diff --git a/notebooks/Enrichment-Results-Analysis_mpj.ipynb b/notebooks/Enrichment-Results-Analysis_mpj.ipynb new file mode 100644 index 000000000..412c900f6 --- /dev/null +++ b/notebooks/Enrichment-Results-Analysis_mpj.ipynb @@ -0,0 +1,71937 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "4327d3f7", + "metadata": {}, + "source": [ + "# Enrichment Analysis Notebook\n", + "\n", + "Compares the results of SPINDOCTOR gene set summarization vs statistical ontological enrichment.\n", + "\n", + "Draft: https://docs.google.com/document/d/1H103ux6Dd1_bPM0un4RwutBLcYJx-0ybil2AwlAvG_Q/edit#" + ] + }, + { + "cell_type": "markdown", + "id": "32c9fa1d", + "metadata": {}, + "source": [ + "## Initial setup\n", + "\n", + "Here we take care of imports, defining the data dictionary for the pandas dataframes" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "3452b4b0", + "metadata": { + "tags": [ + "parameters" + ] + }, + "outputs": [], + "source": [ + "# parameters\n", + "experiment_results = \"../enrichgpt-results/results/enrichment-summary.yaml\"" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "97e39d4a", + "metadata": {}, + "outputs": [], + "source": [ + "import yaml\n", + "from yaml import Loader\n", + "from collections import defaultdict\n", + "import pandas as pd\n", + "from oaklib import get_adapter\n", + "from oaklib.datamodels.vocabulary import IS_A, PART_OF\n", + "from ontogpt.evaluation.enrichment.eval_enrichment import EvalEnrichment\n", + "go = get_adapter(\"sqlite:obo:go\")\n", + "hgnc = get_adapter(\"sqlite:obo:hgnc\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "293db399", + "metadata": {}, + "outputs": [], + "source": [ + "#from ontogpt.utils.gene_set_utils import populate_ids_and_symbols, GeneSet\n", + "#ee = EvalEnrichment()\n", + "#ee.ontology = go\n", + "#ee.load_annotations(\"../tests/input/genes2go.tsv.gz\")" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "a988de3f", + "metadata": {}, + "outputs": [], + "source": [ + "TURBO = \"gpt-3.5-turbo\"\n", + "DAVINCI = \"text-davinci-003\"\n", + "GPT4 = \"gpt-4\"\n", + "MODELS = [TURBO, DAVINCI, GPT4]" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "9b0990c0", + "metadata": {}, + "outputs": [], + "source": [ + "# data dictionary\n", + "MODEL = \"model\"\n", + "METHOD = \"method\"\n", + "HAS_TOP_HIT = \"has top term\"\n", + "IN_TOP_5 = \"in top 5\"\n", + "IN_TOP_10 = \"in top 10\"\n", + "RANK = \"rank\"\n", + "SIZE_OVERLAP = \"size overlap\"\n", + "SIMILARITY = \"similarity\"\n", + "NR_SIZE_OVERLAP = \"nr size overlap\"\n", + "NR_SIMILARITY = \"nr similarity\"\n", + "GENESET = \"geneset\"\n", + "PROMPT_VARIANT = \"prompt_variant\"\n", + "SOURCE_GENESET = \"source geneset\"\n", + "GENESET_DESCRIPTION = \"description\"\n", + "GENESET_SIZE = \"geneset_size\"\n", + "TRUNCATION_FACTOR = \"truncation factor\"\n", + "NUM_TERMS = \"num terms\"\n", + "NUM_GO_TERMS = \"num GO terms\"\n", + "NUM_UNPARSED = \"num unparsed\"\n", + "TERM_IDS = \"term ids\"\n", + "GO_TERM_IDS = \"go term ids\"\n", + "GO_TERM_P_VALUES = \"go term p values\"\n", + "MAX_P_VALUE = \"max p value\"\n", + "MIN_P_VALUE = \"min p value\"\n", + "MEAN_P_VALUE = \"mean p value\"\n", + "PROPOTION_SIGNIFICANT = \"proportion significant\"\n", + "NOVEL = \"unannotated\"\n", + "NOVEL_LABELS = \"unannotated labels\"\n", + "NUM_NOVEL = \"num unannotated\"\n", + "GENE_RANDOMIZATION_FACTOR = \"gene_randomization_factor\"\n", + "SUMMARY = \"summary\"\n", + "\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "e16189b3", + "metadata": {}, + "outputs": [], + "source": [ + "from ontogpt.evaluation.enrichment.eval_enrichment import GeneSetComparison" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "id": "ca76b18a", + "metadata": {}, + "outputs": [], + "source": [ + "# assumes comparisons have been run and concatenated (see Makefile) \n", + "def load_comparisons():\n", + " with open(f\"../{experiment_results}\") as f:\n", + " obj = yaml.load(f, Loader)\n", + " comps = [GeneSetComparison(**x) for x in obj]\n", + " return comps" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "id": "ebab4da5", + "metadata": {}, + "outputs": [], + "source": [ + "comps = load_comparisons()" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "id": "1eec3e01", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['GO:0005773', 'GO:0005634', 'GO:0008150']" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "\n", + "def filter_redundant(term_ids):\n", + " \"\"\"\n", + " find leaf nodes in a set of term ids\n", + " \"\"\"\n", + " cumulative_ancs = set()\n", + " visited = set()\n", + " for t in term_ids:\n", + " visited.add(t)\n", + " if t in cumulative_ancs:\n", + " # a descendant of t has been encountered\n", + " continue\n", + " ancs = list(go.ancestors(t, [IS_A, PART_OF]))\n", + " cumulative_ancs.update(ancs)\n", + " if (visited-{t}).intersection(ancs):\n", + " # t is a descendant of a term that has been encountered\n", + " continue\n", + " yield t\n", + "\n", + "# test\n", + "list(filter_redundant([\"GO:0005773\", \"GO:0005634\", \"GO:0031965\", \"GO:0008150\"]))" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "id": "1ad7746a", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
| \n", + " | model | \n", + "method | \n", + "geneset | \n", + "truncation factor | \n", + "prompt_variant | \n", + "summary | \n", + "source geneset | \n", + "gene_randomization_factor | \n", + "has top term | \n", + "rank | \n", + "... | \n", + "num terms | \n", + "num unparsed | \n", + "go term p values | \n", + "max p value | \n", + "min p value | \n", + "mean p value | \n", + "proportion significant | \n", + "unannotated | \n", + "unannotated labels | \n", + "num unannotated | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "EDS-0 | \n", + "1.0 | \n", + "v1 | \n", + "Summary: The common function of the genes is r... | \n", + "EDS | \n", + "0 | \n", + "True | \n", + "1.0 | \n", + "... | \n", + "3 | \n", + "3 | \n", + "[3.341122685366184e-06, 5.591343976855226e-11,... | \n", + "0.000321 | \n", + "5.591344e-11 | \n", + "0.000108 | \n", + "1.000000 | \n", + "[] | \n", + "[] | \n", + "0 | \n", + "
| 1 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "EDS-0 | \n", + "1.0 | \n", + "v2 | \n", + "Summary: Extracellular matrix organization and... | \n", + "EDS | \n", + "0 | \n", + "True | \n", + "2.0 | \n", + "... | \n", + "6 | \n", + "6 | \n", + "[3.341122685366184e-06, 3.4271478353194616e-06... | \n", + "1.000000 | \n", + "5.591344e-11 | \n", + "0.500001 | \n", + "0.500000 | \n", + "[] | \n", + "[] | \n", + "0 | \n", + "
| 2 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "EDS-0 | \n", + "1.0 | \n", + "v1 | \n", + "Summary: The enriched terms are related to the... | \n", + "EDS | \n", + "0 | \n", + "True | \n", + "0.0 | \n", + "... | \n", + "4 | \n", + "4 | \n", + "[5.591343976855226e-11, 3.341122685366184e-06,... | \n", + "1.000000 | \n", + "5.591344e-11 | \n", + "0.250081 | \n", + "0.750000 | \n", + "[] | \n", + "[] | \n", + "0 | \n", + "
| 3 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "EDS-0 | \n", + "1.0 | \n", + "v2 | \n", + "Summary: The common function of the listed gen... | \n", + "EDS | \n", + "0 | \n", + "True | \n", + "0.0 | \n", + "... | \n", + "5 | \n", + "5 | \n", + "[5.591343976855226e-11, 1.0, 2.2177237867319e-... | \n", + "1.000000 | \n", + "5.591344e-11 | \n", + "0.200065 | \n", + "0.800000 | \n", + "[] | \n", + "[] | \n", + "0 | \n", + "
| 4 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "EDS-0 | \n", + "1.0 | \n", + "v1 | \n", + "Summary: Genes involved in connective tissue d... | \n", + "EDS | \n", + "0 | \n", + "False | \n", + "NaN | \n", + "... | \n", + "7 | \n", + "7 | \n", + "[1.0, 3.341122685366184e-06, 1.0, 1.0, 1.0, 1.... | \n", + "1.000000 | \n", + "3.341123e-06 | \n", + "0.857143 | \n", + "0.142857 | \n", + "[GO:0010712, GO:0043687] | \n", + "[regulation of collagen metabolic process, pos... | \n", + "2 | \n", + "
| ... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "
| 2409 | \n", + "N/A | \n", + "standard | \n", + "tf-downreg-colorectal-1 | \n", + "1.0 | \n", + "None | \n", + "None | \n", + "tf-downreg-colorectal | \n", + "1 | \n", + "True | \n", + "0.0 | \n", + "... | \n", + "180 | \n", + "180 | \n", + "[2.463439488461684e-28, 2.511460888299925e-28,... | \n", + "0.047670 | \n", + "2.463439e-28 | \n", + "0.003428 | \n", + "1.000000 | \n", + "[] | \n", + "[] | \n", + "0 | \n", + "
| 2410 | \n", + "N/A | \n", + "standard_no_ontology | \n", + "tf-downreg-colorectal-1 | \n", + "1.0 | \n", + "None | \n", + "None | \n", + "tf-downreg-colorectal | \n", + "1 | \n", + "False | \n", + "NaN | \n", + "... | \n", + "40 | \n", + "40 | \n", + "[1.0670949536417977e-21, 6.368123603602858e-19... | \n", + "1.000000 | \n", + "6.758362e-27 | \n", + "0.153915 | \n", + "0.850000 | \n", + "[] | \n", + "[] | \n", + "0 | \n", + "
| 2411 | \n", + "N/A | \n", + "random | \n", + "tf-downreg-colorectal-1 | \n", + "1.0 | \n", + "None | \n", + "None | \n", + "tf-downreg-colorectal | \n", + "1 | \n", + "False | \n", + "NaN | \n", + "... | \n", + "42 | \n", + "42 | \n", + "[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 6.26342211... | \n", + "1.000000 | \n", + "6.263422e-13 | \n", + "0.952381 | \n", + "0.047619 | \n", + "[GO:2000095, GO:0006869, GO:0004721, GO:001513... | \n", + "[regulation of Wnt signaling pathway, planar c... | \n", + "25 | \n", + "
| 2412 | \n", + "N/A | \n", + "rank_based | \n", + "tf-downreg-colorectal-1 | \n", + "1.0 | \n", + "None | \n", + "None | \n", + "tf-downreg-colorectal | \n", + "1 | \n", + "False | \n", + "NaN | \n", + "... | \n", + "46 | \n", + "46 | \n", + "[4.966218259085737e-14, 1.0, 1.0, 1.0, 1.0, 6.... | \n", + "1.000000 | \n", + "6.758362e-27 | \n", + "0.673924 | \n", + "0.326087 | \n", + "[GO:0004930, GO:0005509, GO:0007186, GO:000013... | \n", + "[G protein-coupled receptor activity, calcium ... | \n", + "5 | \n", + "
| 2413 | \n", + "N/A | \n", + "closure | \n", + "tf-downreg-colorectal-1 | \n", + "1.0 | \n", + "None | \n", + "None | \n", + "tf-downreg-colorectal | \n", + "1 | \n", + "True | \n", + "505.0 | \n", + "... | \n", + "3523 | \n", + "3523 | \n", + "[1.0, 1.0, 1.0, 3.405746031985595e-10, 1.0, 1.... | \n", + "1.000000 | \n", + "2.463439e-28 | \n", + "0.930224 | \n", + "0.070029 | \n", + "[] | \n", + "[] | \n", + "0 | \n", + "
2414 rows × 32 columns
\n", + "| \n", + " | model | \n", + "method | \n", + "
|---|---|---|
| 0 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "
| 2 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "
| 4 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "
| 6 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "
| 8 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "
| 10 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "
| 12 | \n", + "N/A | \n", + "standard | \n", + "
| 13 | \n", + "N/A | \n", + "standard_no_ontology | \n", + "
| 14 | \n", + "N/A | \n", + "random | \n", + "
| 15 | \n", + "N/A | \n", + "rank_based | \n", + "
| 16 | \n", + "N/A | \n", + "closure | \n", + "
| \n", + " | source geneset | \n", + "
|---|---|
| 0 | \n", + "EDS | \n", + "
| 34 | \n", + "FA | \n", + "
| 68 | \n", + "HALLMARK_ADIPOGENESIS | \n", + "
| 102 | \n", + "HALLMARK_ALLOGRAFT_REJECTION | \n", + "
| 136 | \n", + "HALLMARK_ANDROGEN_RESPONSE | \n", + "
| ... | \n", + "... | \n", + "
| 2244 | \n", + "peroxisome | \n", + "
| 2278 | \n", + "progeria | \n", + "
| 2312 | \n", + "regulation of presynaptic membrane potential | \n", + "
| 2346 | \n", + "sensory ataxia | \n", + "
| 2380 | \n", + "tf-downreg-colorectal | \n", + "
71 rows × 1 columns
\n", + "| source geneset | \n", + "geneset_size | \n", + "
|---|---|
| EDS | \n", + "19 | \n", + "
| EDS | \n", + "18 | \n", + "
| FA | \n", + "19 | \n", + "
| FA | \n", + "18 | \n", + "
| HALLMARK_ADIPOGENESIS | \n", + "200 | \n", + "
| HALLMARK_ADIPOGENESIS | \n", + "180 | \n", + "
| HALLMARK_ALLOGRAFT_REJECTION | \n", + "200 | \n", + "
| HALLMARK_ALLOGRAFT_REJECTION | \n", + "180 | \n", + "
| HALLMARK_ANDROGEN_RESPONSE | \n", + "101 | \n", + "
| HALLMARK_ANDROGEN_RESPONSE | \n", + "90 | \n", + "
| HALLMARK_ANGIOGENESIS | \n", + "36 | \n", + "
| HALLMARK_ANGIOGENESIS | \n", + "33 | \n", + "
| HALLMARK_APICAL_JUNCTION | \n", + "200 | \n", + "
| HALLMARK_APICAL_JUNCTION | \n", + "180 | \n", + "
| HALLMARK_APICAL_SURFACE | \n", + "44 | \n", + "
| HALLMARK_APICAL_SURFACE | \n", + "40 | \n", + "
| HALLMARK_APOPTOSIS | \n", + "161 | \n", + "
| HALLMARK_APOPTOSIS | \n", + "145 | \n", + "
| HALLMARK_BILE_ACID_METABOLISM | \n", + "112 | \n", + "
| HALLMARK_BILE_ACID_METABOLISM | \n", + "101 | \n", + "
| HALLMARK_CHOLESTEROL_HOMEOSTASIS | \n", + "74 | \n", + "
| HALLMARK_CHOLESTEROL_HOMEOSTASIS | \n", + "67 | \n", + "
| HALLMARK_COAGULATION | \n", + "138 | \n", + "
| HALLMARK_COAGULATION | \n", + "125 | \n", + "
| HALLMARK_COMPLEMENT | \n", + "200 | \n", + "
| HALLMARK_COMPLEMENT | \n", + "180 | \n", + "
| HALLMARK_DNA_REPAIR | \n", + "150 | \n", + "
| HALLMARK_DNA_REPAIR | \n", + "135 | \n", + "
| HALLMARK_E2F_TARGETS | \n", + "200 | \n", + "
| HALLMARK_E2F_TARGETS | \n", + "180 | \n", + "
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION | \n", + "200 | \n", + "
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION | \n", + "180 | \n", + "
| HALLMARK_ESTROGEN_RESPONSE_EARLY | \n", + "200 | \n", + "
| HALLMARK_ESTROGEN_RESPONSE_EARLY | \n", + "180 | \n", + "
| HALLMARK_ESTROGEN_RESPONSE_LATE | \n", + "200 | \n", + "
| HALLMARK_ESTROGEN_RESPONSE_LATE | \n", + "180 | \n", + "
| HALLMARK_FATTY_ACID_METABOLISM | \n", + "158 | \n", + "
| HALLMARK_FATTY_ACID_METABOLISM | \n", + "143 | \n", + "
| HALLMARK_G2M_CHECKPOINT | \n", + "200 | \n", + "
| HALLMARK_G2M_CHECKPOINT | \n", + "180 | \n", + "
| HALLMARK_GLYCOLYSIS | \n", + "200 | \n", + "
| HALLMARK_GLYCOLYSIS | \n", + "180 | \n", + "
| HALLMARK_HEDGEHOG_SIGNALING | \n", + "36 | \n", + "
| HALLMARK_HEDGEHOG_SIGNALING | \n", + "33 | \n", + "
| HALLMARK_HEME_METABOLISM | \n", + "200 | \n", + "
| HALLMARK_HEME_METABOLISM | \n", + "180 | \n", + "
| HALLMARK_HYPOXIA | \n", + "200 | \n", + "
| HALLMARK_HYPOXIA | \n", + "180 | \n", + "
| HALLMARK_IL2_STAT5_SIGNALING | \n", + "199 | \n", + "
| HALLMARK_IL2_STAT5_SIGNALING | \n", + "179 | \n", + "
| HALLMARK_IL6_JAK_STAT3_SIGNALING | \n", + "87 | \n", + "
| HALLMARK_IL6_JAK_STAT3_SIGNALING | \n", + "79 | \n", + "
| HALLMARK_INFLAMMATORY_RESPONSE | \n", + "200 | \n", + "
| HALLMARK_INFLAMMATORY_RESPONSE | \n", + "180 | \n", + "
| HALLMARK_INTERFERON_ALPHA_RESPONSE | \n", + "97 | \n", + "
| HALLMARK_INTERFERON_ALPHA_RESPONSE | \n", + "88 | \n", + "
| HALLMARK_INTERFERON_GAMMA_RESPONSE | \n", + "200 | \n", + "
| HALLMARK_INTERFERON_GAMMA_RESPONSE | \n", + "180 | \n", + "
| HALLMARK_KRAS_SIGNALING_DN | \n", + "200 | \n", + "
| HALLMARK_KRAS_SIGNALING_DN | \n", + "180 | \n", + "
| HALLMARK_KRAS_SIGNALING_UP | \n", + "200 | \n", + "
| HALLMARK_KRAS_SIGNALING_UP | \n", + "180 | \n", + "
| HALLMARK_MITOTIC_SPINDLE | \n", + "199 | \n", + "
| HALLMARK_MITOTIC_SPINDLE | \n", + "180 | \n", + "
| HALLMARK_MTORC1_SIGNALING | \n", + "200 | \n", + "
| HALLMARK_MTORC1_SIGNALING | \n", + "180 | \n", + "
| HALLMARK_MYC_TARGETS_V1 | \n", + "200 | \n", + "
| HALLMARK_MYC_TARGETS_V1 | \n", + "180 | \n", + "
| HALLMARK_MYC_TARGETS_V2 | \n", + "58 | \n", + "
| HALLMARK_MYC_TARGETS_V2 | \n", + "53 | \n", + "
| HALLMARK_MYOGENESIS | \n", + "200 | \n", + "
| HALLMARK_MYOGENESIS | \n", + "180 | \n", + "
| HALLMARK_NOTCH_SIGNALING | \n", + "32 | \n", + "
| HALLMARK_NOTCH_SIGNALING | \n", + "29 | \n", + "
| HALLMARK_OXIDATIVE_PHOSPHORYLATION | \n", + "200 | \n", + "
| HALLMARK_OXIDATIVE_PHOSPHORYLATION | \n", + "180 | \n", + "
| HALLMARK_P53_PATHWAY | \n", + "200 | \n", + "
| HALLMARK_P53_PATHWAY | \n", + "180 | \n", + "
| HALLMARK_PANCREAS_BETA_CELLS | \n", + "40 | \n", + "
| HALLMARK_PANCREAS_BETA_CELLS | \n", + "36 | \n", + "
| HALLMARK_PEROXISOME | \n", + "104 | \n", + "
| HALLMARK_PEROXISOME | \n", + "94 | \n", + "
| HALLMARK_PI3K_AKT_MTOR_SIGNALING | \n", + "105 | \n", + "
| HALLMARK_PI3K_AKT_MTOR_SIGNALING | \n", + "95 | \n", + "
| HALLMARK_PROTEIN_SECRETION | \n", + "96 | \n", + "
| HALLMARK_PROTEIN_SECRETION | \n", + "87 | \n", + "
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY | \n", + "49 | \n", + "
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY | \n", + "45 | \n", + "
| HALLMARK_SPERMATOGENESIS | \n", + "135 | \n", + "
| HALLMARK_SPERMATOGENESIS | \n", + "122 | \n", + "
| HALLMARK_TGF_BETA_SIGNALING | \n", + "54 | \n", + "
| HALLMARK_TGF_BETA_SIGNALING | \n", + "49 | \n", + "
| HALLMARK_TNFA_SIGNALING_VIA_NFKB | \n", + "200 | \n", + "
| HALLMARK_TNFA_SIGNALING_VIA_NFKB | \n", + "180 | \n", + "
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE | \n", + "113 | \n", + "
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE | \n", + "101 | \n", + "
| HALLMARK_UV_RESPONSE_DN | \n", + "144 | \n", + "
| HALLMARK_UV_RESPONSE_DN | \n", + "130 | \n", + "
| HALLMARK_UV_RESPONSE_UP | \n", + "158 | \n", + "
| HALLMARK_UV_RESPONSE_UP | \n", + "143 | \n", + "
| HALLMARK_WNT_BETA_CATENIN_SIGNALING | \n", + "42 | \n", + "
| HALLMARK_WNT_BETA_CATENIN_SIGNALING | \n", + "38 | \n", + "
| T cell proliferation | \n", + "72 | \n", + "
| T cell proliferation | \n", + "65 | \n", + "
| Yamanaka-TFs | \n", + "4 | \n", + "
| Yamanaka-TFs | \n", + "3 | \n", + "
| amigo-example | \n", + "36 | \n", + "
| amigo-example | \n", + "32 | \n", + "
| bicluster_RNAseqDB_0 | \n", + "158 | \n", + "
| bicluster_RNAseqDB_0 | \n", + "134 | \n", + "
| bicluster_RNAseqDB_1002 | \n", + "52 | \n", + "
| bicluster_RNAseqDB_1002 | \n", + "43 | \n", + "
| glycolysis-gocam | \n", + "10 | \n", + "
| glycolysis-gocam | \n", + "9 | \n", + "
| term-GO:0007212 | \n", + "28 | \n", + "
| term-GO:0007212 | \n", + "26 | \n", + "
| endocytosis | \n", + "16 | \n", + "
| endocytosis | \n", + "15 | \n", + "
| go-postsynapse-calcium-transmembrane | \n", + "33 | \n", + "
| go-postsynapse-calcium-transmembrane | \n", + "30 | \n", + "
| go-reg-autophagy-pkra | \n", + "17 | \n", + "
| go-reg-autophagy-pkra | \n", + "16 | \n", + "
| hydrolase activity, hydrolyzing O-glycosyl compounds | \n", + "91 | \n", + "
| hydrolase activity, hydrolyzing O-glycosyl compounds | \n", + "81 | \n", + "
| ig-receptor-binding-2022 | \n", + "91 | \n", + "
| ig-receptor-binding-2022 | \n", + "82 | \n", + "
| meiosis I | \n", + "54 | \n", + "
| meiosis I | \n", + "46 | \n", + "
| molecular sequestering | \n", + "30 | \n", + "
| molecular sequestering | \n", + "27 | \n", + "
| mtorc1 | \n", + "200 | \n", + "
| mtorc1 | \n", + "180 | \n", + "
| peroxisome | \n", + "8 | \n", + "
| peroxisome | \n", + "5 | \n", + "
| progeria | \n", + "4 | \n", + "
| progeria | \n", + "3 | \n", + "
| regulation of presynaptic membrane potential | \n", + "30 | \n", + "
| regulation of presynaptic membrane potential | \n", + "27 | \n", + "
| sensory ataxia | \n", + "15 | \n", + "
| sensory ataxia | \n", + "14 | \n", + "
| tf-downreg-colorectal | \n", + "51 | \n", + "
| tf-downreg-colorectal | \n", + "46 | \n", + "
| model | \n", + "method | \n", + "
|---|---|
| gpt-3.5-turbo | \n", + "no_synopsis | \n", + "
| gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "
| gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "
| text-davinci-003 | \n", + "no_synopsis | \n", + "
| text-davinci-003 | \n", + "ontological_synopsis | \n", + "
| text-davinci-003 | \n", + "narrative_synopsis | \n", + "
| N/A | \n", + "standard | \n", + "
| N/A | \n", + "standard_no_ontology | \n", + "
| N/A | \n", + "random | \n", + "
| N/A | \n", + "rank_based | \n", + "
| N/A | \n", + "closure | \n", + "
| model | \n", + "method | \n", + "prompt_variant | \n", + "
|---|---|---|
| gpt-3.5-turbo | \n", + "no_synopsis | \n", + "v1 | \n", + "
| gpt-3.5-turbo | \n", + "no_synopsis | \n", + "v2 | \n", + "
| gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "v1 | \n", + "
| gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "v2 | \n", + "
| gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "v1 | \n", + "
| gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "v2 | \n", + "
| text-davinci-003 | \n", + "no_synopsis | \n", + "v1 | \n", + "
| text-davinci-003 | \n", + "no_synopsis | \n", + "v2 | \n", + "
| text-davinci-003 | \n", + "ontological_synopsis | \n", + "v1 | \n", + "
| text-davinci-003 | \n", + "ontological_synopsis | \n", + "v2 | \n", + "
| text-davinci-003 | \n", + "narrative_synopsis | \n", + "v1 | \n", + "
| text-davinci-003 | \n", + "narrative_synopsis | \n", + "v2 | \n", + "
| N/A | \n", + "standard | \n", + "None | \n", + "
| N/A | \n", + "standard_no_ontology | \n", + "None | \n", + "
| N/A | \n", + "random | \n", + "None | \n", + "
| N/A | \n", + "rank_based | \n", + "None | \n", + "
| N/A | \n", + "closure | \n", + "None | \n", + "
| \n", + " | model | \n", + "method | \n", + "term | \n", + "label | \n", + "goslim_chembl | \n", + "goslim_generic | \n", + "goslim_drosophila | \n", + "goslim_pir | \n", + "anc_of_goslim_chembl | \n", + "anc_of_goslim_generic | \n", + "... | \n", + "anc_of_goslim_flybase_ribbon | \n", + "anc_of_goslim_agr | \n", + "goslim_mouse | \n", + "anc_of_goslim_plant | \n", + "anc_of_goslim_pombe | \n", + "anc_of_gocheck_do_not_manually_annotate | \n", + "anc_of_goslim_mouse | \n", + "gocheck_do_not_annotate | \n", + "gocheck_do_not_manually_annotate | \n", + "goslim_synapse | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "GO:0030198 | \n", + "extracellular matrix organization | \n", + "1.0 | \n", + "1.0 | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "... | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 1 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "GO:0030199 | \n", + "collagen fibril organization | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "... | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 2 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "GO:0006024 | \n", + "glycosaminoglycan biosynthetic process | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "... | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 3 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "GO:0030198 | \n", + "extracellular matrix organization | \n", + "1.0 | \n", + "1.0 | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "... | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 4 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "GO:0043062 | \n", + "extracellular structure organization | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "1.0 | \n", + "1.0 | \n", + "... | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| ... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "
| 756440 | \n", + "N/A | \n", + "closure | \n", + "GO:0032106 | \n", + "positive regulation of response to extracellul... | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "... | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 756441 | \n", + "N/A | \n", + "closure | \n", + "GO:0032109 | \n", + "positive regulation of response to nutrient le... | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "... | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 756442 | \n", + "N/A | \n", + "closure | \n", + "GO:0045848 | \n", + "positive regulation of nitrogen utilization | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "... | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 756443 | \n", + "N/A | \n", + "closure | \n", + "GO:2001248 | \n", + "regulation of ammonia assimilation cycle | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "... | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 756444 | \n", + "N/A | \n", + "closure | \n", + "GO:2001250 | \n", + "positive regulation of ammonia assimilation cycle | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "... | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
756445 rows × 36 columns
\n", + "| \n", + " | \n", + " | goslim_chembl | \n", + "goslim_generic | \n", + "goslim_drosophila | \n", + "goslim_pir | \n", + "anc_of_goslim_chembl | \n", + "anc_of_goslim_generic | \n", + "anc_of_goslim_drosophila | \n", + "prokaryote_subset | \n", + "goslim_yeast | \n", + "goslim_pombe | \n", + "goslim_metagenomics | \n", + "goslim_candida | \n", + "anc_of_goslim_pir | \n", + "anc_of_goslim_synapse | \n", + "anc_of_goslim_yeast | \n", + "anc_of_gocheck_do_not_annotate | \n", + "anc_of_goslim_candida | \n", + "goslim_plant | \n", + "anc_of_goslim_metagenomics | \n", + "anc_of_prokaryote_subset | \n", + "goslim_flybase_ribbon | \n", + "goslim_agr | \n", + "anc_of_goslim_flybase_ribbon | \n", + "anc_of_goslim_agr | \n", + "goslim_mouse | \n", + "anc_of_goslim_plant | \n", + "anc_of_goslim_pombe | \n", + "anc_of_gocheck_do_not_manually_annotate | \n", + "anc_of_goslim_mouse | \n", + "gocheck_do_not_annotate | \n", + "gocheck_do_not_manually_annotate | \n", + "goslim_synapse | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " |
| N/A | \n", + "closure | \n", + "0.050 | \n", + "0.028 | \n", + "0.035 | \n", + "0.051 | \n", + "0.055 | \n", + "0.047 | \n", + "0.053 | \n", + "0.017 | \n", + "0.030 | \n", + "0.009 | \n", + "0.018 | \n", + "0.018 | \n", + "0.079 | \n", + "0.094 | \n", + "0.051 | \n", + "0.043 | \n", + "0.031 | \n", + "0.022 | \n", + "0.036 | \n", + "0.034 | \n", + "0.013 | \n", + "0.015 | \n", + "0.012 | \n", + "0.019 | \n", + "0.013 | \n", + "0.026 | \n", + "0.037 | \n", + "0.032 | \n", + "0.020 | \n", + "0.008 | \n", + "0.008 | \n", + "0.012 | \n", + "
| random | \n", + "0.167 | \n", + "0.099 | \n", + "0.112 | \n", + "0.109 | \n", + "0.047 | \n", + "0.057 | \n", + "0.068 | \n", + "0.056 | \n", + "0.104 | \n", + "0.017 | \n", + "0.069 | \n", + "0.085 | \n", + "0.111 | \n", + "0.164 | \n", + "0.050 | \n", + "0.085 | \n", + "0.027 | \n", + "0.102 | \n", + "0.037 | \n", + "0.035 | \n", + "0.057 | \n", + "0.071 | \n", + "0.026 | \n", + "0.032 | \n", + "0.062 | \n", + "0.021 | \n", + "0.077 | \n", + "0.065 | \n", + "0.033 | \n", + "0.001 | \n", + "0.001 | \n", + "0.016 | \n", + "|
| rank_based | \n", + "0.334 | \n", + "0.186 | \n", + "0.221 | \n", + "0.218 | \n", + "0.108 | \n", + "0.129 | \n", + "0.157 | \n", + "0.100 | \n", + "0.204 | \n", + "0.024 | \n", + "0.118 | \n", + "0.165 | \n", + "0.213 | \n", + "0.315 | \n", + "0.107 | \n", + "0.166 | \n", + "0.071 | \n", + "0.200 | \n", + "0.091 | \n", + "0.082 | \n", + "0.111 | \n", + "0.151 | \n", + "0.046 | \n", + "0.072 | \n", + "0.128 | \n", + "0.055 | \n", + "0.142 | \n", + "0.126 | \n", + "0.075 | \n", + "0.000 | \n", + "0.004 | \n", + "0.022 | \n", + "|
| standard | \n", + "0.087 | \n", + "0.049 | \n", + "0.055 | \n", + "0.095 | \n", + "0.163 | \n", + "0.142 | \n", + "0.158 | \n", + "0.035 | \n", + "0.044 | \n", + "0.013 | \n", + "0.043 | \n", + "0.037 | \n", + "0.172 | \n", + "0.216 | \n", + "0.137 | \n", + "0.116 | \n", + "0.098 | \n", + "0.061 | \n", + "0.103 | \n", + "0.108 | \n", + "0.031 | \n", + "0.036 | \n", + "0.042 | \n", + "0.070 | \n", + "0.032 | \n", + "0.084 | \n", + "0.099 | \n", + "0.118 | \n", + "0.077 | \n", + "0.035 | \n", + "0.037 | \n", + "0.007 | \n", + "|
| standard_no_ontology | \n", + "0.107 | \n", + "0.062 | \n", + "0.063 | \n", + "0.068 | \n", + "0.028 | \n", + "0.034 | \n", + "0.036 | \n", + "0.034 | \n", + "0.059 | \n", + "0.014 | \n", + "0.034 | \n", + "0.042 | \n", + "0.074 | \n", + "0.093 | \n", + "0.027 | \n", + "0.049 | \n", + "0.012 | \n", + "0.051 | \n", + "0.029 | \n", + "0.021 | \n", + "0.030 | \n", + "0.035 | \n", + "0.008 | \n", + "0.010 | \n", + "0.032 | \n", + "0.009 | \n", + "0.042 | \n", + "0.031 | \n", + "0.011 | \n", + "0.001 | \n", + "0.001 | \n", + "0.014 | \n", + "|
| gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "0.266 | \n", + "0.210 | \n", + "0.255 | \n", + "0.242 | \n", + "0.081 | \n", + "0.108 | \n", + "0.109 | \n", + "0.155 | \n", + "0.194 | \n", + "0.113 | \n", + "0.140 | \n", + "0.167 | \n", + "0.172 | \n", + "0.239 | \n", + "0.106 | \n", + "0.172 | \n", + "0.054 | \n", + "0.131 | \n", + "0.076 | \n", + "0.099 | \n", + "0.028 | \n", + "0.059 | \n", + "0.023 | \n", + "0.036 | \n", + "0.044 | \n", + "0.026 | \n", + "0.068 | \n", + "0.076 | \n", + "0.044 | \n", + "0.022 | \n", + "0.009 | \n", + "0.006 | \n", + "
| no_synopsis | \n", + "0.194 | \n", + "0.180 | \n", + "0.215 | \n", + "0.191 | \n", + "0.089 | \n", + "0.102 | \n", + "0.096 | \n", + "0.118 | \n", + "0.154 | \n", + "0.098 | \n", + "0.092 | \n", + "0.102 | \n", + "0.140 | \n", + "0.198 | \n", + "0.112 | \n", + "0.131 | \n", + "0.055 | \n", + "0.080 | \n", + "0.082 | \n", + "0.086 | \n", + "0.028 | \n", + "0.050 | \n", + "0.020 | \n", + "0.035 | \n", + "0.036 | \n", + "0.035 | \n", + "0.090 | \n", + "0.055 | \n", + "0.036 | \n", + "0.021 | \n", + "0.023 | \n", + "0.007 | \n", + "|
| ontological_synopsis | \n", + "0.254 | \n", + "0.135 | \n", + "0.180 | \n", + "0.163 | \n", + "0.071 | \n", + "0.095 | \n", + "0.121 | \n", + "0.097 | \n", + "0.155 | \n", + "0.057 | \n", + "0.134 | \n", + "0.122 | \n", + "0.176 | \n", + "0.214 | \n", + "0.101 | \n", + "0.138 | \n", + "0.064 | \n", + "0.125 | \n", + "0.074 | \n", + "0.088 | \n", + "0.051 | \n", + "0.074 | \n", + "0.036 | \n", + "0.056 | \n", + "0.064 | \n", + "0.035 | \n", + "0.037 | \n", + "0.067 | \n", + "0.063 | \n", + "0.013 | \n", + "0.009 | \n", + "0.009 | \n", + "|
| text-davinci-003 | \n", + "narrative_synopsis | \n", + "0.397 | \n", + "0.253 | \n", + "0.290 | \n", + "0.315 | \n", + "0.115 | \n", + "0.207 | \n", + "0.211 | \n", + "0.231 | \n", + "0.225 | \n", + "0.141 | \n", + "0.244 | \n", + "0.263 | \n", + "0.233 | \n", + "0.272 | \n", + "0.219 | \n", + "0.234 | \n", + "0.120 | \n", + "0.253 | \n", + "0.118 | \n", + "0.163 | \n", + "0.108 | \n", + "0.128 | \n", + "0.082 | \n", + "0.096 | \n", + "0.110 | \n", + "0.063 | \n", + "0.133 | \n", + "0.117 | \n", + "0.105 | \n", + "0.031 | \n", + "0.034 | \n", + "0.002 | \n", + "
| no_synopsis | \n", + "0.329 | \n", + "0.237 | \n", + "0.311 | \n", + "0.355 | \n", + "0.173 | \n", + "0.225 | \n", + "0.240 | \n", + "0.211 | \n", + "0.188 | \n", + "0.150 | \n", + "0.216 | \n", + "0.213 | \n", + "0.230 | \n", + "0.303 | \n", + "0.249 | \n", + "0.301 | \n", + "0.148 | \n", + "0.220 | \n", + "0.113 | \n", + "0.158 | \n", + "0.078 | \n", + "0.117 | \n", + "0.053 | \n", + "0.074 | \n", + "0.075 | \n", + "0.079 | \n", + "0.217 | \n", + "0.159 | \n", + "0.101 | \n", + "0.047 | \n", + "0.036 | \n", + "0.007 | \n", + "|
| ontological_synopsis | \n", + "0.296 | \n", + "0.147 | \n", + "0.186 | \n", + "0.146 | \n", + "0.107 | \n", + "0.110 | \n", + "0.130 | \n", + "0.124 | \n", + "0.152 | \n", + "0.038 | \n", + "0.135 | \n", + "0.130 | \n", + "0.189 | \n", + "0.201 | \n", + "0.122 | \n", + "0.133 | \n", + "0.078 | \n", + "0.129 | \n", + "0.069 | \n", + "0.094 | \n", + "0.071 | \n", + "0.084 | \n", + "0.038 | \n", + "0.056 | \n", + "0.071 | \n", + "0.043 | \n", + "0.040 | \n", + "0.082 | \n", + "0.065 | \n", + "0.012 | \n", + "0.004 | \n", + "0.004 | \n", + "
| \n", + " | \n", + " | goslim_generic | \n", + "anc_of_goslim_generic | \n", + "goslim_agr | \n", + "anc_of_goslim_agr | \n", + "closure_of_goslim_generic | \n", + "closure_of_goslim_agr | \n", + "
|---|---|---|---|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " |
| N/A | \n", + "closure | \n", + "0.028 | \n", + "0.047 | \n", + "0.015 | \n", + "0.019 | \n", + "0.074 | \n", + "0.034 | \n", + "
| random | \n", + "0.099 | \n", + "0.057 | \n", + "0.071 | \n", + "0.032 | \n", + "0.156 | \n", + "0.103 | \n", + "|
| rank_based | \n", + "0.186 | \n", + "0.129 | \n", + "0.151 | \n", + "0.072 | \n", + "0.315 | \n", + "0.223 | \n", + "|
| standard | \n", + "0.049 | \n", + "0.142 | \n", + "0.036 | \n", + "0.070 | \n", + "0.191 | \n", + "0.106 | \n", + "|
| standard_no_ontology | \n", + "0.062 | \n", + "0.034 | \n", + "0.035 | \n", + "0.010 | \n", + "0.096 | \n", + "0.046 | \n", + "|
| gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "0.210 | \n", + "0.108 | \n", + "0.059 | \n", + "0.036 | \n", + "0.318 | \n", + "0.095 | \n", + "
| no_synopsis | \n", + "0.180 | \n", + "0.102 | \n", + "0.050 | \n", + "0.035 | \n", + "0.281 | \n", + "0.085 | \n", + "|
| ontological_synopsis | \n", + "0.135 | \n", + "0.095 | \n", + "0.074 | \n", + "0.056 | \n", + "0.229 | \n", + "0.131 | \n", + "|
| text-davinci-003 | \n", + "narrative_synopsis | \n", + "0.253 | \n", + "0.207 | \n", + "0.128 | \n", + "0.096 | \n", + "0.460 | \n", + "0.225 | \n", + "
| no_synopsis | \n", + "0.237 | \n", + "0.225 | \n", + "0.117 | \n", + "0.074 | \n", + "0.462 | \n", + "0.191 | \n", + "|
| ontological_synopsis | \n", + "0.147 | \n", + "0.110 | \n", + "0.084 | \n", + "0.056 | \n", + "0.257 | \n", + "0.140 | \n", + "
| \n", + " | \n", + " | anc_of_goslim_generic | \n", + "anc_of_goslim_agr | \n", + "
|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " |
| text-davinci-003 | \n", + "no_synopsis | \n", + "0.225 | \n", + "0.074 | \n", + "
| narrative_synopsis | \n", + "0.207 | \n", + "0.096 | \n", + "|
| N/A | \n", + "standard | \n", + "0.142 | \n", + "0.070 | \n", + "
| rank_based | \n", + "0.129 | \n", + "0.072 | \n", + "|
| text-davinci-003 | \n", + "ontological_synopsis | \n", + "0.110 | \n", + "0.056 | \n", + "
| gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "0.108 | \n", + "0.036 | \n", + "
| no_synopsis | \n", + "0.102 | \n", + "0.035 | \n", + "|
| ontological_synopsis | \n", + "0.095 | \n", + "0.056 | \n", + "|
| N/A | \n", + "random | \n", + "0.057 | \n", + "0.032 | \n", + "
| closure | \n", + "0.047 | \n", + "0.019 | \n", + "|
| standard_no_ontology | \n", + "0.034 | \n", + "0.010 | \n", + "
| \n", + " | \n", + " | anc_of_goslim_generic | \n", + "anc_of_goslim_agr | \n", + "
|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " |
| N/A | \n", + "standard_no_ontology | \n", + "0.034 | \n", + "0.010 | \n", + "
| closure | \n", + "0.047 | \n", + "0.019 | \n", + "|
| random | \n", + "0.057 | \n", + "0.032 | \n", + "|
| gpt-3.5-turbo | \n", + "no_synopsis | \n", + "0.102 | \n", + "0.035 | \n", + "
| narrative_synopsis | \n", + "0.108 | \n", + "0.036 | \n", + "|
| text-davinci-003 | \n", + "ontological_synopsis | \n", + "0.110 | \n", + "0.056 | \n", + "
| gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "0.095 | \n", + "0.056 | \n", + "
| N/A | \n", + "standard | \n", + "0.142 | \n", + "0.070 | \n", + "
| rank_based | \n", + "0.129 | \n", + "0.072 | \n", + "|
| text-davinci-003 | \n", + "no_synopsis | \n", + "0.225 | \n", + "0.074 | \n", + "
| narrative_synopsis | \n", + "0.207 | \n", + "0.096 | \n", + "
| \n", + " | \n", + " | num GO terms | \n", + "size overlap | \n", + "nr size overlap | \n", + "
|---|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " | \n", + " |
| N/A | \n", + "closure | \n", + "4910.606 | \n", + "240.014 | \n", + "2.239 | \n", + "
| random | \n", + "100.690 | \n", + "7.535 | \n", + "0.563 | \n", + "|
| rank based | \n", + "114.930 | \n", + "16.225 | \n", + "0.901 | \n", + "|
| standard no ontology | \n", + "59.394 | \n", + "49.451 | \n", + "5.070 | \n", + "|
| gpt-3.5-turbo | \n", + "narrative synopsis | \n", + "3.782 | \n", + "2.415 | \n", + "0.507 | \n", + "
| no synopsis | \n", + "4.690 | \n", + "2.965 | \n", + "0.585 | \n", + "|
| ontological synopsis | \n", + "3.408 | \n", + "2.120 | \n", + "0.486 | \n", + "|
| text-davinci-003 | \n", + "narrative synopsis | \n", + "3.915 | \n", + "1.423 | \n", + "0.345 | \n", + "
| no synopsis | \n", + "3.063 | \n", + "1.155 | \n", + "0.268 | \n", + "|
| ontological synopsis | \n", + "6.563 | \n", + "2.070 | \n", + "0.345 | \n", + "
| \n", + " | \n", + " | has top term | \n", + "in top 5 | \n", + "in top 10 | \n", + "size overlap | \n", + "similarity | \n", + "num terms | \n", + "num GO terms | \n", + "nr size overlap | \n", + "nr similarity | \n", + "mean p value | \n", + "min p value | \n", + "max p value | \n", + "proportion significant | \n", + "num unannotated | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " |
| N/A | \n", + "closure | \n", + "1.000 | \n", + "0.014 | \n", + "0.028 | \n", + "240.014 | \n", + "0.073 | \n", + "4972.718 | \n", + "4910.606 | \n", + "2.239 | \n", + "0.011 | \n", + "0.924 | \n", + "0.000 | \n", + "1.000 | \n", + "0.077 | \n", + "0.000 | \n", + "
| random | \n", + "0.042 | \n", + "0.000 | \n", + "0.000 | \n", + "7.535 | \n", + "0.017 | \n", + "100.690 | \n", + "100.690 | \n", + "0.563 | \n", + "0.005 | \n", + "0.936 | \n", + "0.142 | \n", + "1.000 | \n", + "0.064 | \n", + "41.704 | \n", + "|
| rank based | \n", + "0.169 | \n", + "0.014 | \n", + "0.028 | \n", + "16.225 | \n", + "0.038 | \n", + "114.930 | \n", + "114.930 | \n", + "0.901 | \n", + "0.014 | \n", + "0.874 | \n", + "0.085 | \n", + "1.000 | \n", + "0.126 | \n", + "9.493 | \n", + "|
| standard | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "240.014 | \n", + "0.969 | \n", + "246.831 | \n", + "240.014 | \n", + "18.282 | \n", + "0.934 | \n", + "0.007 | \n", + "0.000 | \n", + "0.047 | \n", + "1.000 | \n", + "0.000 | \n", + "|
| standard no ontology | \n", + "0.535 | \n", + "0.394 | \n", + "0.423 | \n", + "49.451 | \n", + "0.200 | \n", + "59.394 | \n", + "59.394 | \n", + "5.070 | \n", + "0.138 | \n", + "0.212 | \n", + "0.000 | \n", + "1.000 | \n", + "0.792 | \n", + "0.000 | \n", + "|
| gpt-3.5-turbo | \n", + "narrative synopsis | \n", + "0.134 | \n", + "0.127 | \n", + "0.134 | \n", + "2.415 | \n", + "0.014 | \n", + "5.500 | \n", + "3.782 | \n", + "0.507 | \n", + "0.027 | \n", + "0.341 | \n", + "0.114 | \n", + "0.613 | \n", + "0.661 | \n", + "0.197 | \n", + "
| no synopsis | \n", + "0.218 | \n", + "0.197 | \n", + "0.218 | \n", + "2.965 | \n", + "0.017 | \n", + "7.246 | \n", + "4.690 | \n", + "0.585 | \n", + "0.030 | \n", + "0.367 | \n", + "0.121 | \n", + "0.715 | \n", + "0.634 | \n", + "0.218 | \n", + "|
| ontological synopsis | \n", + "0.148 | \n", + "0.134 | \n", + "0.148 | \n", + "2.120 | \n", + "0.016 | \n", + "5.838 | \n", + "3.408 | \n", + "0.486 | \n", + "0.030 | \n", + "0.389 | \n", + "0.163 | \n", + "0.649 | \n", + "0.612 | \n", + "0.085 | \n", + "|
| text-davinci-003 | \n", + "narrative synopsis | \n", + "0.085 | \n", + "0.070 | \n", + "0.085 | \n", + "1.423 | \n", + "0.008 | \n", + "11.359 | \n", + "3.915 | \n", + "0.345 | \n", + "0.017 | \n", + "0.629 | \n", + "0.316 | \n", + "0.885 | \n", + "0.372 | \n", + "0.331 | \n", + "
| no synopsis | \n", + "0.092 | \n", + "0.085 | \n", + "0.092 | \n", + "1.155 | \n", + "0.006 | \n", + "10.324 | \n", + "3.063 | \n", + "0.268 | \n", + "0.013 | \n", + "0.587 | \n", + "0.324 | \n", + "0.807 | \n", + "0.414 | \n", + "0.225 | \n", + "|
| ontological synopsis | \n", + "0.099 | \n", + "0.056 | \n", + "0.085 | \n", + "2.070 | \n", + "0.011 | \n", + "13.070 | \n", + "6.563 | \n", + "0.345 | \n", + "0.016 | \n", + "0.685 | \n", + "0.269 | \n", + "0.949 | \n", + "0.316 | \n", + "0.338 | \n", + "
| \n", + " | \n", + " | proportion significant | \n", + "has top term | \n", + "num GO terms | \n", + "num unannotated | \n", + "num unparsed | \n", + "
|---|---|---|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " | \n", + " | \n", + " | \n", + " |
| gpt-3.5-turbo | \n", + "narrative synopsis | \n", + "0.661 | \n", + "0.134 | \n", + "3.782 | \n", + "0.197 | \n", + "5.500 | \n", + "
| no synopsis | \n", + "0.634 | \n", + "0.218 | \n", + "4.690 | \n", + "0.218 | \n", + "7.246 | \n", + "|
| ontological synopsis | \n", + "0.612 | \n", + "0.148 | \n", + "3.408 | \n", + "0.085 | \n", + "5.838 | \n", + "|
| text-davinci-003 | \n", + "narrative synopsis | \n", + "0.372 | \n", + "0.085 | \n", + "3.915 | \n", + "0.331 | \n", + "11.359 | \n", + "
| no synopsis | \n", + "0.414 | \n", + "0.092 | \n", + "3.063 | \n", + "0.225 | \n", + "10.324 | \n", + "|
| ontological synopsis | \n", + "0.316 | \n", + "0.099 | \n", + "6.563 | \n", + "0.338 | \n", + "13.070 | \n", + "
| \n", + " | \n", + " | proportion significant | \n", + "has top term | \n", + "num GO terms | \n", + "num unannotated | \n", + "num unparsed | \n", + "
|---|---|---|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " | \n", + " | \n", + " | \n", + " |
| gpt-3.5-turbo | \n", + "narrative synopsis | \n", + "0.661 | \n", + "0.134 | \n", + "3.782 | \n", + "0.197 | \n", + "5.500 | \n", + "
| no synopsis | \n", + "0.634 | \n", + "0.218 | \n", + "4.690 | \n", + "0.218 | \n", + "7.246 | \n", + "|
| ontological synopsis | \n", + "0.612 | \n", + "0.148 | \n", + "3.408 | \n", + "0.085 | \n", + "5.838 | \n", + "|
| text-davinci-003 | \n", + "narrative synopsis | \n", + "0.372 | \n", + "0.085 | \n", + "3.915 | \n", + "0.331 | \n", + "11.359 | \n", + "
| no synopsis | \n", + "0.414 | \n", + "0.092 | \n", + "3.063 | \n", + "0.225 | \n", + "10.324 | \n", + "|
| ontological synopsis | \n", + "0.316 | \n", + "0.099 | \n", + "6.563 | \n", + "0.338 | \n", + "13.070 | \n", + "
| \n", + " | \n", + " | has top term | \n", + "in top 5 | \n", + "in top 10 | \n", + "size overlap | \n", + "similarity | \n", + "num terms | \n", + "num GO terms | \n", + "nr size overlap | \n", + "nr similarity | \n", + "mean p value | \n", + "min p value | \n", + "max p value | \n", + "proportion significant | \n", + "num unannotated | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " |
| N/A | \n", + "closure | \n", + "True | \n", + "True | \n", + "True | \n", + "872 | \n", + "0.239 | \n", + "9056 | \n", + "8977 | \n", + "9 | \n", + "0.140 | \n", + "0.996 | \n", + "0.011 | \n", + "1.000 | \n", + "0.266 | \n", + "0 | \n", + "
| random | \n", + "True | \n", + "False | \n", + "False | \n", + "33 | \n", + "0.043 | \n", + "181 | \n", + "181 | \n", + "3 | \n", + "0.062 | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "0.186 | \n", + "98 | \n", + "|
| rank_based | \n", + "True | \n", + "True | \n", + "True | \n", + "58 | \n", + "0.090 | \n", + "200 | \n", + "200 | \n", + "7 | \n", + "0.071 | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "0.343 | \n", + "61 | \n", + "|
| standard | \n", + "True | \n", + "True | \n", + "True | \n", + "872 | \n", + "1.000 | \n", + "873 | \n", + "872 | \n", + "40 | \n", + "1.000 | \n", + "0.024 | \n", + "0.011 | \n", + "0.050 | \n", + "1.000 | \n", + "0 | \n", + "|
| standard_no_ontology | \n", + "True | \n", + "True | \n", + "True | \n", + "199 | \n", + "0.449 | \n", + "227 | \n", + "227 | \n", + "18 | \n", + "0.800 | \n", + "0.877 | \n", + "0.023 | \n", + "1.000 | \n", + "0.969 | \n", + "0 | \n", + "|
| gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "True | \n", + "True | \n", + "True | \n", + "15 | \n", + "0.333 | \n", + "20 | \n", + "20 | \n", + "4 | \n", + "0.500 | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "2 | \n", + "
| no_synopsis | \n", + "True | \n", + "True | \n", + "True | \n", + "16 | \n", + "0.200 | \n", + "53 | \n", + "19 | \n", + "5 | \n", + "0.250 | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "3 | \n", + "|
| ontological_synopsis | \n", + "True | \n", + "True | \n", + "True | \n", + "10 | \n", + "0.200 | \n", + "39 | \n", + "19 | \n", + "3 | \n", + "0.667 | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "2 | \n", + "|
| text-davinci-003 | \n", + "narrative_synopsis | \n", + "True | \n", + "True | \n", + "True | \n", + "9 | \n", + "0.111 | \n", + "48 | \n", + "15 | \n", + "2 | \n", + "0.125 | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "3 | \n", + "
| no_synopsis | \n", + "True | \n", + "True | \n", + "True | \n", + "6 | \n", + "0.083 | \n", + "60 | \n", + "17 | \n", + "3 | \n", + "0.167 | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "5 | \n", + "|
| ontological_synopsis | \n", + "True | \n", + "True | \n", + "True | \n", + "12 | \n", + "0.103 | \n", + "36 | \n", + "25 | \n", + "4 | \n", + "0.333 | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "1.000 | \n", + "7 | \n", + "
| \n", + " | source geneset | \n", + "
|---|---|
| 0 | \n", + "EDS | \n", + "
| 34 | \n", + "FA | \n", + "
| 170 | \n", + "HALLMARK_ANGIOGENESIS | \n", + "
| 238 | \n", + "HALLMARK_APICAL_SURFACE | \n", + "
| 714 | \n", + "HALLMARK_HEDGEHOG_SIGNALING | \n", + "
| ... | \n", + "... | \n", + "
| 2244 | \n", + "peroxisome | \n", + "
| 2278 | \n", + "progeria | \n", + "
| 2312 | \n", + "regulation of presynaptic membrane potential | \n", + "
| 2346 | \n", + "sensory ataxia | \n", + "
| 2397 | \n", + "tf-downreg-colorectal | \n", + "
25 rows × 1 columns
\n", + "| \n", + " | \n", + " | has top term | \n", + "in top 5 | \n", + "in top 10 | \n", + "size overlap | \n", + "similarity | \n", + "num terms | \n", + "num GO terms | \n", + "nr size overlap | \n", + "nr similarity | \n", + "mean p value | \n", + "min p value | \n", + "max p value | \n", + "proportion significant | \n", + "num unannotated | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " |
| N/A | \n", + "closure | \n", + "1.00 | \n", + "0.04 | \n", + "0.09 | \n", + "132.61 | \n", + "7.95e-02 | \n", + "2389.76 | \n", + "2346.59 | \n", + "3.41 | \n", + "2.27e-02 | \n", + "9.15e-01 | \n", + "2.59e-04 | \n", + "1.00 | \n", + "0.09 | \n", + "0.00 | \n", + "
| random | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "1.41 | \n", + "7.41e-03 | \n", + "26.07 | \n", + "26.07 | \n", + "0.26 | \n", + "6.58e-03 | \n", + "9.54e-01 | \n", + "3.71e-01 | \n", + "1.00 | \n", + "0.05 | \n", + "14.74 | \n", + "|
| rank_based | \n", + "0.04 | \n", + "0.04 | \n", + "0.04 | \n", + "2.85 | \n", + "1.70e-02 | \n", + "26.72 | \n", + "26.72 | \n", + "0.28 | \n", + "8.75e-03 | \n", + "9.11e-01 | \n", + "2.62e-01 | \n", + "1.00 | \n", + "0.09 | \n", + "2.70 | \n", + "|
| standard | \n", + "1.00 | \n", + "1.00 | \n", + "1.00 | \n", + "132.61 | \n", + "9.83e-01 | \n", + "135.43 | \n", + "132.61 | \n", + "15.70 | \n", + "9.78e-01 | \n", + "8.28e-03 | \n", + "2.59e-04 | \n", + "0.05 | \n", + "1.00 | \n", + "0.00 | \n", + "|
| standard_no_ontology | \n", + "0.63 | \n", + "0.54 | \n", + "0.57 | \n", + "28.80 | \n", + "2.14e-01 | \n", + "38.37 | \n", + "38.37 | \n", + "5.63 | \n", + "1.92e-01 | \n", + "2.96e-01 | \n", + "7.75e-04 | \n", + "1.00 | \n", + "0.71 | \n", + "0.00 | \n", + "|
| ... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "
| gpt-3.5-turbo | \n", + "no_synopsis | \n", + "0.20 | \n", + "0.18 | \n", + "0.20 | \n", + "2.45 | \n", + "2.44e-02 | \n", + "5.27 | \n", + "4.33 | \n", + "0.71 | \n", + "4.12e-02 | \n", + "4.27e-01 | \n", + "1.48e-01 | \n", + "0.75 | \n", + "0.57 | \n", + "0.33 | \n", + "
| ontological_synopsis | \n", + "0.34 | \n", + "0.34 | \n", + "0.34 | \n", + "2.27 | \n", + "3.10e-02 | \n", + "5.35 | \n", + "3.90 | \n", + "0.77 | \n", + "5.47e-02 | \n", + "3.90e-01 | \n", + "1.16e-01 | \n", + "0.69 | \n", + "0.61 | \n", + "0.12 | \n", + "|
| text-davinci-003 | \n", + "narrative_synopsis | \n", + "0.12 | \n", + "0.12 | \n", + "0.12 | \n", + "1.18 | \n", + "1.07e-02 | \n", + "11.34 | \n", + "3.35 | \n", + "0.35 | \n", + "1.97e-02 | \n", + "6.75e-01 | \n", + "3.87e-01 | \n", + "0.90 | \n", + "0.33 | \n", + "0.33 | \n", + "
| no_synopsis | \n", + "0.12 | \n", + "0.11 | \n", + "0.12 | \n", + "1.00 | \n", + "7.48e-03 | \n", + "7.36 | \n", + "2.62 | \n", + "0.28 | \n", + "1.57e-02 | \n", + "5.95e-01 | \n", + "3.95e-01 | \n", + "0.79 | \n", + "0.41 | \n", + "0.25 | \n", + "|
| ontological_synopsis | \n", + "0.22 | \n", + "0.12 | \n", + "0.17 | \n", + "2.51 | \n", + "2.36e-02 | \n", + "12.59 | \n", + "7.91 | \n", + "0.52 | \n", + "2.67e-02 | \n", + "6.63e-01 | \n", + "2.13e-01 | \n", + "0.94 | \n", + "0.34 | \n", + "0.45 | \n", + "
11 rows × 14 columns
\n", + "| \n", + " | \n", + " | has top term | \n", + "in top 5 | \n", + "in top 10 | \n", + "size overlap | \n", + "similarity | \n", + "num terms | \n", + "num GO terms | \n", + "nr size overlap | \n", + "nr similarity | \n", + "mean p value | \n", + "min p value | \n", + "max p value | \n", + "proportion significant | \n", + "num unannotated | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " |
| N/A | \n", + "closure | \n", + "1.000 | \n", + "0.043 | \n", + "0.087 | \n", + "132.609 | \n", + "0.080 | \n", + "2389.761 | \n", + "2346.587 | \n", + "3.413 | \n", + "0.023 | \n", + "0.915 | \n", + "0.000 | \n", + "1.000 | \n", + "0.085 | \n", + "0.000 | \n", + "
| random | \n", + "0.000 | \n", + "0.000 | \n", + "0.000 | \n", + "1.413 | \n", + "0.007 | \n", + "26.065 | \n", + "26.065 | \n", + "0.261 | \n", + "0.007 | \n", + "0.954 | \n", + "0.371 | \n", + "1.000 | \n", + "0.046 | \n", + "14.739 | \n", + "|
| rank_based | \n", + "0.043 | \n", + "0.043 | \n", + "0.043 | \n", + "2.848 | \n", + "0.017 | \n", + "26.717 | \n", + "26.717 | \n", + "0.283 | \n", + "0.009 | \n", + "0.911 | \n", + "0.262 | \n", + "1.000 | \n", + "0.090 | \n", + "2.696 | \n", + "|
| standard_no_ontology | \n", + "0.630 | \n", + "0.543 | \n", + "0.565 | \n", + "28.804 | \n", + "0.214 | \n", + "38.370 | \n", + "38.370 | \n", + "5.630 | \n", + "0.192 | \n", + "0.296 | \n", + "0.001 | \n", + "1.000 | \n", + "0.710 | \n", + "0.000 | \n", + "|
| gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "0.163 | \n", + "0.152 | \n", + "0.163 | \n", + "1.663 | \n", + "0.021 | \n", + "4.935 | \n", + "3.043 | \n", + "0.587 | \n", + "0.043 | \n", + "0.400 | \n", + "0.152 | \n", + "0.622 | \n", + "0.602 | \n", + "0.228 | \n", + "
| no_synopsis | \n", + "0.196 | \n", + "0.185 | \n", + "0.196 | \n", + "2.446 | \n", + "0.024 | \n", + "5.272 | \n", + "4.326 | \n", + "0.707 | \n", + "0.041 | \n", + "0.427 | \n", + "0.148 | \n", + "0.750 | \n", + "0.574 | \n", + "0.326 | \n", + "|
| ontological_synopsis | \n", + "0.337 | \n", + "0.337 | \n", + "0.337 | \n", + "2.272 | \n", + "0.031 | \n", + "5.348 | \n", + "3.902 | \n", + "0.772 | \n", + "0.055 | \n", + "0.390 | \n", + "0.116 | \n", + "0.692 | \n", + "0.611 | \n", + "0.120 | \n", + "|
| text-davinci-003 | \n", + "narrative_synopsis | \n", + "0.120 | \n", + "0.120 | \n", + "0.120 | \n", + "1.185 | \n", + "0.011 | \n", + "11.337 | \n", + "3.348 | \n", + "0.348 | \n", + "0.020 | \n", + "0.675 | \n", + "0.387 | \n", + "0.904 | \n", + "0.326 | \n", + "0.326 | \n", + "
| no_synopsis | \n", + "0.120 | \n", + "0.109 | \n", + "0.120 | \n", + "1.000 | \n", + "0.007 | \n", + "7.359 | \n", + "2.620 | \n", + "0.283 | \n", + "0.016 | \n", + "0.595 | \n", + "0.395 | \n", + "0.786 | \n", + "0.406 | \n", + "0.250 | \n", + "|
| ontological_synopsis | \n", + "0.217 | \n", + "0.120 | \n", + "0.174 | \n", + "2.511 | \n", + "0.024 | \n", + "12.587 | \n", + "7.913 | \n", + "0.522 | \n", + "0.027 | \n", + "0.663 | \n", + "0.213 | \n", + "0.945 | \n", + "0.338 | \n", + "0.446 | \n", + "
| \n", + " | \n", + " | proportion significant | \n", + "has top term | \n", + "num GO terms | \n", + "num unannotated | \n", + "num unparsed | \n", + "
|---|---|---|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " | \n", + " | \n", + " | \n", + " |
| gpt-3.5-turbo | \n", + "narrative synopsis | \n", + "0.602 | \n", + "0.163 | \n", + "3.043 | \n", + "0.228 | \n", + "4.935 | \n", + "
| no synopsis | \n", + "0.574 | \n", + "0.196 | \n", + "4.326 | \n", + "0.326 | \n", + "5.272 | \n", + "|
| ontological synopsis | \n", + "0.611 | \n", + "0.337 | \n", + "3.902 | \n", + "0.120 | \n", + "5.348 | \n", + "|
| text-davinci-003 | \n", + "narrative synopsis | \n", + "0.326 | \n", + "0.120 | \n", + "3.348 | \n", + "0.326 | \n", + "11.337 | \n", + "
| no synopsis | \n", + "0.406 | \n", + "0.120 | \n", + "2.620 | \n", + "0.250 | \n", + "7.359 | \n", + "|
| ontological synopsis | \n", + "0.338 | \n", + "0.217 | \n", + "7.913 | \n", + "0.446 | \n", + "12.587 | \n", + "
| \n", + " | id | \n", + "label | \n", + "redundant | \n", + "standard | \n", + "standard no ontology | \n", + "turbo no synopsis | \n", + "turbo narrative synopsis | \n", + "dav ontological synopsis | \n", + "turbo ontological synopsis | \n", + "dav no synopsis | \n", + "dav narrative synopsis | \n", + "rank based | \n", + "p_label | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", + "GO:0006625 | \n", + "protein targeting to peroxisome | \n", + "False | \n", + "0.0 | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "protein targeting to peroxisome 1.983967326142... | \n", + "
| 1 | \n", + "GO:0072663 | \n", + "establishment of protein localization to perox... | \n", + "True | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "establishment of protein localization to perox... | \n", + "
| 2 | \n", + "GO:0072662 | \n", + "protein localization to peroxisome | \n", + "True | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "protein localization to peroxisome 1.983967326... | \n", + "
| 3 | \n", + "GO:0015919 | \n", + "peroxisomal membrane transport | \n", + "False | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "peroxisomal membrane transport 3.8191371028307... | \n", + "
| 4 | \n", + "GO:0043574 | \n", + "peroxisomal transport | \n", + "True | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "peroxisomal transport 6.889423793379416e-16 | \n", + "
| ... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "
| 92 | \n", + "GO:0016020 | \n", + "membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "membrane | \n", + "
| 93 | \n", + "GO:0005829 | \n", + "cytosol | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "cytosol | \n", + "
| 94 | \n", + "GO:0005634 | \n", + "nucleus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "nucleus | \n", + "
| 95 | \n", + "GO:0005654 | \n", + "nucleoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "nucleoplasm | \n", + "
| 96 | \n", + "GO:0046872 | \n", + "metal ion binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "metal ion binding | \n", + "
97 rows × 13 columns
\n", + "| \n", + " | model | \n", + "method | \n", + "has top term | \n", + "in top 5 | \n", + "in top 10 | \n", + "size overlap | \n", + "similarity | \n", + "num terms | \n", + "num GO terms | \n", + "nr size overlap | \n", + "nr similarity | \n", + "mean p value | \n", + "min p value | \n", + "max p value | \n", + "proportion significant | \n", + "num unannotated | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2256 | \n", + "N/A | \n", + "standard | \n", + "True | \n", + "True | \n", + "True | \n", + "62 | \n", + "1.00 | \n", + "62 | \n", + "62 | \n", + "10 | \n", + "1.00 | \n", + "5.64e-03 | \n", + "1.98e-16 | \n", + "0.04 | \n", + "1.00 | \n", + "0 | \n", + "
| 2257 | \n", + "N/A | \n", + "standard_no_ontology | \n", + "True | \n", + "False | \n", + "False | \n", + "15 | \n", + "0.22 | \n", + "21 | \n", + "21 | \n", + "7 | \n", + "0.41 | \n", + "2.89e-01 | \n", + "1.98e-16 | \n", + "1.00 | \n", + "0.71 | \n", + "0 | \n", + "
| 2260 | \n", + "N/A | \n", + "closure | \n", + "True | \n", + "True | \n", + "True | \n", + "62 | \n", + "0.19 | \n", + "419 | \n", + "391 | \n", + "7 | \n", + "0.14 | \n", + "8.02e-01 | \n", + "1.98e-16 | \n", + "1.00 | \n", + "0.20 | \n", + "0 | \n", + "
| 2252 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "5 | \n", + "0.08 | \n", + "10 | \n", + "6 | \n", + "4 | \n", + "0.33 | \n", + "1.73e-01 | \n", + "2.87e-04 | \n", + "1.00 | \n", + "0.83 | \n", + "0 | \n", + "
| 2253 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "True | \n", + "False | \n", + "True | \n", + "4 | \n", + "0.06 | \n", + "10 | \n", + "6 | \n", + "2 | \n", + "0.15 | \n", + "3.33e-01 | \n", + "1.98e-16 | \n", + "1.00 | \n", + "0.67 | \n", + "0 | \n", + "
| ... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "
| 2254 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "8 | \n", + "0 | \n", + "0 | \n", + "0.00 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0 | \n", + "
| 2255 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "3 | \n", + "0 | \n", + "0 | \n", + "0.00 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0 | \n", + "
| 2247 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "3 | \n", + "1 | \n", + "0 | \n", + "0.00 | \n", + "1.00e+00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "1 | \n", + "
| 2258 | \n", + "N/A | \n", + "random | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "8 | \n", + "8 | \n", + "0 | \n", + "0.00 | \n", + "1.00e+00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "7 | \n", + "
| 2259 | \n", + "N/A | \n", + "rank_based | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "8 | \n", + "8 | \n", + "0 | \n", + "0.00 | \n", + "1.00e+00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "1 | \n", + "
17 rows × 16 columns
\n", + "| \n", + " | id | \n", + "label | \n", + "redundant | \n", + "standard | \n", + "standard no ontology | \n", + "turbo no synopsis | \n", + "turbo narrative synopsis | \n", + "dav ontological synopsis | \n", + "turbo ontological synopsis | \n", + "dav no synopsis | \n", + "dav narrative synopsis | \n", + "rank based | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", + "GO:0006625 | \n", + "protein targeting to peroxisome | \n", + "False | \n", + "0.0 | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 1 | \n", + "GO:0072663 | \n", + "establishment of protein localization to perox... | \n", + "True | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 2 | \n", + "GO:0072662 | \n", + "protein localization to peroxisome | \n", + "True | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 3 | \n", + "GO:0015919 | \n", + "peroxisomal membrane transport | \n", + "False | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 4 | \n", + "GO:0043574 | \n", + "peroxisomal transport | \n", + "True | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| ... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "
| 92 | \n", + "GO:0016020 | \n", + "membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "
| 93 | \n", + "GO:0005829 | \n", + "cytosol | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "
| 94 | \n", + "GO:0005634 | \n", + "nucleus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "
| 95 | \n", + "GO:0005654 | \n", + "nucleoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "
| 96 | \n", + "GO:0046872 | \n", + "metal ion binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "
97 rows × 12 columns
\n", + "| \n", + " | id | \n", + "label | \n", + "redundant | \n", + "standard | \n", + "standard no ontology | \n", + "dav ontological synopsis | \n", + "turbo no synopsis | \n", + "turbo narrative synopsis | \n", + "dav no synopsis | \n", + "dav narrative synopsis | \n", + "turbo ontological synopsis | \n", + "rank based | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", + "GO:0006625 | \n", + "protein targeting to peroxisome | \n", + "False | \n", + "0.0 | \n", + "10.0 | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 1 | \n", + "GO:0072663 | \n", + "establishment of protein localization to perox... | \n", + "True | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 2 | \n", + "GO:0072662 | \n", + "protein localization to peroxisome | \n", + "True | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 3 | \n", + "GO:0015919 | \n", + "peroxisomal membrane transport | \n", + "False | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 4 | \n", + "GO:0043574 | \n", + "peroxisomal transport | \n", + "True | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| ... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "
| 95 | \n", + "GO:0016020 | \n", + "membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "
| 96 | \n", + "GO:0005829 | \n", + "cytosol | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "
| 97 | \n", + "GO:0005634 | \n", + "nucleus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "
| 98 | \n", + "GO:0005654 | \n", + "nucleoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "
| 99 | \n", + "GO:0046872 | \n", + "metal ion binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "
100 rows × 12 columns
\n", + "| \n", + " | model | \n", + "method | \n", + "has top term | \n", + "in top 5 | \n", + "in top 10 | \n", + "size overlap | \n", + "similarity | \n", + "num terms | \n", + "num GO terms | \n", + "nr size overlap | \n", + "nr similarity | \n", + "mean p value | \n", + "min p value | \n", + "max p value | \n", + "proportion significant | \n", + "num unannotated | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2358 | \n", + "N/A | \n", + "standard | \n", + "True | \n", + "True | \n", + "True | \n", + "9 | \n", + "1.00 | \n", + "9 | \n", + "9 | \n", + "3 | \n", + "1.00 | \n", + "0.01 | \n", + "1.95e-05 | \n", + "0.04 | \n", + "1.00 | \n", + "0 | \n", + "
| 2359 | \n", + "N/A | \n", + "standard_no_ontology | \n", + "False | \n", + "False | \n", + "False | \n", + "3 | \n", + "0.30 | \n", + "4 | \n", + "4 | \n", + "1 | \n", + "0.20 | \n", + "0.26 | \n", + "3.13e-04 | \n", + "1.00 | \n", + "0.75 | \n", + "0 | \n", + "
| 2348 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "True | \n", + "True | \n", + "True | \n", + "2 | \n", + "0.20 | \n", + "5 | \n", + "3 | \n", + "2 | \n", + "0.67 | \n", + "0.33 | \n", + "1.95e-05 | \n", + "1.00 | \n", + "0.67 | \n", + "0 | \n", + "
| 2349 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "True | \n", + "True | \n", + "True | \n", + "2 | \n", + "0.18 | \n", + "7 | \n", + "4 | \n", + "2 | \n", + "0.40 | \n", + "0.50 | \n", + "1.95e-05 | \n", + "1.00 | \n", + "0.50 | \n", + "0 | \n", + "
| 2351 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "1 | \n", + "0.11 | \n", + "5 | \n", + "1 | \n", + "1 | \n", + "0.33 | \n", + "0.03 | \n", + "2.80e-02 | \n", + "0.03 | \n", + "1.00 | \n", + "0 | \n", + "
| ... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "... | \n", + "
| 2357 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "11 | \n", + "4 | \n", + "0 | \n", + "0.00 | \n", + "1.00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "1 | \n", + "
| 2356 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "8 | \n", + "2 | \n", + "0 | \n", + "0.00 | \n", + "1.00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "0 | \n", + "
| 2353 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "5 | \n", + "3 | \n", + "0 | \n", + "0.00 | \n", + "1.00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "1 | \n", + "
| 2352 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "5 | \n", + "3 | \n", + "0 | \n", + "0.00 | \n", + "1.00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "0 | \n", + "
| 2354 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "9 | \n", + "6 | \n", + "0 | \n", + "0.00 | \n", + "1.00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "0 | \n", + "
17 rows × 16 columns
\n", + "| \n", + " | model | \n", + "method | \n", + "prompt_variant | \n", + "go term ids | \n", + "unannotated labels | \n", + "
|---|---|---|---|---|---|
| 2358 | \n", + "N/A | \n", + "standard | \n", + "None | \n", + "[GO:0042552, GO:0008366, GO:0007272, GO:0007422, GO:0014037, GO:0010001, GO:0032287, GO:0006264, GO:0042063] | \n", + "[] | \n", + "
| 2359 | \n", + "N/A | \n", + "standard_no_ontology | \n", + "None | \n", + "[GO:0021680, GO:0032287, GO:0006264, GO:0007422] | \n", + "[] | \n", + "
| 2348 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "v1 | \n", + "[GO:0042552, GO:0007422, GO:0022011] | \n", + "[] | \n", + "
| 2349 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "v2 | \n", + "[GO:0042552, GO:0007422, GO:0006457, GO:0007600] | \n", + "[] | \n", + "
| 2351 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "v2 | \n", + "[GO:0006264] | \n", + "[] | \n", + "
| 2350 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "v1 | \n", + "[GO:0043209, GO:0006264] | \n", + "[] | \n", + "
| 2347 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "v2 | \n", + "[GO:0042552, GO:0007411, GO:0007399, GO:0008104, GO:0031175] | \n", + "[] | \n", + "
| 2355 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "v2 | \n", + "[GO:0031625, GO:0003677, GO:0006027, GO:0043583, GO:0045475, GO:0007399, GO:0006457, GO:0043066, GO:0010595, GO:0002639, GO:0034214, GO:0050974, GO:0006812, GO:0015886, GO:0071260, GO:0042552, GO:0098742, GO:0006839, GO:0019226, GO:0008380, GO:0003774, GO:0061608, GO:0006607, GO:0003887, GO:0006284] | \n", + "[glycosaminoglycan catabolic process, transmission of nerve impulse, RNA splicing, cytoskeletal motor activity] | \n", + "
| 2362 | \n", + "N/A | \n", + "closure | \n", + "None | \n", + "[GO:0005654, GO:0140018, GO:0008381, GO:0032060, GO:0009611, GO:0006915, GO:0043484, GO:0006400, GO:0046620, GO:0035994, GO:0071310, GO:0043139, GO:0048168, GO:0055085, GO:0005760, GO:0032963, GO:0042982, GO:0030278, GO:0043218, GO:0000981, GO:0061608, GO:0032570, GO:0032868, GO:0034975, GO:0048536, GO:0006959, GO:0000976, GO:0008270, GO:0003158, GO:0034101, GO:0009612, GO:0060173, GO:0042391, GO:0033157, GO:0021675, GO:0004860, GO:0042564, GO:0099022, GO:0006611, GO:0043565, GO:0002020, GO:0006094, GO:0045182, GO:0046872, GO:0005576, GO:0007165, GO:0035264, GO:0010595, GO:0016597, GO:0014037, GO:0032496, GO:0032355, GO:0002161, GO:0006914, GO:0007399, GO:0034142, GO:0106074, GO:1904390, GO:0050885, GO:0043154, GO:0002639, GO:0006096, GO:0006259, GO:0098743, GO:0035284, GO:0007611, GO:0006390, GO:0035640, GO:0014040, GO:0033574, GO:0006801, GO:0071260, GO:0031069, GO:0006287, GO:0007268, GO:0001701, GO:0007040, GO:0005739, GO:0035578, GO:0006419, GO:0005759, GO:0035633, GO:0034774, GO:0097577, GO:0046548, GO:0005783, GO:0001707, GO:0031625, GO:0051787, GO:0005125, GO:0051607, GO:0004561, GO:0030201, GO:0003697, GO:0008366, GO:0008033, GO:0008408, GO:0005643, GO:0003700, GO:0006812, ...] | \n", + "[] | \n", + "
| 2361 | \n", + "N/A | \n", + "rank_based | \n", + "None | \n", + "[GO:0005654, GO:0006357, GO:0070062, GO:0042802, GO:0016020, GO:0046872, GO:0005576, GO:0005737, GO:0005829, GO:0005634, GO:0005739, GO:0005615, GO:0005524, GO:0005886, GO:0003723] | \n", + "[] | \n", + "
| 2360 | \n", + "N/A | \n", + "random | \n", + "None | \n", + "[GO:0007169, GO:0042132, GO:0007207, GO:0045944, GO:0001916, GO:0007229, GO:1990889, GO:0097546, GO:0050878, GO:0044772, GO:0006413, GO:0001525, GO:0005615, GO:0036064, GO:0072686] | \n", + "[transmembrane receptor protein tyrosine kinase signaling pathway, fructose 1,6-bisphosphate 1-phosphatase activity, phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway, positive regulation of T cell mediated cytotoxicity, integrin-mediated signaling pathway, H4K20me3 modified histone binding, ciliary base, mitotic cell cycle phase transition, translational initiation, angiogenesis, ciliary basal body, mitotic spindle] | \n", + "
| 2346 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "v1 | \n", + "[GO:0006457, GO:0030163, GO:0055085] | \n", + "[] | \n", + "
| 2357 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "v2 | \n", + "[GO:0000981, GO:0009056, GO:0002377, GO:0005643] | \n", + "[immunoglobulin production] | \n", + "
| 2356 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "v1 | \n", + "[GO:0030218, GO:0036211] | \n", + "[] | \n", + "
| 2353 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "v2 | \n", + "[GO:0006412, GO:0008152, GO:0006936] | \n", + "[muscle contraction] | \n", + "
| 2352 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "v1 | \n", + "[GO:0015031, GO:0006629, GO:0009653] | \n", + "[] | \n", + "
| 2354 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "v1 | \n", + "[GO:0046872, GO:0031625, GO:0045944, GO:0002639, GO:1901184, GO:0033157] | \n", + "[] | \n", + "
| \n", + " | id | \n", + "label | \n", + "redundant | \n", + "standard | \n", + "turbo ontological synopsis | \n", + "standard no ontology | \n", + "turbo narrative synopsis | \n", + "rank based | \n", + "dav ontological synopsis | \n", + "turbo no synopsis | \n", + "dav narrative synopsis | \n", + "dav no synopsis | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", + "GO:0042552 | \n", + "myelination | \n", + "False | \n", + "0.0 | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 1 | \n", + "GO:0008366 | \n", + "axon ensheathment | \n", + "True | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 2 | \n", + "GO:0007272 | \n", + "ensheathment of neurons | \n", + "True | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 3 | \n", + "GO:0007422 | \n", + "peripheral nervous system development | \n", + "False | \n", + "3.0 | \n", + "1.0 | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 4 | \n", + "GO:0014037 | \n", + "Schwann cell differentiation | \n", + "True | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 5 | \n", + "GO:0010001 | \n", + "glial cell differentiation | \n", + "True | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 6 | \n", + "GO:0032287 | \n", + "peripheral nervous system myelin maintenance | \n", + "True | \n", + "6.0 | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 7 | \n", + "GO:0006264 | \n", + "mitochondrial DNA replication | \n", + "False | \n", + "7.0 | \n", + "NaN | \n", + "2.0 | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 8 | \n", + "GO:0042063 | \n", + "gliogenesis | \n", + "True | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 9 | \n", + "GO:0021680 | \n", + "cerebellar Purkinje cell layer development | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 10 | \n", + "MONDO:0005071 | \n", + "None | \n", + "False | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 11 | \n", + "GO:0022011 | \n", + "myelination in peripheral nervous system | \n", + "False | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 12 | \n", + "MONDO:0005244 | \n", + "None | \n", + "False | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 13 | \n", + "MONDO:0015626 | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 14 | \n", + "MONDO:0007790 | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 15 | \n", + "GO:0043209 | \n", + "myelin sheath | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 16 | \n", + "tetratricopeptide repeat | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 17 | \n", + "transporter protein\\n\\nmechanism: these genes are involved in myelin upkeep and various neurological diseases associated with defects in myelin sheath synthesis and functions. they play roles in mitochondrial dna replication and transport, as well as protein transportation across the nuclear membrane. the presence of tetratricopeptide repeat motifs in these genes suggests their roles in protein-protein interactions and chaperone functions | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 18 | \n", + "GO:0005654 | \n", + "nucleoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 19 | \n", + "GO:0006357 | \n", + "regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 20 | \n", + "GO:0070062 | \n", + "extracellular exosome | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 21 | \n", + "GO:0042802 | \n", + "identical protein binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 22 | \n", + "GO:0016020 | \n", + "membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 23 | \n", + "GO:0046872 | \n", + "metal ion binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 24 | \n", + "GO:0005576 | \n", + "extracellular region | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 25 | \n", + "GO:0005737 | \n", + "cytoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 26 | \n", + "GO:0005829 | \n", + "cytosol | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 27 | \n", + "GO:0005634 | \n", + "nucleus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 28 | \n", + "GO:0005739 | \n", + "mitochondrion | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 29 | \n", + "GO:0005615 | \n", + "extracellular space | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "11.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 30 | \n", + "GO:0005524 | \n", + "ATP binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "12.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 31 | \n", + "GO:0005886 | \n", + "plasma membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "13.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 32 | \n", + "GO:0003723 | \n", + "RNA binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "14.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 33 | \n", + "mitochondrial function | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 34 | \n", + "GO:0006457 | \n", + "protein folding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 35 | \n", + "GO:0030163 | \n", + "protein catabolic process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 36 | \n", + "GO:0055085 | \n", + "transmembrane transport | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 37 | \n", + "transcriptional regulation | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "
| 38 | \n", + "mitochondrial rna synthesis | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "
| 39 | \n", + "neurodevelopment | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "
| 40 | \n", + "GO:0030218 | \n", + "erythrocyte differentiation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "
| 41 | \n", + "GO:0036211 | \n", + "protein modification process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "
| 42 | \n", + "nucleolar function | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "
| 43 | \n", + "neuronal network formation | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "
| 44 | \n", + "sensory receptor function | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "
| 45 | \n", + "MESH:D024510 | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "
| 46 | \n", + "neuronal development | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "
| 47 | \n", + "GO:0015031 | \n", + "protein transport | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "
| 48 | \n", + "GO:0006629 | \n", + "lipid metabolic process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "
| 49 | \n", + "GO:0009653 | \n", + "anatomical structure morphogenesis | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "
| 50 | \n", + "dna-binding | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 51 | \n", + "rna polymerase ii-specific activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 52 | \n", + "GO:0031625 | \n", + "ubiquitin protein ligase binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 53 | \n", + "GO:0045944 | \n", + "positive regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 54 | \n", + "GO:0002639 | \n", + "positive regulation of immunoglobulin production | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 55 | \n", + "GO:1901184 | \n", + "regulation of ERBB signaling pathway | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 56 | \n", + "GO:0033157 | \n", + "regulation of intracellular protein transport | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 57 | \n", + "monoatomic cation | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| \n", + " | model | \n", + "method | \n", + "has top term | \n", + "in top 5 | \n", + "in top 10 | \n", + "size overlap | \n", + "similarity | \n", + "num terms | \n", + "num GO terms | \n", + "nr size overlap | \n", + "nr similarity | \n", + "mean p value | \n", + "min p value | \n", + "max p value | \n", + "proportion significant | \n", + "num unannotated | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1746 | \n", + "N/A | \n", + "standard | \n", + "True | \n", + "True | \n", + "True | \n", + "491 | \n", + "1.00e+00 | \n", + "491 | \n", + "491 | \n", + "15 | \n", + "1.00e+00 | \n", + "2.96e-03 | \n", + "2.66e-193 | \n", + "4.96e-02 | \n", + "1.00 | \n", + "0 | \n", + "
| 1747 | \n", + "N/A | \n", + "standard_no_ontology | \n", + "True | \n", + "True | \n", + "True | \n", + "79 | \n", + "1.56e-01 | \n", + "95 | \n", + "95 | \n", + "3 | \n", + "4.62e-02 | \n", + "1.71e-01 | \n", + "2.66e-193 | \n", + "1.00e+00 | \n", + "0.83 | \n", + "0 | \n", + "
| 1750 | \n", + "N/A | \n", + "closure | \n", + "True | \n", + "False | \n", + "False | \n", + "491 | \n", + "1.11e-01 | \n", + "6315 | \n", + "6255 | \n", + "1 | \n", + "1.47e-03 | \n", + "8.93e-01 | \n", + "2.66e-193 | \n", + "1.00e+00 | \n", + "0.11 | \n", + "0 | \n", + "
| 1749 | \n", + "N/A | \n", + "rank_based | \n", + "False | \n", + "False | \n", + "False | \n", + "15 | \n", + "2.74e-02 | \n", + "72 | \n", + "72 | \n", + "1 | \n", + "2.63e-02 | \n", + "7.92e-01 | \n", + "3.40e-19 | \n", + "1.00e+00 | \n", + "0.21 | \n", + "4 | \n", + "
| 1736 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "5 | \n", + "1.02e-02 | \n", + "8 | \n", + "5 | \n", + "0 | \n", + "0.00e+00 | \n", + "1.08e-02 | \n", + "1.22e-28 | \n", + "4.94e-02 | \n", + "1.00 | \n", + "0 | \n", + "
| 1735 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "5 | \n", + "1.02e-02 | \n", + "6 | \n", + "6 | \n", + "0 | \n", + "0.00e+00 | \n", + "1.67e-01 | \n", + "4.13e-126 | \n", + "1.00e+00 | \n", + "0.83 | \n", + "0 | \n", + "
| 1748 | \n", + "N/A | \n", + "random | \n", + "False | \n", + "False | \n", + "False | \n", + "4 | \n", + "7.22e-03 | \n", + "67 | \n", + "67 | \n", + "0 | \n", + "0.00e+00 | \n", + "9.41e-01 | \n", + "1.18e-03 | \n", + "1.00e+00 | \n", + "0.06 | \n", + "29 | \n", + "
| 1741 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "3 | \n", + "6.11e-03 | \n", + "5 | \n", + "3 | \n", + "0 | \n", + "0.00e+00 | \n", + "9.86e-04 | \n", + "1.59e-14 | \n", + "2.96e-03 | \n", + "1.00 | \n", + "0 | \n", + "
| 1738 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "3 | \n", + "6.10e-03 | \n", + "5 | \n", + "4 | \n", + "0 | \n", + "0.00e+00 | \n", + "2.50e-01 | \n", + "1.50e-18 | \n", + "1.00e+00 | \n", + "0.75 | \n", + "0 | \n", + "
| 1740 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "3 | \n", + "6.07e-03 | \n", + "10 | \n", + "6 | \n", + "0 | \n", + "0.00e+00 | \n", + "5.00e-01 | \n", + "1.50e-18 | \n", + "1.00e+00 | \n", + "0.50 | \n", + "0 | \n", + "
| 1743 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "3 | \n", + "6.06e-03 | \n", + "15 | \n", + "7 | \n", + "0 | \n", + "0.00e+00 | \n", + "5.75e-01 | \n", + "7.76e-05 | \n", + "1.00e+00 | \n", + "0.43 | \n", + "0 | \n", + "
| 1737 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "2 | \n", + "4.07e-03 | \n", + "5 | \n", + "2 | \n", + "0 | \n", + "0.00e+00 | \n", + "3.88e-05 | \n", + "7.43e-13 | \n", + "7.76e-05 | \n", + "1.00 | \n", + "0 | \n", + "
| 1734 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "1 | \n", + "2.04e-03 | \n", + "3 | \n", + "1 | \n", + "0 | \n", + "0.00e+00 | \n", + "4.13e-126 | \n", + "4.13e-126 | \n", + "4.13e-126 | \n", + "1.00 | \n", + "0 | \n", + "
| 1742 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "1 | \n", + "2.02e-03 | \n", + "6 | \n", + "4 | \n", + "0 | \n", + "0.00e+00 | \n", + "7.50e-01 | \n", + "8.79e-09 | \n", + "1.00e+00 | \n", + "0.25 | \n", + "0 | \n", + "
| 1745 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00e+00 | \n", + "17 | \n", + "0 | \n", + "0 | \n", + "0.00e+00 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0 | \n", + "
| 1744 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00e+00 | \n", + "10 | \n", + "6 | \n", + "0 | \n", + "0.00e+00 | \n", + "1.00e+00 | \n", + "1.00e+00 | \n", + "1.00e+00 | \n", + "0.00 | \n", + "0 | \n", + "
| 1739 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00e+00 | \n", + "9 | \n", + "4 | \n", + "0 | \n", + "0.00e+00 | \n", + "1.00e+00 | \n", + "1.00e+00 | \n", + "1.00e+00 | \n", + "0.00 | \n", + "2 | \n", + "
| \n", + " | id | \n", + "label | \n", + "redundant | \n", + "standard | \n", + "standard no ontology | \n", + "turbo ontological synopsis | \n", + "dav narrative synopsis | \n", + "dav ontological synopsis | \n", + "turbo no synopsis | \n", + "turbo narrative synopsis | \n", + "dav no synopsis | \n", + "rank based | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", + "GO:0006907 | \n", + "pinocytosis | \n", + "False | \n", + "0.0 | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 1 | \n", + "GO:0006897 | \n", + "endocytosis | \n", + "True | \n", + "1.0 | \n", + "6.0 | \n", + "0.0 | \n", + "0.0 | \n", + "5.0 | \n", + "0.0 | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 2 | \n", + "GO:0044351 | \n", + "macropinocytosis | \n", + "True | \n", + "2.0 | \n", + "0.0 | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 3 | \n", + "GO:0016192 | \n", + "vesicle-mediated transport | \n", + "True | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 4 | \n", + "GO:0030100 | \n", + "regulation of endocytosis | \n", + "False | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 5 | \n", + "GO:0006810 | \n", + "transport | \n", + "True | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 6 | \n", + "GO:0051234 | \n", + "establishment of localization | \n", + "True | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 7 | \n", + "GO:0045807 | \n", + "positive regulation of endocytosis | \n", + "True | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 8 | \n", + "GO:0060627 | \n", + "regulation of vesicle-mediated transport | \n", + "True | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 9 | \n", + "GO:0051179 | \n", + "localization | \n", + "True | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 10 | \n", + "GO:0031410 | \n", + "cytoplasmic vesicle | \n", + "False | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 11 | \n", + "GO:0097708 | \n", + "intracellular vesicle | \n", + "True | \n", + "11.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 12 | \n", + "GO:0050766 | \n", + "positive regulation of phagocytosis | \n", + "True | \n", + "12.0 | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 13 | \n", + "GO:0048518 | \n", + "positive regulation of biological process | \n", + "True | \n", + "13.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 14 | \n", + "GO:0050764 | \n", + "regulation of phagocytosis | \n", + "True | \n", + "14.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 15 | \n", + "GO:0051128 | \n", + "regulation of cellular component organization | \n", + "True | \n", + "15.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 16 | \n", + "GO:0031982 | \n", + "vesicle | \n", + "True | \n", + "16.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 17 | \n", + "GO:0150094 | \n", + "amyloid-beta clearance by cellular catabolic process | \n", + "False | \n", + "17.0 | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 18 | \n", + "GO:0006909 | \n", + "phagocytosis | \n", + "True | \n", + "18.0 | \n", + "17.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 19 | \n", + "GO:0051049 | \n", + "regulation of transport | \n", + "True | \n", + "19.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 20 | \n", + "GO:0006898 | \n", + "receptor-mediated endocytosis | \n", + "True | \n", + "20.0 | \n", + "2.0 | \n", + "2.0 | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 21 | \n", + "GO:0051050 | \n", + "positive regulation of transport | \n", + "True | \n", + "21.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 22 | \n", + "GO:0005041 | \n", + "low-density lipoprotein particle receptor activity | \n", + "True | \n", + "22.0 | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 23 | \n", + "GO:0030139 | \n", + "endocytic vesicle | \n", + "True | \n", + "23.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 24 | \n", + "GO:0030228 | \n", + "lipoprotein particle receptor activity | \n", + "True | \n", + "24.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 25 | \n", + "GO:0030666 | \n", + "endocytic vesicle membrane | \n", + "True | \n", + "25.0 | \n", + "18.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 26 | \n", + "GO:0097242 | \n", + "amyloid-beta clearance | \n", + "True | \n", + "26.0 | \n", + "22.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 27 | \n", + "GO:0051130 | \n", + "positive regulation of cellular component organization | \n", + "True | \n", + "27.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 28 | \n", + "GO:0060907 | \n", + "positive regulation of macrophage cytokine production | \n", + "True | \n", + "28.0 | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 29 | \n", + "GO:0032879 | \n", + "regulation of localization | \n", + "True | \n", + "29.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 30 | \n", + "GO:0048522 | \n", + "positive regulation of cellular process | \n", + "True | \n", + "30.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 31 | \n", + "GO:0002277 | \n", + "myeloid dendritic cell activation involved in immune response | \n", + "False | \n", + "31.0 | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 32 | \n", + "GO:0030659 | \n", + "cytoplasmic vesicle membrane | \n", + "True | \n", + "32.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 33 | \n", + "GO:0012506 | \n", + "vesicle membrane | \n", + "True | \n", + "33.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 34 | \n", + "GO:0061081 | \n", + "positive regulation of myeloid leukocyte cytokine production involved in immune response | \n", + "True | \n", + "34.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 35 | \n", + "GO:0010935 | \n", + "regulation of macrophage cytokine production | \n", + "True | \n", + "35.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 36 | \n", + "GO:0048583 | \n", + "regulation of response to stimulus | \n", + "False | \n", + "36.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 37 | \n", + "GO:1905167 | \n", + "positive regulation of lysosomal protein catabolic process | \n", + "True | \n", + "37.0 | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 38 | \n", + "GO:0009894 | \n", + "regulation of catabolic process | \n", + "True | \n", + "38.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 39 | \n", + "GO:0023051 | \n", + "regulation of signaling | \n", + "False | \n", + "39.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 40 | \n", + "GO:0051641 | \n", + "cellular localization | \n", + "True | \n", + "40.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 41 | \n", + "GO:1904352 | \n", + "positive regulation of protein catabolic process in the vacuole | \n", + "True | \n", + "41.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 42 | \n", + "GO:0070508 | \n", + "cholesterol import | \n", + "True | \n", + "42.0 | \n", + "13.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 43 | \n", + "GO:0031347 | \n", + "regulation of defense response | \n", + "True | \n", + "43.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 44 | \n", + "GO:0005794 | \n", + "Golgi apparatus | \n", + "False | \n", + "44.0 | \n", + "14.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 45 | \n", + "GO:1901700 | \n", + "response to oxygen-containing compound | \n", + "False | \n", + "45.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 46 | \n", + "GO:0061024 | \n", + "membrane organization | \n", + "False | \n", + "46.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 47 | \n", + "GO:0009966 | \n", + "regulation of signal transduction | \n", + "True | \n", + "47.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 48 | \n", + "GO:0015031 | \n", + "protein transport | \n", + "True | \n", + "48.0 | \n", + "NaN | \n", + "1.0 | \n", + "1.0 | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 49 | \n", + "GO:0048523 | \n", + "negative regulation of cellular process | \n", + "False | \n", + "49.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 50 | \n", + "GO:0032429 | \n", + "regulation of phospholipase A2 activity | \n", + "False | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 51 | \n", + "GO:0034381 | \n", + "plasma lipoprotein particle clearance | \n", + "False | \n", + "NaN | \n", + "11.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 52 | \n", + "GO:0031623 | \n", + "receptor internalization | \n", + "False | \n", + "NaN | \n", + "12.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 53 | \n", + "GO:0009931 | \n", + "calcium-dependent protein serine/threonine kinase activity | \n", + "False | \n", + "NaN | \n", + "15.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 54 | \n", + "GO:0005905 | \n", + "clathrin-coated pit | \n", + "False | \n", + "NaN | \n", + "16.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 55 | \n", + "GO:0032050 | \n", + "clathrin heavy chain binding | \n", + "False | \n", + "NaN | \n", + "19.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 56 | \n", + "GO:0030299 | \n", + "intestinal cholesterol absorption | \n", + "False | \n", + "NaN | \n", + "20.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 57 | \n", + "GO:0001540 | \n", + "amyloid-beta binding | \n", + "False | \n", + "NaN | \n", + "21.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 58 | \n", + "GO:0034383 | \n", + "low-density lipoprotein particle clearance | \n", + "False | \n", + "NaN | \n", + "23.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 59 | \n", + "GO:0032760 | \n", + "positive regulation of tumor necrosis factor production | \n", + "False | \n", + "NaN | \n", + "24.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 60 | \n", + "GO:0071404 | \n", + "cellular response to low-density lipoprotein particle stimulus | \n", + "False | \n", + "NaN | \n", + "25.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 61 | \n", + "GO:0042953 | \n", + "lipoprotein transport | \n", + "False | \n", + "NaN | \n", + "26.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 62 | \n", + "GO:0030169 | \n", + "low-density lipoprotein particle binding | \n", + "False | \n", + "NaN | \n", + "27.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 63 | \n", + "GO:0051639 | \n", + "actin filament network formation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 64 | \n", + "endoplasmic reticulum and recycling endosome membrane organization | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 65 | \n", + "GO:0016043 | \n", + "cellular component organization | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 66 | \n", + "intracellular signaling | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 67 | \n", + "GO:0051260 | \n", + "protein homooligomerization | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 68 | \n", + "protein signaling | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 69 | \n", + "GO:0006468 | \n", + "protein phosphorylation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 70 | \n", + "GO:0016567 | \n", + "protein ubiquitination | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 71 | \n", + "GO:0030030 | \n", + "cell projection organization | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 72 | \n", + "GO:0035091 | \n", + "phosphatidylinositol binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 73 | \n", + "GO:0001766 | \n", + "membrane raft polarization | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 74 | \n", + "GO:0097320 | \n", + "plasma membrane tubulation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 75 | \n", + "GO:0007041 | \n", + "lysosomal transport | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 76 | \n", + "GO:0007032 | \n", + "endosome organization | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 77 | \n", + "GO:0030163 | \n", + "protein catabolic process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 78 | \n", + "intracellular trafficking | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 79 | \n", + "cytoskeleton reorganization | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 80 | \n", + "GO:0007165 | \n", + "signal transduction | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "
| 81 | \n", + "vesicle/lipid trafficking | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "
| 82 | \n", + "cellular adhesion | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "
| 83 | \n", + "nutrient regulation | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "
| 84 | \n", + "cell metabolism | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "
| 85 | \n", + "cytoskeletal organization | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "
| 86 | \n", + "endocytosis/exocytosis | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "
| 87 | \n", + "intercellular adhesion/motility | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "
| 88 | \n", + "GO:0005654 | \n", + "nucleoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "
| 89 | \n", + "GO:0005634 | \n", + "nucleus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "
| 90 | \n", + "GO:0046872 | \n", + "metal ion binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "
| 91 | \n", + "GO:0005886 | \n", + "plasma membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "
| 92 | \n", + "GO:0005524 | \n", + "ATP binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "
| 93 | \n", + "GO:0045944 | \n", + "positive regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "
| 94 | \n", + "GO:0070062 | \n", + "extracellular exosome | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "
| 95 | \n", + "GO:0005576 | \n", + "extracellular region | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "
| 96 | \n", + "GO:0042802 | \n", + "identical protein binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "8.0 | \n", + "
| 97 | \n", + "GO:0005829 | \n", + "cytosol | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "9.0 | \n", + "
| 98 | \n", + "GO:0006357 | \n", + "regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "10.0 | \n", + "
| 99 | \n", + "GO:0005739 | \n", + "mitochondrion | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "11.0 | \n", + "
| 100 | \n", + "GO:0005737 | \n", + "cytoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "12.0 | \n", + "
| 101 | \n", + "GO:0016020 | \n", + "membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "13.0 | \n", + "
| 102 | \n", + "GO:0003723 | \n", + "RNA binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "14.0 | \n", + "
| 103 | \n", + "GO:0005615 | \n", + "extracellular space | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "15.0 | \n", + "
| \n", + " | id | \n", + "label | \n", + "redundant | \n", + "standard | \n", + "standard no ontology | \n", + "dav ontological synopsis | \n", + "dav narrative synopsis | \n", + "turbo narrative synopsis | \n", + "turbo no synopsis | \n", + "turbo ontological synopsis | \n", + "rank based | \n", + "dav no synopsis | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", + "GO:0004553 | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds | \n", + "False | \n", + "0.0 | \n", + "62.0 | \n", + "14.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 1 | \n", + "GO:0016798 | \n", + "hydrolase activity, acting on glycosyl bonds | \n", + "True | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 2 | \n", + "GO:0005975 | \n", + "carbohydrate metabolic process | \n", + "False | \n", + "2.0 | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 3 | \n", + "GO:0016787 | \n", + "hydrolase activity | \n", + "True | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 4 | \n", + "GO:1901136 | \n", + "carbohydrate derivative catabolic process | \n", + "False | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 5 | \n", + "GO:0009311 | \n", + "oligosaccharide metabolic process | \n", + "True | \n", + "5.0 | \n", + "22.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 6 | \n", + "GO:1901135 | \n", + "carbohydrate derivative metabolic process | \n", + "True | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 7 | \n", + "GO:0003824 | \n", + "catalytic activity | \n", + "True | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 8 | \n", + "GO:0006026 | \n", + "aminoglycan catabolic process | \n", + "True | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 9 | \n", + "GO:0009313 | \n", + "oligosaccharide catabolic process | \n", + "True | \n", + "9.0 | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 10 | \n", + "GO:0015929 | \n", + "hexosaminidase activity | \n", + "True | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 11 | \n", + "GO:0015923 | \n", + "mannosidase activity | \n", + "True | \n", + "11.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 12 | \n", + "GO:0016052 | \n", + "carbohydrate catabolic process | \n", + "True | \n", + "12.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 13 | \n", + "GO:1901575 | \n", + "organic substance catabolic process | \n", + "True | \n", + "13.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 14 | \n", + "GO:0004559 | \n", + "alpha-mannosidase activity | \n", + "True | \n", + "14.0 | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 15 | \n", + "GO:0015926 | \n", + "glucosidase activity | \n", + "True | \n", + "15.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 16 | \n", + "GO:0019377 | \n", + "glycolipid catabolic process | \n", + "True | \n", + "16.0 | \n", + "70.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 17 | \n", + "GO:0046514 | \n", + "ceramide catabolic process | \n", + "True | \n", + "17.0 | \n", + "59.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 18 | \n", + "GO:0046466 | \n", + "membrane lipid catabolic process | \n", + "True | \n", + "18.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 19 | \n", + "GO:0006022 | \n", + "aminoglycan metabolic process | \n", + "True | \n", + "19.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 20 | \n", + "GO:0009056 | \n", + "catabolic process | \n", + "True | \n", + "20.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 21 | \n", + "GO:1901565 | \n", + "organonitrogen compound catabolic process | \n", + "True | \n", + "21.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 22 | \n", + "GO:0046479 | \n", + "glycosphingolipid catabolic process | \n", + "True | \n", + "22.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 23 | \n", + "GO:0006027 | \n", + "glycosaminoglycan catabolic process | \n", + "True | \n", + "23.0 | \n", + "15.0 | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 24 | \n", + "GO:0030149 | \n", + "sphingolipid catabolic process | \n", + "True | \n", + "24.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 25 | \n", + "GO:0009100 | \n", + "glycoprotein metabolic process | \n", + "True | \n", + "25.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 26 | \n", + "GO:0006516 | \n", + "glycoprotein catabolic process | \n", + "True | \n", + "26.0 | \n", + "49.0 | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 27 | \n", + "GO:0043202 | \n", + "lysosomal lumen | \n", + "False | \n", + "27.0 | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 28 | \n", + "GO:0005775 | \n", + "vacuolar lumen | \n", + "True | \n", + "28.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 29 | \n", + "GO:0006517 | \n", + "protein deglycosylation | \n", + "True | \n", + "29.0 | \n", + "26.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 30 | \n", + "GO:0009057 | \n", + "macromolecule catabolic process | \n", + "True | \n", + "30.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 31 | \n", + "GO:0008152 | \n", + "metabolic process | \n", + "True | \n", + "31.0 | \n", + "24.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 32 | \n", + "GO:0015924 | \n", + "mannosyl-oligosaccharide mannosidase activity | \n", + "True | \n", + "32.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 33 | \n", + "GO:0003796 | \n", + "lysozyme activity | \n", + "True | \n", + "33.0 | \n", + "3.0 | \n", + "20.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 34 | \n", + "GO:0030203 | \n", + "glycosaminoglycan metabolic process | \n", + "True | \n", + "34.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 35 | \n", + "GO:0006672 | \n", + "ceramide metabolic process | \n", + "True | \n", + "35.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 36 | \n", + "GO:0006687 | \n", + "glycosphingolipid metabolic process | \n", + "True | \n", + "36.0 | \n", + "21.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 37 | \n", + "GO:0005764 | \n", + "lysosome | \n", + "True | \n", + "37.0 | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 38 | \n", + "GO:0000323 | \n", + "lytic vacuole | \n", + "True | \n", + "38.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 39 | \n", + "GO:0030214 | \n", + "hyaluronan catabolic process | \n", + "True | \n", + "39.0 | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 40 | \n", + "GO:0006664 | \n", + "glycolipid metabolic process | \n", + "True | \n", + "40.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 41 | \n", + "GO:1903509 | \n", + "liposaccharide metabolic process | \n", + "True | \n", + "41.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 42 | \n", + "GO:0005773 | \n", + "vacuole | \n", + "True | \n", + "42.0 | \n", + "50.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 43 | \n", + "GO:0006643 | \n", + "membrane lipid metabolic process | \n", + "True | \n", + "43.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 44 | \n", + "GO:0004415 | \n", + "hyalurononglucosaminidase activity | \n", + "True | \n", + "44.0 | \n", + "6.0 | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 45 | \n", + "GO:0061783 | \n", + "peptidoglycan muralytic activity | \n", + "True | \n", + "45.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 46 | \n", + "GO:0006665 | \n", + "sphingolipid metabolic process | \n", + "True | \n", + "46.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 47 | \n", + "GO:0044242 | \n", + "cellular lipid catabolic process | \n", + "True | \n", + "47.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 48 | \n", + "GO:0005576 | \n", + "extracellular region | \n", + "False | \n", + "48.0 | \n", + "38.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "42.0 | \n", + "NaN | \n", + "
| 49 | \n", + "GO:0071704 | \n", + "organic substance metabolic process | \n", + "True | \n", + "49.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 50 | \n", + "GO:1903510 | \n", + "mucopolysaccharide metabolic process | \n", + "True | \n", + "50.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 51 | \n", + "GO:0006689 | \n", + "ganglioside catabolic process | \n", + "True | \n", + "51.0 | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 52 | \n", + "GO:0004571 | \n", + "mannosyl-oligosaccharide 1,2-alpha-mannosidase activity | \n", + "True | \n", + "52.0 | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 53 | \n", + "GO:0090599 | \n", + "alpha-glucosidase activity | \n", + "True | \n", + "53.0 | \n", + "76.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 54 | \n", + "GO:0015925 | \n", + "galactosidase activity | \n", + "True | \n", + "54.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 55 | \n", + "GO:0030212 | \n", + "hyaluronan metabolic process | \n", + "True | \n", + "55.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 56 | \n", + "GO:0005984 | \n", + "disaccharide metabolic process | \n", + "True | \n", + "56.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 57 | \n", + "GO:0044238 | \n", + "primary metabolic process | \n", + "True | \n", + "57.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 58 | \n", + "GO:0016139 | \n", + "glycoside catabolic process | \n", + "True | \n", + "58.0 | \n", + "12.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 59 | \n", + "GO:0016042 | \n", + "lipid catabolic process | \n", + "True | \n", + "59.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 60 | \n", + "GO:0006032 | \n", + "chitin catabolic process | \n", + "True | \n", + "60.0 | \n", + "11.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 61 | \n", + "GO:0006030 | \n", + "chitin metabolic process | \n", + "True | \n", + "61.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 62 | \n", + "GO:0016160 | \n", + "amylase activity | \n", + "True | \n", + "62.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 63 | \n", + "GO:0006491 | \n", + "N-glycan processing | \n", + "True | \n", + "63.0 | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 64 | \n", + "GO:1901564 | \n", + "organonitrogen compound metabolic process | \n", + "True | \n", + "64.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 65 | \n", + "GO:0044273 | \n", + "sulfur compound catabolic process | \n", + "True | \n", + "65.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 66 | \n", + "GO:0030246 | \n", + "carbohydrate binding | \n", + "False | \n", + "66.0 | \n", + "13.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 67 | \n", + "GO:0005996 | \n", + "monosaccharide metabolic process | \n", + "True | \n", + "67.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 68 | \n", + "GO:0008061 | \n", + "chitin binding | \n", + "False | \n", + "68.0 | \n", + "14.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 69 | \n", + "GO:0031982 | \n", + "vesicle | \n", + "False | \n", + "69.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 70 | \n", + "GO:0001573 | \n", + "ganglioside metabolic process | \n", + "True | \n", + "70.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 71 | \n", + "GO:0036508 | \n", + "protein alpha-1,2-demannosylation | \n", + "True | \n", + "71.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 72 | \n", + "GO:0036507 | \n", + "protein demannosylation | \n", + "True | \n", + "72.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 73 | \n", + "GO:1901072 | \n", + "glucosamine-containing compound catabolic process | \n", + "True | \n", + "73.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 74 | \n", + "GO:1903561 | \n", + "extracellular vesicle | \n", + "True | \n", + "74.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 75 | \n", + "GO:0065010 | \n", + "extracellular membrane-bounded organelle | \n", + "True | \n", + "75.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 76 | \n", + "GO:0043230 | \n", + "extracellular organelle | \n", + "True | \n", + "76.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 77 | \n", + "CL:0000775 | \n", + "neutrophil | \n", + "False | \n", + "77.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 78 | \n", + "CL:0000094 | \n", + "granulocyte | \n", + "True | \n", + "78.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 79 | \n", + "CL:0000766 | \n", + "myeloid leukocyte | \n", + "True | \n", + "79.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 80 | \n", + "CL:0000738 | \n", + "leukocyte | \n", + "True | \n", + "80.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 81 | \n", + "CL:0002242 | \n", + "nucleate cell | \n", + "True | \n", + "81.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 82 | \n", + "CL:0000219 | \n", + "motile cell | \n", + "True | \n", + "82.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 83 | \n", + "UBERON:0002405 | \n", + "immune system | \n", + "True | \n", + "83.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 84 | \n", + "GO:0030141 | \n", + "secretory granule | \n", + "True | \n", + "84.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 85 | \n", + "UBERON:0015203 | \n", + "non-connected functional system | \n", + "True | \n", + "85.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 86 | \n", + "UBERON:0034923 | \n", + "disconnected anatomical group | \n", + "True | \n", + "86.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 87 | \n", + "GO:1904382 | \n", + "mannose trimming involved in glycoprotein ERAD pathway | \n", + "True | \n", + "87.0 | \n", + "19.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 88 | \n", + "GO:0097466 | \n", + "ubiquitin-dependent glycoprotein ERAD pathway | \n", + "True | \n", + "88.0 | \n", + "67.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 89 | \n", + "GO:0046477 | \n", + "glycosylceramide catabolic process | \n", + "True | \n", + "89.0 | \n", + "42.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 90 | \n", + "GO:0035977 | \n", + "protein deglycosylation involved in glycoprotein catabolic process | \n", + "True | \n", + "90.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 91 | \n", + "GO:0004558 | \n", + "alpha-1,4-glucosidase activity | \n", + "True | \n", + "91.0 | \n", + "20.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 92 | \n", + "GO:0004563 | \n", + "beta-N-acetylhexosaminidase activity | \n", + "True | \n", + "92.0 | \n", + "35.0 | \n", + "16.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 93 | \n", + "GO:0004565 | \n", + "beta-galactosidase activity | \n", + "True | \n", + "93.0 | \n", + "16.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 94 | \n", + "GO:0008422 | \n", + "beta-glucosidase activity | \n", + "True | \n", + "94.0 | \n", + "17.0 | \n", + "11.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 95 | \n", + "GO:0004556 | \n", + "alpha-amylase activity | \n", + "True | \n", + "95.0 | \n", + "18.0 | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 96 | \n", + "GO:0016137 | \n", + "glycoside metabolic process | \n", + "True | \n", + "96.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 97 | \n", + "GO:0005615 | \n", + "extracellular space | \n", + "True | \n", + "97.0 | \n", + "65.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "77.0 | \n", + "NaN | \n", + "
| 98 | \n", + "GO:0042582 | \n", + "azurophil granule | \n", + "True | \n", + "98.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 99 | \n", + "GO:0005766 | \n", + "primary lysosome | \n", + "True | \n", + "99.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 100 | \n", + "GO:0044248 | \n", + "cellular catabolic process | \n", + "True | \n", + "100.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 101 | \n", + "GO:1901071 | \n", + "glucosamine-containing compound metabolic process | \n", + "True | \n", + "101.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 102 | \n", + "GO:0070062 | \n", + "extracellular exosome | \n", + "True | \n", + "102.0 | \n", + "23.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "64.0 | \n", + "NaN | \n", + "
| 103 | \n", + "CL:0000763 | \n", + "myeloid cell | \n", + "True | \n", + "103.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 104 | \n", + "CL:0000081 | \n", + "blood cell | \n", + "True | \n", + "104.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 105 | \n", + "CL:0000988 | \n", + "hematopoietic cell | \n", + "True | \n", + "105.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 106 | \n", + "GO:0046348 | \n", + "amino sugar catabolic process | \n", + "True | \n", + "106.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 107 | \n", + "GO:0099503 | \n", + "secretory vesicle | \n", + "True | \n", + "107.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 108 | \n", + "GO:1901658 | \n", + "glycosyl compound catabolic process | \n", + "True | \n", + "108.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 109 | \n", + "GO:0030200 | \n", + "heparan sulfate proteoglycan catabolic process | \n", + "True | \n", + "109.0 | \n", + "27.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 110 | \n", + "GO:0006013 | \n", + "mannose metabolic process | \n", + "True | \n", + "110.0 | \n", + "25.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 111 | \n", + "GO:1904587 | \n", + "response to glycoprotein | \n", + "True | \n", + "111.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 112 | \n", + "GO:0034774 | \n", + "secretory granule lumen | \n", + "True | \n", + "112.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 113 | \n", + "GO:0060205 | \n", + "cytoplasmic vesicle lumen | \n", + "True | \n", + "113.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 114 | \n", + "GO:0012505 | \n", + "endomembrane system | \n", + "True | \n", + "114.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 115 | \n", + "GO:0031983 | \n", + "vesicle lumen | \n", + "True | \n", + "115.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 116 | \n", + "GO:0035578 | \n", + "azurophil granule lumen | \n", + "True | \n", + "116.0 | \n", + "28.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 117 | \n", + "GO:0006029 | \n", + "proteoglycan metabolic process | \n", + "True | \n", + "117.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 118 | \n", + "GO:0030207 | \n", + "chondroitin sulfate catabolic process | \n", + "True | \n", + "118.0 | \n", + "31.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 119 | \n", + "GO:0046352 | \n", + "disaccharide catabolic process | \n", + "True | \n", + "119.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 120 | \n", + "GO:0052795 | \n", + "exo-alpha-(2->6)-sialidase activity | \n", + "True | \n", + "120.0 | \n", + "33.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 121 | \n", + "GO:0052794 | \n", + "exo-alpha-(2->3)-sialidase activity | \n", + "True | \n", + "121.0 | \n", + "30.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 122 | \n", + "GO:0052796 | \n", + "exo-alpha-(2->8)-sialidase activity | \n", + "True | \n", + "122.0 | \n", + "34.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 123 | \n", + "GO:0004308 | \n", + "exo-alpha-sialidase activity | \n", + "True | \n", + "123.0 | \n", + "32.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 124 | \n", + "GO:0004336 | \n", + "galactosylceramidase activity | \n", + "True | \n", + "124.0 | \n", + "29.0 | \n", + "13.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 125 | \n", + "GO:0016997 | \n", + "alpha-sialidase activity | \n", + "True | \n", + "125.0 | \n", + "73.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 126 | \n", + "GO:0004568 | \n", + "chitinase activity | \n", + "True | \n", + "126.0 | \n", + "36.0 | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 127 | \n", + "GO:0044245 | \n", + "polysaccharide digestion | \n", + "False | \n", + "127.0 | \n", + "37.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 128 | \n", + "GO:0030167 | \n", + "proteoglycan catabolic process | \n", + "True | \n", + "128.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 129 | \n", + "GO:0006040 | \n", + "amino sugar metabolic process | \n", + "True | \n", + "129.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 130 | \n", + "GO:0006677 | \n", + "glycosylceramide metabolic process | \n", + "True | \n", + "130.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 131 | \n", + "GO:0000272 | \n", + "polysaccharide catabolic process | \n", + "True | \n", + "131.0 | \n", + "69.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 132 | \n", + "GO:0031410 | \n", + "cytoplasmic vesicle | \n", + "True | \n", + "132.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 133 | \n", + "GO:0097708 | \n", + "intracellular vesicle | \n", + "True | \n", + "133.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 134 | \n", + "GO:0070085 | \n", + "glycosylation | \n", + "True | \n", + "134.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 135 | \n", + "GO:0044255 | \n", + "cellular lipid metabolic process | \n", + "True | \n", + "135.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 136 | \n", + "GO:0019318 | \n", + "hexose metabolic process | \n", + "True | \n", + "136.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 137 | \n", + "GO:0006486 | \n", + "protein glycosylation | \n", + "True | \n", + "137.0 | \n", + "39.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 138 | \n", + "GO:0043413 | \n", + "macromolecule glycosylation | \n", + "True | \n", + "138.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 139 | \n", + "GO:0032450 | \n", + "maltose alpha-glucosidase activity | \n", + "True | \n", + "139.0 | \n", + "41.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 140 | \n", + "GO:0036510 | \n", + "trimming of terminal mannose on C branch | \n", + "True | \n", + "140.0 | \n", + "44.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 141 | \n", + "GO:1904381 | \n", + "Golgi apparatus mannose trimming | \n", + "True | \n", + "141.0 | \n", + "45.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 142 | \n", + "GO:0071633 | \n", + "dihydroceramidase activity | \n", + "True | \n", + "142.0 | \n", + "47.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 143 | \n", + "GO:0000023 | \n", + "maltose metabolic process | \n", + "True | \n", + "143.0 | \n", + "77.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 144 | \n", + "GO:0004566 | \n", + "beta-glucuronidase activity | \n", + "True | \n", + "144.0 | \n", + "40.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 145 | \n", + "GO:0102148 | \n", + "N-acetyl-beta-D-galactosaminidase activity | \n", + "True | \n", + "145.0 | \n", + "46.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 146 | \n", + "GO:0004348 | \n", + "glucosylceramidase activity | \n", + "True | \n", + "146.0 | \n", + "43.0 | \n", + "12.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 147 | \n", + "GO:0007342 | \n", + "fusion of sperm to egg plasma membrane involved in single fertilization | \n", + "False | \n", + "147.0 | \n", + "48.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 148 | \n", + "GO:1901657 | \n", + "glycosyl compound metabolic process | \n", + "True | \n", + "148.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 149 | \n", + "GO:0045026 | \n", + "plasma membrane fusion | \n", + "True | \n", + "149.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 150 | \n", + "GO:0030209 | \n", + "dermatan sulfate catabolic process | \n", + "True | \n", + "150.0 | \n", + "51.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 151 | \n", + "GO:0052782 | \n", + "amino disaccharide catabolic process | \n", + "True | \n", + "151.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 152 | \n", + "GO:1904380 | \n", + "endoplasmic reticulum mannose trimming | \n", + "True | \n", + "152.0 | \n", + "53.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 153 | \n", + "GO:0031404 | \n", + "chloride ion binding | \n", + "False | \n", + "153.0 | \n", + "54.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 154 | \n", + "GO:0007338 | \n", + "single fertilization | \n", + "True | \n", + "154.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 155 | \n", + "GO:0009101 | \n", + "glycoprotein biosynthetic process | \n", + "True | \n", + "155.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 156 | \n", + "GO:0043603 | \n", + "amide metabolic process | \n", + "True | \n", + "156.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 157 | \n", + "GO:0102121 | \n", + "ceramidase activity | \n", + "True | \n", + "157.0 | \n", + "56.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 158 | \n", + "GO:0006629 | \n", + "lipid metabolic process | \n", + "True | \n", + "158.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 159 | \n", + "CL:0000096 | \n", + "mature neutrophil | \n", + "True | \n", + "159.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 160 | \n", + "CL:0000234 | \n", + "phagocyte | \n", + "True | \n", + "160.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 161 | \n", + "CL:0000473 | \n", + "defensive cell | \n", + "True | \n", + "161.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 162 | \n", + "GO:0009566 | \n", + "fertilization | \n", + "True | \n", + "162.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 163 | \n", + "GO:0017040 | \n", + "N-acylsphingosine amidohydrolase activity | \n", + "True | \n", + "163.0 | \n", + "58.0 | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 164 | \n", + "GO:1901137 | \n", + "carbohydrate derivative biosynthetic process | \n", + "True | \n", + "164.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 165 | \n", + "GO:0005509 | \n", + "calcium ion binding | \n", + "False | \n", + "165.0 | \n", + "60.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "45.0 | \n", + "NaN | \n", + "
| 166 | \n", + "GO:0001669 | \n", + "acrosomal vesicle | \n", + "True | \n", + "166.0 | \n", + "55.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 167 | \n", + "GO:0044322 | \n", + "endoplasmic reticulum quality control compartment | \n", + "True | \n", + "167.0 | \n", + "61.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 168 | \n", + "GO:0003674 | \n", + "molecular_function | \n", + "True | \n", + "168.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "47.0 | \n", + "NaN | \n", + "
| 169 | \n", + "CL:0000325 | \n", + "stuff accumulating cell | \n", + "True | \n", + "169.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 170 | \n", + "GO:0030205 | \n", + "dermatan sulfate metabolic process | \n", + "True | \n", + "170.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 171 | \n", + "GO:0052779 | \n", + "amino disaccharide metabolic process | \n", + "True | \n", + "171.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 172 | \n", + "GO:0035580 | \n", + "specific granule lumen | \n", + "True | \n", + "172.0 | \n", + "63.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 173 | \n", + "GO:0030163 | \n", + "protein catabolic process | \n", + "True | \n", + "173.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 174 | \n", + "GO:0030204 | \n", + "chondroitin sulfate metabolic process | \n", + "True | \n", + "174.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 175 | \n", + "GO:0019082 | \n", + "viral protein processing | \n", + "False | \n", + "175.0 | \n", + "64.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 176 | \n", + "GO:0006790 | \n", + "sulfur compound metabolic process | \n", + "True | \n", + "176.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 177 | \n", + "GO:0006807 | \n", + "nitrogen compound metabolic process | \n", + "True | \n", + "177.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 178 | \n", + "GO:0005976 | \n", + "polysaccharide metabolic process | \n", + "True | \n", + "178.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 179 | \n", + "GO:0071493 | \n", + "cellular response to UV-B | \n", + "False | \n", + "179.0 | \n", + "66.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 180 | \n", + "GO:0050655 | \n", + "dermatan sulfate proteoglycan metabolic process | \n", + "True | \n", + "180.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 181 | \n", + "GO:0006683 | \n", + "galactosylceramide catabolic process | \n", + "True | \n", + "181.0 | \n", + "82.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 182 | \n", + "GO:0006680 | \n", + "glucosylceramide catabolic process | \n", + "True | \n", + "182.0 | \n", + "84.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 183 | \n", + "GO:0036511 | \n", + "trimming of first mannose on A branch | \n", + "True | \n", + "183.0 | \n", + "74.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 184 | \n", + "GO:0036509 | \n", + "trimming of terminal mannose on B branch | \n", + "True | \n", + "184.0 | \n", + "87.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 185 | \n", + "GO:0036512 | \n", + "trimming of second mannose on A branch | \n", + "True | \n", + "185.0 | \n", + "71.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 186 | \n", + "GO:0046373 | \n", + "L-arabinose metabolic process | \n", + "True | \n", + "186.0 | \n", + "75.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 187 | \n", + "GO:0019566 | \n", + "arabinose metabolic process | \n", + "True | \n", + "187.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 188 | \n", + "GO:0004572 | \n", + "mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity | \n", + "True | \n", + "188.0 | \n", + "79.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 189 | \n", + "GO:0004339 | \n", + "glucan 1,4-alpha-glucosidase activity | \n", + "True | \n", + "189.0 | \n", + "80.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 190 | \n", + "GO:0004557 | \n", + "alpha-galactosidase activity | \n", + "True | \n", + "190.0 | \n", + "88.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 191 | \n", + "GO:0004560 | \n", + "alpha-L-fucosidase activity | \n", + "True | \n", + "191.0 | \n", + "81.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 192 | \n", + "GO:0033906 | \n", + "hyaluronoglucuronidase activity | \n", + "True | \n", + "192.0 | \n", + "89.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 193 | \n", + "GO:0030305 | \n", + "heparanase activity | \n", + "True | \n", + "193.0 | \n", + "68.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 194 | \n", + "GO:0017042 | \n", + "glycosylceramidase activity | \n", + "True | \n", + "194.0 | \n", + "72.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 195 | \n", + "GO:1905379 | \n", + "beta-N-acetylhexosaminidase complex | \n", + "False | \n", + "195.0 | \n", + "83.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 196 | \n", + "GO:0015928 | \n", + "fucosidase activity | \n", + "True | \n", + "196.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 197 | \n", + "GO:0046556 | \n", + "alpha-L-arabinofuranosidase activity | \n", + "True | \n", + "197.0 | \n", + "85.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 198 | \n", + "GO:0004649 | \n", + "poly(ADP-ribose) glycohydrolase activity | \n", + "True | \n", + "198.0 | \n", + "78.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 199 | \n", + "GO:0050654 | \n", + "chondroitin sulfate proteoglycan metabolic process | \n", + "True | \n", + "199.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 200 | \n", + "GO:0046512 | \n", + "sphingosine biosynthetic process | \n", + "True | \n", + "200.0 | \n", + "90.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 201 | \n", + "GO:0046520 | \n", + "sphingoid biosynthetic process | \n", + "True | \n", + "201.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 202 | \n", + "GO:0009251 | \n", + "glucan catabolic process | \n", + "True | \n", + "202.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 203 | \n", + "GO:0030433 | \n", + "ubiquitin-dependent ERAD pathway | \n", + "True | \n", + "203.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 204 | \n", + "GO:0051651 | \n", + "maintenance of location in cell | \n", + "False | \n", + "NaN | \n", + "52.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 205 | \n", + "GO:0007040 | \n", + "lysosome organization | \n", + "False | \n", + "NaN | \n", + "57.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 206 | \n", + "GO:0016799 | \n", + "hydrolase activity, hydrolyzing N-glycosyl compounds | \n", + "False | \n", + "NaN | \n", + "86.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 207 | \n", + "GO:0050885 | \n", + "neuromuscular process controlling balance | \n", + "False | \n", + "NaN | \n", + "91.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 208 | \n", + "GO:1904154 | \n", + "positive regulation of retrograde protein transport, ER to cytosol | \n", + "False | \n", + "NaN | \n", + "92.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 209 | \n", + "GO:0042552 | \n", + "myelination | \n", + "False | \n", + "NaN | \n", + "93.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 210 | \n", + "the genes in this list share functions involving glycoprotein and carbohydrate metabolic processes and structural functions related to extracellular matrix organization. enriched terms include: dihydroceramidase activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 211 | \n", + "GO:0061463 | \n", + "O-acetyl-ADP-ribose deacetylase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 212 | \n", + "GO:0004134 | \n", + "4-alpha-glucanotransferase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 213 | \n", + "GO:0004135 | \n", + "amylo-alpha-1,6-glucosidase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 214 | \n", + "hyaluronic acid binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 215 | \n", + "GO:0008843 | \n", + "endochitinase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 216 | \n", + "clathrin heavy chain binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 217 | \n", + "GO:0008375 | \n", + "acetylglucosaminyltransferase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "15.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 218 | \n", + "identical protein binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "17.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 219 | \n", + "syndecan binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "18.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 220 | \n", + "heparan sulfate proteoglycan binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "19.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 221 | \n", + "GO:0004567 | \n", + "beta-mannosidase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "21.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 222 | \n", + "glycoside hydrolase activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 223 | \n", + "GO:0005980 | \n", + "glycogen catabolic process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 224 | \n", + "acid hydrolase activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 225 | \n", + "chitin catabolic process\\n\\nmechanism: these genes participate in the lysosomal degradation of various carbohydrate molecules, breaking them down into their component parts for further processing by the cell | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 226 | \n", + "GO:0005783 | \n", + "endoplasmic reticulum | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "28.0 | \n", + "NaN | \n", + "
| 227 | \n", + "catabolism of carbohydrate | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 228 | \n", + "MONDO:0019249 | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 229 | \n", + "GO:0007155 | \n", + "cell adhesion | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "
| 230 | \n", + "GO:0007399 | \n", + "nervous system development | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "
| 231 | \n", + "GO:0009986 | \n", + "cell surface | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "
| 232 | \n", + "GO:0046872 | \n", + "metal ion binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "
| 233 | \n", + "GO:0008270 | \n", + "zinc ion binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "
| 234 | \n", + "GO:0043066 | \n", + "negative regulation of apoptotic process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "
| 235 | \n", + "GO:0045087 | \n", + "innate immune response | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "
| 236 | \n", + "GO:0042803 | \n", + "protein homodimerization activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "
| 237 | \n", + "GO:0005654 | \n", + "nucleoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "8.0 | \n", + "NaN | \n", + "
| 238 | \n", + "GO:0019899 | \n", + "enzyme binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "9.0 | \n", + "NaN | \n", + "
| 239 | \n", + "GO:0006954 | \n", + "inflammatory response | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "10.0 | \n", + "NaN | \n", + "
| 240 | \n", + "GO:0008284 | \n", + "positive regulation of cell population proliferation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "11.0 | \n", + "NaN | \n", + "
| 241 | \n", + "GO:0004984 | \n", + "olfactory receptor activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "12.0 | \n", + "NaN | \n", + "
| 242 | \n", + "GO:0016607 | \n", + "nuclear speck | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "13.0 | \n", + "NaN | \n", + "
| 243 | \n", + "GO:0000785 | \n", + "chromatin | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "14.0 | \n", + "NaN | \n", + "
| 244 | \n", + "GO:0051301 | \n", + "cell division | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "15.0 | \n", + "NaN | \n", + "
| 245 | \n", + "GO:0042802 | \n", + "identical protein binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "16.0 | \n", + "NaN | \n", + "
| 246 | \n", + "GO:0045944 | \n", + "positive regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "17.0 | \n", + "NaN | \n", + "
| 247 | \n", + "GO:0106310 | \n", + "protein serine kinase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "18.0 | \n", + "NaN | \n", + "
| 248 | \n", + "GO:0043231 | \n", + "intracellular membrane-bounded organelle | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "19.0 | \n", + "NaN | \n", + "
| 249 | \n", + "GO:0043025 | \n", + "neuronal cell body | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "20.0 | \n", + "NaN | \n", + "
| 250 | \n", + "GO:0010628 | \n", + "positive regulation of gene expression | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "21.0 | \n", + "NaN | \n", + "
| 251 | \n", + "GO:0016020 | \n", + "membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "22.0 | \n", + "NaN | \n", + "
| 252 | \n", + "GO:0008150 | \n", + "biological_process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "23.0 | \n", + "NaN | \n", + "
| 253 | \n", + "GO:0006508 | \n", + "proteolysis | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "24.0 | \n", + "NaN | \n", + "
| 254 | \n", + "GO:0005524 | \n", + "ATP binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "25.0 | \n", + "NaN | \n", + "
| 255 | \n", + "GO:0005856 | \n", + "cytoskeleton | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "26.0 | \n", + "NaN | \n", + "
| 256 | \n", + "GO:0061630 | \n", + "ubiquitin protein ligase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "27.0 | \n", + "NaN | \n", + "
| 257 | \n", + "GO:0016567 | \n", + "protein ubiquitination | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "29.0 | \n", + "NaN | \n", + "
| 258 | \n", + "GO:0006357 | \n", + "regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "30.0 | \n", + "NaN | \n", + "
| 259 | \n", + "GO:0030154 | \n", + "cell differentiation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "31.0 | \n", + "NaN | \n", + "
| 260 | \n", + "GO:0003723 | \n", + "RNA binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "32.0 | \n", + "NaN | \n", + "
| 261 | \n", + "GO:0016887 | \n", + "ATP hydrolysis activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "33.0 | \n", + "NaN | \n", + "
| 262 | \n", + "GO:0006355 | \n", + "regulation of DNA-templated transcription | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "34.0 | \n", + "NaN | \n", + "
| 263 | \n", + "GO:0000981 | \n", + "DNA-binding transcription factor activity, RNA polymerase II-specific | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "35.0 | \n", + "NaN | \n", + "
| 264 | \n", + "GO:0005765 | \n", + "lysosomal membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "36.0 | \n", + "NaN | \n", + "
| 265 | \n", + "GO:0005739 | \n", + "mitochondrion | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "37.0 | \n", + "NaN | \n", + "
| 266 | \n", + "GO:0005102 | \n", + "signaling receptor binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "38.0 | \n", + "NaN | \n", + "
| 267 | \n", + "GO:0044877 | \n", + "protein-containing complex binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "39.0 | \n", + "NaN | \n", + "
| 268 | \n", + "GO:0048471 | \n", + "perinuclear region of cytoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "40.0 | \n", + "NaN | \n", + "
| 269 | \n", + "GO:0006915 | \n", + "apoptotic process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "41.0 | \n", + "NaN | \n", + "
| 270 | \n", + "GO:0005743 | \n", + "mitochondrial inner membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "43.0 | \n", + "NaN | \n", + "
| 271 | \n", + "GO:0009897 | \n", + "external side of plasma membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "44.0 | \n", + "NaN | \n", + "
| 272 | \n", + "GO:0003682 | \n", + "chromatin binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "46.0 | \n", + "NaN | \n", + "
| 273 | \n", + "GO:0002250 | \n", + "adaptive immune response | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "48.0 | \n", + "NaN | \n", + "
| 274 | \n", + "GO:0008285 | \n", + "negative regulation of cell population proliferation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "49.0 | \n", + "NaN | \n", + "
| 275 | \n", + "GO:0045892 | \n", + "negative regulation of DNA-templated transcription | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "50.0 | \n", + "NaN | \n", + "
| 276 | \n", + "GO:0001228 | \n", + "DNA-binding transcription activator activity, RNA polymerase II-specific | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "51.0 | \n", + "NaN | \n", + "
| 277 | \n", + "GO:0050911 | \n", + "detection of chemical stimulus involved in sensory perception of smell | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "52.0 | \n", + "NaN | \n", + "
| 278 | \n", + "GO:0062023 | \n", + "collagen-containing extracellular matrix | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "53.0 | \n", + "NaN | \n", + "
| 279 | \n", + "GO:0035556 | \n", + "intracellular signal transduction | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "54.0 | \n", + "NaN | \n", + "
| 280 | \n", + "GO:0005925 | \n", + "focal adhesion | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "55.0 | \n", + "NaN | \n", + "
| 281 | \n", + "GO:0006468 | \n", + "protein phosphorylation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "56.0 | \n", + "NaN | \n", + "
| 282 | \n", + "GO:0004674 | \n", + "protein serine/threonine kinase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "57.0 | \n", + "NaN | \n", + "
| 283 | \n", + "GO:0005886 | \n", + "plasma membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "58.0 | \n", + "NaN | \n", + "
| 284 | \n", + "GO:0006955 | \n", + "immune response | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "59.0 | \n", + "NaN | \n", + "
| 285 | \n", + "GO:0005575 | \n", + "cellular_component | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "60.0 | \n", + "NaN | \n", + "
| 286 | \n", + "GO:0007165 | \n", + "signal transduction | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "61.0 | \n", + "NaN | \n", + "
| 287 | \n", + "GO:0005813 | \n", + "centrosome | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "62.0 | \n", + "NaN | \n", + "
| 288 | \n", + "GO:0005730 | \n", + "nucleolus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "63.0 | \n", + "NaN | \n", + "
| 289 | \n", + "GO:0007186 | \n", + "G protein-coupled receptor signaling pathway | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "65.0 | \n", + "NaN | \n", + "
| 290 | \n", + "GO:0004930 | \n", + "G protein-coupled receptor activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "66.0 | \n", + "NaN | \n", + "
| 291 | \n", + "GO:1990837 | \n", + "sequence-specific double-stranded DNA binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "67.0 | \n", + "NaN | \n", + "
| 292 | \n", + "GO:0015031 | \n", + "protein transport | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "68.0 | \n", + "NaN | \n", + "
| 293 | \n", + "GO:0019901 | \n", + "protein kinase binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "69.0 | \n", + "NaN | \n", + "
| 294 | \n", + "GO:0005829 | \n", + "cytosol | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "70.0 | \n", + "NaN | \n", + "
| 295 | \n", + "GO:0000978 | \n", + "RNA polymerase II cis-regulatory region sequence-specific DNA binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "71.0 | \n", + "NaN | \n", + "
| 296 | \n", + "GO:0045893 | \n", + "positive regulation of DNA-templated transcription | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "72.0 | \n", + "NaN | \n", + "
| 297 | \n", + "GO:0005737 | \n", + "cytoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "73.0 | \n", + "NaN | \n", + "
| 298 | \n", + "GO:0016324 | \n", + "apical plasma membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "74.0 | \n", + "NaN | \n", + "
| 299 | \n", + "GO:0007283 | \n", + "spermatogenesis | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "75.0 | \n", + "NaN | \n", + "
| 300 | \n", + "GO:0005794 | \n", + "Golgi apparatus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "76.0 | \n", + "NaN | \n", + "
| 301 | \n", + "GO:0003677 | \n", + "DNA binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "78.0 | \n", + "NaN | \n", + "
| 302 | \n", + "GO:0003700 | \n", + "DNA-binding transcription factor activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "79.0 | \n", + "NaN | \n", + "
| 303 | \n", + "GO:0098978 | \n", + "glutamatergic synapse | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "80.0 | \n", + "NaN | \n", + "
| 304 | \n", + "GO:0005759 | \n", + "mitochondrial matrix | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "81.0 | \n", + "NaN | \n", + "
| 305 | \n", + "GO:0000122 | \n", + "negative regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "82.0 | \n", + "NaN | \n", + "
| 306 | \n", + "GO:0032991 | \n", + "protein-containing complex | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "83.0 | \n", + "NaN | \n", + "
| 307 | \n", + "GO:0045202 | \n", + "synapse | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "84.0 | \n", + "NaN | \n", + "
| 308 | \n", + "GO:0005789 | \n", + "endoplasmic reticulum membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "85.0 | \n", + "NaN | \n", + "
| 309 | \n", + "GO:0005525 | \n", + "GTP binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "86.0 | \n", + "NaN | \n", + "
| 310 | \n", + "GO:0000139 | \n", + "Golgi membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "87.0 | \n", + "NaN | \n", + "
| 311 | \n", + "GO:0016604 | \n", + "nuclear body | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "88.0 | \n", + "NaN | \n", + "
| 312 | \n", + "GO:0030425 | \n", + "dendrite | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "89.0 | \n", + "NaN | \n", + "
| 313 | \n", + "GO:0005634 | \n", + "nucleus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "90.0 | \n", + "NaN | \n", + "
| 314 | \n", + "GO:0051787 | \n", + "misfolded protein binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 315 | \n", + "GO:0036503 | \n", + "ERAD pathway | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 316 | \n", + "glycosaminoglycan hydrolysis | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 317 | \n", + "heparan sulfate hydrolysis | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 318 | \n", + "cell surface hyaluronidase.\\nhpyothesis: the genes listed serve key roles in the degradation of polysaccharides and glycoproteins, the recognition of misfolded proteins and their subsequent degradation by endoplasmic reticulum-associated degradation, the hydrolysis of glycosaminoglycans, and the hydrolysis of heparan sulfate for the maintenance of cell proteins and structure | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 319 | \n", + "carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomal | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "
| 320 | \n", + "GO:0005777 | \n", + "peroxisome | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "
| 321 | \n", + "and catabolic processes; digit | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "
| 322 | \n", + "skeletal | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "
| 323 | \n", + "GO:0035108 | \n", + "limb morphogenesis | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "
| \n", + " | \n", + " | prompt_variant | \n", + "v1 | \n", + "v2 | \n", + "diff | \n", + "
|---|---|---|---|---|---|
| model | \n", + "method | \n", + "geneset | \n", + "\n", + " | \n", + " | \n", + " |
| gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "EDS-0 | \n", + "0.14 | \n", + "0.50 | \n", + "-0.36 | \n", + "
| EDS-1 | \n", + "0.50 | \n", + "0.25 | \n", + "0.25 | \n", + "||
| FA-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| FA-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ADIPOGENESIS-0 | \n", + "1.00 | \n", + "0.67 | \n", + "0.33 | \n", + "||
| HALLMARK_ADIPOGENESIS-1 | \n", + "0.33 | \n", + "1.00 | \n", + "-0.67 | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "1.00 | \n", + "0.87 | \n", + "0.13 | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "0.20 | \n", + "0.00 | \n", + "0.20 | \n", + "||
| HALLMARK_ANGIOGENESIS-0 | \n", + "0.50 | \n", + "0.33 | \n", + "0.17 | \n", + "||
| HALLMARK_ANGIOGENESIS-1 | \n", + "0.50 | \n", + "0.50 | \n", + "0.00 | \n", + "||
| HALLMARK_APICAL_JUNCTION-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_APICAL_JUNCTION-1 | \n", + "0.80 | \n", + "0.67 | \n", + "0.13 | \n", + "||
| HALLMARK_APICAL_SURFACE-0 | \n", + "0.25 | \n", + "0.08 | \n", + "0.17 | \n", + "||
| HALLMARK_APICAL_SURFACE-1 | \n", + "0.33 | \n", + "0.00 | \n", + "0.33 | \n", + "||
| HALLMARK_APOPTOSIS-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_APOPTOSIS-1 | \n", + "NaN | \n", + "0.71 | \n", + "NaN | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "1.00 | \n", + "0.60 | \n", + "0.40 | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "0.83 | \n", + "1.00 | \n", + "-0.17 | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "0.67 | \n", + "0.67 | \n", + "0.00 | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "0.67 | \n", + "0.75 | \n", + "-0.08 | \n", + "||
| HALLMARK_COAGULATION-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_COAGULATION-1 | \n", + "0.50 | \n", + "1.00 | \n", + "-0.50 | \n", + "||
| HALLMARK_COMPLEMENT-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_COMPLEMENT-1 | \n", + "0.80 | \n", + "0.80 | \n", + "0.00 | \n", + "||
| HALLMARK_DNA_REPAIR-0 | \n", + "0.67 | \n", + "1.00 | \n", + "-0.33 | \n", + "||
| HALLMARK_DNA_REPAIR-1 | \n", + "0.38 | \n", + "1.00 | \n", + "-0.62 | \n", + "||
| HALLMARK_E2F_TARGETS-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_E2F_TARGETS-1 | \n", + "0.75 | \n", + "1.00 | \n", + "-0.25 | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "1.00 | \n", + "0.79 | \n", + "0.21 | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "0.83 | \n", + "0.67 | \n", + "0.17 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "0.00 | \n", + "0.38 | \n", + "-0.38 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "0.20 | \n", + "0.17 | \n", + "0.03 | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "0.80 | \n", + "1.00 | \n", + "-0.20 | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "1.00 | \n", + "0.88 | \n", + "0.12 | \n", + "||
| HALLMARK_G2M_CHECKPOINT-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_G2M_CHECKPOINT-1 | \n", + "0.83 | \n", + "1.00 | \n", + "-0.17 | \n", + "||
| HALLMARK_GLYCOLYSIS-0 | \n", + "0.64 | \n", + "1.00 | \n", + "-0.36 | \n", + "||
| HALLMARK_GLYCOLYSIS-1 | \n", + "0.40 | \n", + "0.50 | \n", + "-0.10 | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "1.00 | \n", + "0.80 | \n", + "0.20 | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_HEME_METABOLISM-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_HEME_METABOLISM-1 | \n", + "0.10 | \n", + "0.00 | \n", + "0.10 | \n", + "||
| HALLMARK_HYPOXIA-0 | \n", + "0.67 | \n", + "1.00 | \n", + "-0.33 | \n", + "||
| HALLMARK_HYPOXIA-1 | \n", + "0.50 | \n", + "0.40 | \n", + "0.10 | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "1.00 | \n", + "0.20 | \n", + "0.80 | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "0.67 | \n", + "0.75 | \n", + "-0.08 | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "NaN | \n", + "0.80 | \n", + "NaN | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "0.33 | \n", + "1.00 | \n", + "-0.67 | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "1.00 | \n", + "0.80 | \n", + "0.20 | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "0.75 | \n", + "1.00 | \n", + "-0.25 | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "NaN | \n", + "1.00 | \n", + "NaN | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "0.75 | \n", + "1.00 | \n", + "-0.25 | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "0.20 | \n", + "0.12 | \n", + "0.08 | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "0.20 | \n", + "0.33 | \n", + "-0.13 | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "0.25 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-0 | \n", + "0.80 | \n", + "1.00 | \n", + "-0.20 | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_MTORC1_SIGNALING-0 | \n", + "0.60 | \n", + "0.60 | \n", + "0.00 | \n", + "||
| HALLMARK_MTORC1_SIGNALING-1 | \n", + "0.50 | \n", + "0.67 | \n", + "-0.17 | \n", + "||
| HALLMARK_MYC_TARGETS_V1-0 | \n", + "0.83 | \n", + "0.80 | \n", + "0.03 | \n", + "||
| HALLMARK_MYC_TARGETS_V1-1 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| HALLMARK_MYC_TARGETS_V2-0 | \n", + "1.00 | \n", + "0.67 | \n", + "0.33 | \n", + "||
| HALLMARK_MYC_TARGETS_V2-1 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| HALLMARK_MYOGENESIS-0 | \n", + "0.78 | \n", + "1.00 | \n", + "-0.22 | \n", + "||
| HALLMARK_MYOGENESIS-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_NOTCH_SIGNALING-0 | \n", + "0.75 | \n", + "0.33 | \n", + "0.42 | \n", + "||
| HALLMARK_NOTCH_SIGNALING-1 | \n", + "1.00 | \n", + "0.67 | \n", + "0.33 | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_P53_PATHWAY-0 | \n", + "0.67 | \n", + "0.25 | \n", + "0.42 | \n", + "||
| HALLMARK_P53_PATHWAY-1 | \n", + "0.75 | \n", + "0.67 | \n", + "0.08 | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "1.00 | \n", + "0.40 | \n", + "0.60 | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_PEROXISOME-0 | \n", + "0.60 | \n", + "0.80 | \n", + "-0.20 | \n", + "||
| HALLMARK_PEROXISOME-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_PROTEIN_SECRETION-0 | \n", + "0.67 | \n", + "0.83 | \n", + "-0.17 | \n", + "||
| HALLMARK_PROTEIN_SECRETION-1 | \n", + "1.00 | \n", + "0.83 | \n", + "0.17 | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "1.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_SPERMATOGENESIS-0 | \n", + "0.25 | \n", + "0.60 | \n", + "-0.35 | \n", + "||
| HALLMARK_SPERMATOGENESIS-1 | \n", + "0.00 | \n", + "0.33 | \n", + "-0.33 | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "NaN | \n", + "1.00 | \n", + "NaN | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "1.00 | \n", + "0.67 | \n", + "0.33 | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "1.00 | \n", + "0.83 | \n", + "0.17 | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "1.00 | \n", + "0.50 | \n", + "0.50 | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "1.00 | \n", + "0.67 | \n", + "0.33 | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "1.00 | \n", + "0.86 | \n", + "0.14 | \n", + "||
| HALLMARK_UV_RESPONSE_DN-0 | \n", + "0.00 | \n", + "0.75 | \n", + "-0.75 | \n", + "||
| HALLMARK_UV_RESPONSE_DN-1 | \n", + "0.67 | \n", + "0.60 | \n", + "0.07 | \n", + "||
| HALLMARK_UV_RESPONSE_UP-0 | \n", + "0.30 | \n", + "0.67 | \n", + "-0.37 | \n", + "||
| HALLMARK_UV_RESPONSE_UP-1 | \n", + "0.20 | \n", + "0.00 | \n", + "0.20 | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "0.00 | \n", + "1.00 | \n", + "-1.00 | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "1.00 | \n", + "0.50 | \n", + "0.50 | \n", + "||
| T cell proliferation-0 | \n", + "0.75 | \n", + "0.00 | \n", + "0.75 | \n", + "||
| T cell proliferation-1 | \n", + "1.00 | \n", + "0.67 | \n", + "0.33 | \n", + "||
| Yamanaka-TFs-0 | \n", + "NaN | \n", + "0.00 | \n", + "NaN | \n", + "||
| Yamanaka-TFs-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| amigo-example-0 | \n", + "0.20 | \n", + "0.33 | \n", + "-0.13 | \n", + "||
| amigo-example-1 | \n", + "0.50 | \n", + "0.67 | \n", + "-0.17 | \n", + "||
| bicluster_RNAseqDB_0-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| bicluster_RNAseqDB_0-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| bicluster_RNAseqDB_1002-0 | \n", + "0.55 | \n", + "0.40 | \n", + "0.15 | \n", + "||
| bicluster_RNAseqDB_1002-1 | \n", + "0.67 | \n", + "0.17 | \n", + "0.50 | \n", + "||
| endocytosis-0 | \n", + "1.00 | \n", + "0.20 | \n", + "0.80 | \n", + "||
| endocytosis-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| glycolysis-gocam-0 | \n", + "NaN | \n", + "1.00 | \n", + "NaN | \n", + "||
| glycolysis-gocam-1 | \n", + "1.00 | \n", + "0.40 | \n", + "0.60 | \n", + "||
| go-postsynapse-calcium-transmembrane-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| go-postsynapse-calcium-transmembrane-1 | \n", + "0.67 | \n", + "0.67 | \n", + "0.00 | \n", + "||
| go-reg-autophagy-pkra-0 | \n", + "0.50 | \n", + "0.67 | \n", + "-0.17 | \n", + "||
| go-reg-autophagy-pkra-1 | \n", + "0.67 | \n", + "0.17 | \n", + "0.50 | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "0.86 | \n", + "0.75 | \n", + "0.11 | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "0.75 | \n", + "1.00 | \n", + "-0.25 | \n", + "||
| ig-receptor-binding-2022-0 | \n", + "0.33 | \n", + "0.33 | \n", + "0.00 | \n", + "||
| ig-receptor-binding-2022-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| meiosis I-0 | \n", + "NaN | \n", + "1.00 | \n", + "NaN | \n", + "||
| meiosis I-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| molecular sequestering-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| molecular sequestering-1 | \n", + "0.00 | \n", + "0.33 | \n", + "-0.33 | \n", + "||
| mtorc1-0 | \n", + "0.60 | \n", + "0.60 | \n", + "0.00 | \n", + "||
| mtorc1-1 | \n", + "1.00 | \n", + "0.60 | \n", + "0.40 | \n", + "||
| peroxisome-0 | \n", + "1.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| peroxisome-1 | \n", + "NaN | \n", + "0.50 | \n", + "NaN | \n", + "||
| progeria-0 | \n", + "1.00 | \n", + "0.33 | \n", + "0.67 | \n", + "||
| progeria-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| regulation of presynaptic membrane potential-0 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| regulation of presynaptic membrane potential-1 | \n", + "0.67 | \n", + "1.00 | \n", + "-0.33 | \n", + "||
| sensory ataxia-0 | \n", + "0.50 | \n", + "1.00 | \n", + "-0.50 | \n", + "||
| sensory ataxia-1 | \n", + "0.00 | \n", + "0.67 | \n", + "-0.67 | \n", + "||
| term-GO:0007212-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| term-GO:0007212-1 | \n", + "0.67 | \n", + "0.50 | \n", + "0.17 | \n", + "||
| tf-downreg-colorectal-0 | \n", + "0.50 | \n", + "1.00 | \n", + "-0.50 | \n", + "||
| tf-downreg-colorectal-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| no_synopsis | \n", + "EDS-0 | \n", + "1.00 | \n", + "0.50 | \n", + "0.50 | \n", + "|
| EDS-1 | \n", + "0.67 | \n", + "1.00 | \n", + "-0.33 | \n", + "||
| FA-0 | \n", + "NaN | \n", + "0.67 | \n", + "NaN | \n", + "||
| FA-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ADIPOGENESIS-0 | \n", + "0.64 | \n", + "0.88 | \n", + "-0.24 | \n", + "||
| HALLMARK_ADIPOGENESIS-1 | \n", + "0.36 | \n", + "1.00 | \n", + "-0.64 | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ANGIOGENESIS-0 | \n", + "0.33 | \n", + "0.75 | \n", + "-0.42 | \n", + "||
| HALLMARK_ANGIOGENESIS-1 | \n", + "0.50 | \n", + "0.67 | \n", + "-0.17 | \n", + "||
| HALLMARK_APICAL_JUNCTION-0 | \n", + "0.75 | \n", + "0.50 | \n", + "0.25 | \n", + "||
| HALLMARK_APICAL_JUNCTION-1 | \n", + "0.89 | \n", + "1.00 | \n", + "-0.11 | \n", + "||
| HALLMARK_APICAL_SURFACE-0 | \n", + "0.14 | \n", + "0.33 | \n", + "-0.19 | \n", + "||
| HALLMARK_APICAL_SURFACE-1 | \n", + "0.12 | \n", + "0.10 | \n", + "0.02 | \n", + "||
| HALLMARK_APOPTOSIS-0 | \n", + "0.70 | \n", + "1.00 | \n", + "-0.30 | \n", + "||
| HALLMARK_APOPTOSIS-1 | \n", + "1.00 | \n", + "0.70 | \n", + "0.30 | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "0.50 | \n", + "0.50 | \n", + "0.00 | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "0.67 | \n", + "0.80 | \n", + "-0.13 | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "0.88 | \n", + "1.00 | \n", + "-0.12 | \n", + "||
| HALLMARK_COAGULATION-0 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| HALLMARK_COAGULATION-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_COMPLEMENT-0 | \n", + "0.40 | \n", + "0.75 | \n", + "-0.35 | \n", + "||
| HALLMARK_COMPLEMENT-1 | \n", + "0.89 | \n", + "1.00 | \n", + "-0.11 | \n", + "||
| HALLMARK_DNA_REPAIR-0 | \n", + "0.80 | \n", + "0.75 | \n", + "0.05 | \n", + "||
| HALLMARK_DNA_REPAIR-1 | \n", + "0.75 | \n", + "0.80 | \n", + "-0.05 | \n", + "||
| HALLMARK_E2F_TARGETS-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_E2F_TARGETS-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "0.82 | \n", + "1.00 | \n", + "-0.18 | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "0.89 | \n", + "0.86 | \n", + "0.03 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "0.50 | \n", + "0.09 | \n", + "0.41 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "0.20 | \n", + "0.25 | \n", + "-0.05 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "0.30 | \n", + "0.00 | \n", + "0.30 | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "NaN | \n", + "1.00 | \n", + "NaN | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_G2M_CHECKPOINT-0 | \n", + "1.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_G2M_CHECKPOINT-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_GLYCOLYSIS-0 | \n", + "NaN | \n", + "0.50 | \n", + "NaN | \n", + "||
| HALLMARK_GLYCOLYSIS-1 | \n", + "0.50 | \n", + "0.43 | \n", + "0.07 | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "0.80 | \n", + "0.25 | \n", + "0.55 | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_HEME_METABOLISM-0 | \n", + "0.33 | \n", + "0.00 | \n", + "0.33 | \n", + "||
| HALLMARK_HEME_METABOLISM-1 | \n", + "0.38 | \n", + "1.00 | \n", + "-0.62 | \n", + "||
| HALLMARK_HYPOXIA-0 | \n", + "0.56 | \n", + "0.44 | \n", + "0.11 | \n", + "||
| HALLMARK_HYPOXIA-1 | \n", + "1.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "0.67 | \n", + "0.33 | \n", + "0.33 | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "1.00 | \n", + "0.44 | \n", + "0.56 | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "0.71 | \n", + "1.00 | \n", + "-0.29 | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "0.67 | \n", + "0.92 | \n", + "-0.25 | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "0.29 | \n", + "1.00 | \n", + "-0.71 | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "1.00 | \n", + "0.63 | \n", + "0.37 | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "1.00 | \n", + "0.86 | \n", + "0.14 | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "0.50 | \n", + "0.00 | \n", + "0.50 | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "0.86 | \n", + "0.50 | \n", + "0.36 | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "0.40 | \n", + "0.00 | \n", + "0.40 | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-1 | \n", + "1.00 | \n", + "0.94 | \n", + "0.06 | \n", + "||
| HALLMARK_MTORC1_SIGNALING-0 | \n", + "0.75 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_MTORC1_SIGNALING-1 | \n", + "0.50 | \n", + "0.75 | \n", + "-0.25 | \n", + "||
| HALLMARK_MYC_TARGETS_V1-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_MYC_TARGETS_V1-1 | \n", + "1.00 | \n", + "0.89 | \n", + "0.11 | \n", + "||
| HALLMARK_MYC_TARGETS_V2-0 | \n", + "0.67 | \n", + "0.60 | \n", + "0.07 | \n", + "||
| HALLMARK_MYC_TARGETS_V2-1 | \n", + "0.67 | \n", + "0.78 | \n", + "-0.11 | \n", + "||
| HALLMARK_MYOGENESIS-0 | \n", + "0.60 | \n", + "1.00 | \n", + "-0.40 | \n", + "||
| HALLMARK_MYOGENESIS-1 | \n", + "NaN | \n", + "1.00 | \n", + "NaN | \n", + "||
| HALLMARK_NOTCH_SIGNALING-0 | \n", + "0.45 | \n", + "0.71 | \n", + "-0.26 | \n", + "||
| HALLMARK_NOTCH_SIGNALING-1 | \n", + "0.25 | \n", + "0.25 | \n", + "0.00 | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "0.67 | \n", + "0.67 | \n", + "0.00 | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "1.00 | \n", + "0.89 | \n", + "0.11 | \n", + "||
| HALLMARK_P53_PATHWAY-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_P53_PATHWAY-1 | \n", + "0.50 | \n", + "0.60 | \n", + "-0.10 | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "0.67 | \n", + "0.75 | \n", + "-0.08 | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "0.50 | \n", + "0.57 | \n", + "-0.07 | \n", + "||
| HALLMARK_PEROXISOME-0 | \n", + "0.50 | \n", + "0.60 | \n", + "-0.10 | \n", + "||
| HALLMARK_PEROXISOME-1 | \n", + "0.50 | \n", + "0.71 | \n", + "-0.21 | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "0.00 | \n", + "1.00 | \n", + "-1.00 | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| HALLMARK_PROTEIN_SECRETION-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_PROTEIN_SECRETION-1 | \n", + "0.62 | \n", + "1.00 | \n", + "-0.38 | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "0.80 | \n", + "1.00 | \n", + "-0.20 | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "0.33 | \n", + "1.00 | \n", + "-0.67 | \n", + "||
| HALLMARK_SPERMATOGENESIS-0 | \n", + "0.80 | \n", + "0.40 | \n", + "0.40 | \n", + "||
| HALLMARK_SPERMATOGENESIS-1 | \n", + "0.17 | \n", + "0.00 | \n", + "0.17 | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "0.86 | \n", + "0.83 | \n", + "0.02 | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "0.50 | \n", + "1.00 | \n", + "-0.50 | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "0.00 | \n", + "0.42 | \n", + "-0.42 | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "0.67 | \n", + "0.80 | \n", + "-0.13 | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "1.00 | \n", + "0.60 | \n", + "0.40 | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "0.53 | \n", + "0.75 | \n", + "-0.22 | \n", + "||
| HALLMARK_UV_RESPONSE_DN-0 | \n", + "1.00 | \n", + "0.67 | \n", + "0.33 | \n", + "||
| HALLMARK_UV_RESPONSE_DN-1 | \n", + "0.40 | \n", + "0.50 | \n", + "-0.10 | \n", + "||
| HALLMARK_UV_RESPONSE_UP-0 | \n", + "0.50 | \n", + "0.75 | \n", + "-0.25 | \n", + "||
| HALLMARK_UV_RESPONSE_UP-1 | \n", + "0.33 | \n", + "0.43 | \n", + "-0.10 | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "1.00 | \n", + "0.00 | \n", + "1.00 | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "0.75 | \n", + "1.00 | \n", + "-0.25 | \n", + "||
| T cell proliferation-0 | \n", + "1.00 | \n", + "0.83 | \n", + "0.17 | \n", + "||
| T cell proliferation-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| Yamanaka-TFs-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| Yamanaka-TFs-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| amigo-example-0 | \n", + "0.43 | \n", + "NaN | \n", + "NaN | \n", + "||
| amigo-example-1 | \n", + "0.50 | \n", + "0.71 | \n", + "-0.21 | \n", + "||
| bicluster_RNAseqDB_0-0 | \n", + "0.00 | \n", + "0.12 | \n", + "-0.12 | \n", + "||
| bicluster_RNAseqDB_0-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| bicluster_RNAseqDB_1002-0 | \n", + "0.50 | \n", + "0.75 | \n", + "-0.25 | \n", + "||
| bicluster_RNAseqDB_1002-1 | \n", + "1.00 | \n", + "0.40 | \n", + "0.60 | \n", + "||
| endocytosis-0 | \n", + "0.40 | \n", + "0.25 | \n", + "0.15 | \n", + "||
| endocytosis-1 | \n", + "0.57 | \n", + "0.60 | \n", + "-0.03 | \n", + "||
| glycolysis-gocam-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| glycolysis-gocam-1 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| go-postsynapse-calcium-transmembrane-0 | \n", + "0.80 | \n", + "1.00 | \n", + "-0.20 | \n", + "||
| go-postsynapse-calcium-transmembrane-1 | \n", + "0.56 | \n", + "0.75 | \n", + "-0.19 | \n", + "||
| go-reg-autophagy-pkra-0 | \n", + "1.00 | \n", + "0.60 | \n", + "0.40 | \n", + "||
| go-reg-autophagy-pkra-1 | \n", + "0.33 | \n", + "1.00 | \n", + "-0.67 | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "0.80 | \n", + "0.86 | \n", + "-0.06 | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "0.75 | \n", + "1.00 | \n", + "-0.25 | \n", + "||
| ig-receptor-binding-2022-0 | \n", + "0.00 | \n", + "0.60 | \n", + "-0.60 | \n", + "||
| ig-receptor-binding-2022-1 | \n", + "0.33 | \n", + "0.00 | \n", + "0.33 | \n", + "||
| meiosis I-0 | \n", + "1.00 | \n", + "0.69 | \n", + "0.31 | \n", + "||
| meiosis I-1 | \n", + "0.80 | \n", + "1.00 | \n", + "-0.20 | \n", + "||
| molecular sequestering-0 | \n", + "0.12 | \n", + "0.00 | \n", + "0.12 | \n", + "||
| molecular sequestering-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| mtorc1-0 | \n", + "0.75 | \n", + "NaN | \n", + "NaN | \n", + "||
| mtorc1-1 | \n", + "0.33 | \n", + "0.67 | \n", + "-0.33 | \n", + "||
| peroxisome-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| peroxisome-1 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| progeria-0 | \n", + "0.00 | \n", + "0.25 | \n", + "-0.25 | \n", + "||
| progeria-1 | \n", + "0.33 | \n", + "0.00 | \n", + "0.33 | \n", + "||
| regulation of presynaptic membrane potential-0 | \n", + "0.86 | \n", + "0.80 | \n", + "0.06 | \n", + "||
| regulation of presynaptic membrane potential-1 | \n", + "0.86 | \n", + "0.80 | \n", + "0.06 | \n", + "||
| sensory ataxia-0 | \n", + "0.00 | \n", + "0.20 | \n", + "-0.20 | \n", + "||
| sensory ataxia-1 | \n", + "NaN | \n", + "0.00 | \n", + "NaN | \n", + "||
| term-GO:0007212-0 | \n", + "0.80 | \n", + "0.50 | \n", + "0.30 | \n", + "||
| term-GO:0007212-1 | \n", + "NaN | \n", + "0.75 | \n", + "NaN | \n", + "||
| tf-downreg-colorectal-0 | \n", + "1.00 | \n", + "0.25 | \n", + "0.75 | \n", + "||
| tf-downreg-colorectal-1 | \n", + "1.00 | \n", + "0.89 | \n", + "0.11 | \n", + "||
| ontological_synopsis | \n", + "EDS-0 | \n", + "0.75 | \n", + "0.80 | \n", + "-0.05 | \n", + "|
| EDS-1 | \n", + "0.75 | \n", + "0.80 | \n", + "-0.05 | \n", + "||
| FA-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| FA-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ADIPOGENESIS-0 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| HALLMARK_ADIPOGENESIS-1 | \n", + "1.00 | \n", + "0.50 | \n", + "0.50 | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "0.75 | \n", + "1.00 | \n", + "-0.25 | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "0.60 | \n", + "0.57 | \n", + "0.03 | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "0.50 | \n", + "0.00 | \n", + "0.50 | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "0.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_ANGIOGENESIS-1 | \n", + "NaN | \n", + "1.00 | \n", + "NaN | \n", + "||
| HALLMARK_APICAL_JUNCTION-0 | \n", + "1.00 | \n", + "0.33 | \n", + "0.67 | \n", + "||
| HALLMARK_APICAL_SURFACE-0 | \n", + "0.00 | \n", + "0.43 | \n", + "-0.43 | \n", + "||
| HALLMARK_APICAL_SURFACE-1 | \n", + "0.43 | \n", + "0.00 | \n", + "0.43 | \n", + "||
| HALLMARK_APOPTOSIS-0 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| HALLMARK_APOPTOSIS-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "1.00 | \n", + "0.80 | \n", + "0.20 | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "0.80 | \n", + "1.00 | \n", + "-0.20 | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "0.33 | \n", + "0.80 | \n", + "-0.47 | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "0.25 | \n", + "0.67 | \n", + "-0.42 | \n", + "||
| HALLMARK_COAGULATION-0 | \n", + "0.67 | \n", + "1.00 | \n", + "-0.33 | \n", + "||
| HALLMARK_COAGULATION-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_COMPLEMENT-0 | \n", + "0.00 | \n", + "0.67 | \n", + "-0.67 | \n", + "||
| HALLMARK_COMPLEMENT-1 | \n", + "1.00 | \n", + "0.50 | \n", + "0.50 | \n", + "||
| HALLMARK_DNA_REPAIR-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_DNA_REPAIR-1 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| HALLMARK_E2F_TARGETS-0 | \n", + "1.00 | \n", + "0.88 | \n", + "0.12 | \n", + "||
| HALLMARK_E2F_TARGETS-1 | \n", + "NaN | \n", + "0.00 | \n", + "NaN | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "0.50 | \n", + "0.25 | \n", + "0.25 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "0.00 | \n", + "0.33 | \n", + "-0.33 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "NaN | \n", + "0.00 | \n", + "NaN | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "0.29 | \n", + "0.80 | \n", + "-0.51 | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_G2M_CHECKPOINT-0 | \n", + "1.00 | \n", + "0.50 | \n", + "0.50 | \n", + "||
| HALLMARK_G2M_CHECKPOINT-1 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| HALLMARK_GLYCOLYSIS-0 | \n", + "0.67 | \n", + "0.80 | \n", + "-0.13 | \n", + "||
| HALLMARK_GLYCOLYSIS-1 | \n", + "0.67 | \n", + "0.40 | \n", + "0.27 | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "0.29 | \n", + "1.00 | \n", + "-0.71 | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_HEME_METABOLISM-0 | \n", + "0.33 | \n", + "0.00 | \n", + "0.33 | \n", + "||
| HALLMARK_HEME_METABOLISM-1 | \n", + "NaN | \n", + "0.00 | \n", + "NaN | \n", + "||
| HALLMARK_HYPOXIA-0 | \n", + "0.20 | \n", + "0.00 | \n", + "0.20 | \n", + "||
| HALLMARK_HYPOXIA-1 | \n", + "0.33 | \n", + "0.17 | \n", + "0.17 | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "0.80 | \n", + "0.25 | \n", + "0.55 | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "0.12 | \n", + "0.50 | \n", + "-0.38 | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "0.67 | \n", + "1.00 | \n", + "-0.33 | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "0.50 | \n", + "0.55 | \n", + "-0.05 | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "0.33 | \n", + "0.33 | \n", + "0.00 | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "NaN | \n", + "0.33 | \n", + "NaN | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "0.40 | \n", + "0.00 | \n", + "0.40 | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_MTORC1_SIGNALING-0 | \n", + "0.33 | \n", + "0.00 | \n", + "0.33 | \n", + "||
| HALLMARK_MTORC1_SIGNALING-1 | \n", + "0.00 | \n", + "0.75 | \n", + "-0.75 | \n", + "||
| HALLMARK_MYC_TARGETS_V1-0 | \n", + "1.00 | \n", + "0.67 | \n", + "0.33 | \n", + "||
| HALLMARK_MYC_TARGETS_V1-1 | \n", + "1.00 | \n", + "0.80 | \n", + "0.20 | \n", + "||
| HALLMARK_MYC_TARGETS_V2-0 | \n", + "0.33 | \n", + "1.00 | \n", + "-0.67 | \n", + "||
| HALLMARK_MYC_TARGETS_V2-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_MYOGENESIS-0 | \n", + "0.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_MYOGENESIS-1 | \n", + "NaN | \n", + "0.50 | \n", + "NaN | \n", + "||
| HALLMARK_NOTCH_SIGNALING-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_NOTCH_SIGNALING-1 | \n", + "NaN | \n", + "1.00 | \n", + "NaN | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "1.00 | \n", + "0.50 | \n", + "0.50 | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "0.50 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_P53_PATHWAY-0 | \n", + "0.50 | \n", + "0.25 | \n", + "0.25 | \n", + "||
| HALLMARK_P53_PATHWAY-1 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "0.67 | \n", + "0.75 | \n", + "-0.08 | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_PEROXISOME-0 | \n", + "0.60 | \n", + "0.80 | \n", + "-0.20 | \n", + "||
| HALLMARK_PEROXISOME-1 | \n", + "0.40 | \n", + "0.50 | \n", + "-0.10 | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "0.50 | \n", + "0.60 | \n", + "-0.10 | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "0.67 | \n", + "1.00 | \n", + "-0.33 | \n", + "||
| HALLMARK_PROTEIN_SECRETION-0 | \n", + "0.62 | \n", + "0.33 | \n", + "0.29 | \n", + "||
| HALLMARK_PROTEIN_SECRETION-1 | \n", + "0.40 | \n", + "0.75 | \n", + "-0.35 | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "0.75 | \n", + "0.83 | \n", + "-0.08 | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "0.88 | \n", + "1.00 | \n", + "-0.12 | \n", + "||
| HALLMARK_SPERMATOGENESIS-0 | \n", + "0.40 | \n", + "0.25 | \n", + "0.15 | \n", + "||
| HALLMARK_SPERMATOGENESIS-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "NaN | \n", + "1.00 | \n", + "NaN | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "1.00 | \n", + "0.86 | \n", + "0.14 | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "0.75 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "NaN | \n", + "0.67 | \n", + "NaN | \n", + "||
| HALLMARK_UV_RESPONSE_DN-0 | \n", + "0.50 | \n", + "1.00 | \n", + "-0.50 | \n", + "||
| HALLMARK_UV_RESPONSE_DN-1 | \n", + "0.50 | \n", + "0.50 | \n", + "0.00 | \n", + "||
| HALLMARK_UV_RESPONSE_UP-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_UV_RESPONSE_UP-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "0.33 | \n", + "1.00 | \n", + "-0.67 | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "0.40 | \n", + "1.00 | \n", + "-0.60 | \n", + "||
| T cell proliferation-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| T cell proliferation-1 | \n", + "0.47 | \n", + "0.88 | \n", + "-0.41 | \n", + "||
| Yamanaka-TFs-0 | \n", + "0.67 | \n", + "0.25 | \n", + "0.42 | \n", + "||
| Yamanaka-TFs-1 | \n", + "0.25 | \n", + "0.00 | \n", + "0.25 | \n", + "||
| amigo-example-0 | \n", + "1.00 | \n", + "0.25 | \n", + "0.75 | \n", + "||
| amigo-example-1 | \n", + "0.75 | \n", + "0.33 | \n", + "0.42 | \n", + "||
| bicluster_RNAseqDB_0-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| bicluster_RNAseqDB_0-1 | \n", + "0.00 | \n", + "0.25 | \n", + "-0.25 | \n", + "||
| bicluster_RNAseqDB_1002-0 | \n", + "1.00 | \n", + "0.67 | \n", + "0.33 | \n", + "||
| bicluster_RNAseqDB_1002-1 | \n", + "0.50 | \n", + "0.67 | \n", + "-0.17 | \n", + "||
| endocytosis-0 | \n", + "1.00 | \n", + "0.20 | \n", + "0.80 | \n", + "||
| endocytosis-1 | \n", + "0.25 | \n", + "1.00 | \n", + "-0.75 | \n", + "||
| glycolysis-gocam-0 | \n", + "0.50 | \n", + "0.67 | \n", + "-0.17 | \n", + "||
| glycolysis-gocam-1 | \n", + "0.67 | \n", + "0.75 | \n", + "-0.08 | \n", + "||
| go-postsynapse-calcium-transmembrane-0 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| go-postsynapse-calcium-transmembrane-1 | \n", + "0.29 | \n", + "1.00 | \n", + "-0.71 | \n", + "||
| go-reg-autophagy-pkra-0 | \n", + "0.60 | \n", + "0.60 | \n", + "0.00 | \n", + "||
| go-reg-autophagy-pkra-1 | \n", + "0.60 | \n", + "0.80 | \n", + "-0.20 | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "0.80 | \n", + "1.00 | \n", + "-0.20 | \n", + "||
| ig-receptor-binding-2022-0 | \n", + "1.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| ig-receptor-binding-2022-1 | \n", + "0.14 | \n", + "0.50 | \n", + "-0.36 | \n", + "||
| meiosis I-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| meiosis I-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| molecular sequestering-0 | \n", + "0.33 | \n", + "0.50 | \n", + "-0.17 | \n", + "||
| molecular sequestering-1 | \n", + "0.25 | \n", + "0.00 | \n", + "0.25 | \n", + "||
| mtorc1-0 | \n", + "0.33 | \n", + "0.00 | \n", + "0.33 | \n", + "||
| mtorc1-1 | \n", + "0.58 | \n", + "0.33 | \n", + "0.25 | \n", + "||
| peroxisome-0 | \n", + "0.50 | \n", + "0.00 | \n", + "0.50 | \n", + "||
| peroxisome-1 | \n", + "0.60 | \n", + "0.33 | \n", + "0.27 | \n", + "||
| progeria-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| progeria-1 | \n", + "0.25 | \n", + "0.00 | \n", + "0.25 | \n", + "||
| regulation of presynaptic membrane potential-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| regulation of presynaptic membrane potential-1 | \n", + "0.80 | \n", + "1.00 | \n", + "-0.20 | \n", + "||
| sensory ataxia-0 | \n", + "0.67 | \n", + "0.50 | \n", + "0.17 | \n", + "||
| sensory ataxia-1 | \n", + "0.25 | \n", + "0.50 | \n", + "-0.25 | \n", + "||
| term-GO:0007212-0 | \n", + "1.00 | \n", + "0.50 | \n", + "0.50 | \n", + "||
| term-GO:0007212-1 | \n", + "0.13 | \n", + "0.29 | \n", + "-0.15 | \n", + "||
| tf-downreg-colorectal-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| tf-downreg-colorectal-1 | \n", + "0.60 | \n", + "1.00 | \n", + "-0.40 | \n", + "||
| text-davinci-003 | \n", + "narrative_synopsis | \n", + "EDS-0 | \n", + "0.33 | \n", + "0.00 | \n", + "0.33 | \n", + "
| EDS-1 | \n", + "0.50 | \n", + "0.00 | \n", + "0.50 | \n", + "||
| FA-0 | \n", + "0.67 | \n", + "1.00 | \n", + "-0.33 | \n", + "||
| FA-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ADIPOGENESIS-0 | \n", + "0.80 | \n", + "0.31 | \n", + "0.49 | \n", + "||
| HALLMARK_ADIPOGENESIS-1 | \n", + "0.33 | \n", + "0.14 | \n", + "0.19 | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "0.33 | \n", + "0.50 | \n", + "-0.17 | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "0.50 | \n", + "1.00 | \n", + "-0.50 | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ANGIOGENESIS-0 | \n", + "0.00 | \n", + "0.30 | \n", + "-0.30 | \n", + "||
| HALLMARK_ANGIOGENESIS-1 | \n", + "0.50 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_APICAL_JUNCTION-0 | \n", + "0.50 | \n", + "0.00 | \n", + "0.50 | \n", + "||
| HALLMARK_APICAL_JUNCTION-1 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| HALLMARK_APICAL_SURFACE-0 | \n", + "0.00 | \n", + "0.20 | \n", + "-0.20 | \n", + "||
| HALLMARK_APICAL_SURFACE-1 | \n", + "0.14 | \n", + "0.00 | \n", + "0.14 | \n", + "||
| HALLMARK_APOPTOSIS-0 | \n", + "1.00 | \n", + "0.50 | \n", + "0.50 | \n", + "||
| HALLMARK_APOPTOSIS-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "0.33 | \n", + "0.40 | \n", + "-0.07 | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "0.43 | \n", + "1.00 | \n", + "-0.57 | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "NaN | \n", + "0.25 | \n", + "NaN | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "0.50 | \n", + "0.33 | \n", + "0.17 | \n", + "||
| HALLMARK_COAGULATION-0 | \n", + "1.00 | \n", + "0.00 | \n", + "1.00 | \n", + "||
| HALLMARK_COAGULATION-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_COMPLEMENT-0 | \n", + "0.75 | \n", + "0.33 | \n", + "0.42 | \n", + "||
| HALLMARK_COMPLEMENT-1 | \n", + "1.00 | \n", + "0.67 | \n", + "0.33 | \n", + "||
| HALLMARK_DNA_REPAIR-0 | \n", + "0.00 | \n", + "1.00 | \n", + "-1.00 | \n", + "||
| HALLMARK_DNA_REPAIR-1 | \n", + "0.36 | \n", + "0.17 | \n", + "0.20 | \n", + "||
| HALLMARK_E2F_TARGETS-0 | \n", + "0.70 | \n", + "0.67 | \n", + "0.03 | \n", + "||
| HALLMARK_E2F_TARGETS-1 | \n", + "0.71 | \n", + "0.80 | \n", + "-0.09 | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "1.00 | \n", + "0.50 | \n", + "0.50 | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "0.00 | \n", + "0.67 | \n", + "-0.67 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "0.00 | \n", + "0.20 | \n", + "-0.20 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "0.33 | \n", + "0.00 | \n", + "0.33 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "0.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "0.20 | \n", + "0.20 | \n", + "0.00 | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "0.40 | \n", + "0.67 | \n", + "-0.27 | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "0.25 | \n", + "0.33 | \n", + "-0.08 | \n", + "||
| HALLMARK_G2M_CHECKPOINT-0 | \n", + "0.67 | \n", + "0.60 | \n", + "0.07 | \n", + "||
| HALLMARK_G2M_CHECKPOINT-1 | \n", + "0.62 | \n", + "0.57 | \n", + "0.05 | \n", + "||
| HALLMARK_GLYCOLYSIS-0 | \n", + "0.50 | \n", + "0.00 | \n", + "0.50 | \n", + "||
| HALLMARK_GLYCOLYSIS-1 | \n", + "0.46 | \n", + "0.20 | \n", + "0.26 | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "0.33 | \n", + "0.33 | \n", + "0.00 | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "0.60 | \n", + "0.50 | \n", + "0.10 | \n", + "||
| HALLMARK_HEME_METABOLISM-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_HEME_METABOLISM-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_HYPOXIA-0 | \n", + "0.12 | \n", + "0.00 | \n", + "0.12 | \n", + "||
| HALLMARK_HYPOXIA-1 | \n", + "0.25 | \n", + "0.25 | \n", + "0.00 | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "0.38 | \n", + "0.33 | \n", + "0.04 | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "0.33 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "0.40 | \n", + "0.50 | \n", + "-0.10 | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "0.33 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "0.67 | \n", + "0.50 | \n", + "0.17 | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "0.25 | \n", + "0.00 | \n", + "0.25 | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "0.22 | \n", + "0.22 | \n", + "0.00 | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "0.25 | \n", + "0.67 | \n", + "-0.42 | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "0.25 | \n", + "0.00 | \n", + "0.25 | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "0.00 | \n", + "0.11 | \n", + "-0.11 | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "0.27 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-0 | \n", + "0.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-1 | \n", + "0.50 | \n", + "0.40 | \n", + "0.10 | \n", + "||
| HALLMARK_MTORC1_SIGNALING-0 | \n", + "0.25 | \n", + "0.44 | \n", + "-0.19 | \n", + "||
| HALLMARK_MTORC1_SIGNALING-1 | \n", + "0.43 | \n", + "1.00 | \n", + "-0.57 | \n", + "||
| HALLMARK_MYC_TARGETS_V1-0 | \n", + "0.50 | \n", + "0.60 | \n", + "-0.10 | \n", + "||
| HALLMARK_MYC_TARGETS_V1-1 | \n", + "0.62 | \n", + "0.64 | \n", + "-0.01 | \n", + "||
| HALLMARK_MYC_TARGETS_V2-0 | \n", + "0.20 | \n", + "0.33 | \n", + "-0.13 | \n", + "||
| HALLMARK_MYC_TARGETS_V2-1 | \n", + "0.00 | \n", + "0.33 | \n", + "-0.33 | \n", + "||
| HALLMARK_MYOGENESIS-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_MYOGENESIS-1 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| HALLMARK_NOTCH_SIGNALING-0 | \n", + "0.80 | \n", + "1.00 | \n", + "-0.20 | \n", + "||
| HALLMARK_NOTCH_SIGNALING-1 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "1.00 | \n", + "0.80 | \n", + "0.20 | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "1.00 | \n", + "0.67 | \n", + "0.33 | \n", + "||
| HALLMARK_P53_PATHWAY-0 | \n", + "0.50 | \n", + "0.67 | \n", + "-0.17 | \n", + "||
| HALLMARK_P53_PATHWAY-1 | \n", + "0.38 | \n", + "0.29 | \n", + "0.09 | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "0.00 | \n", + "0.33 | \n", + "-0.33 | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "0.00 | \n", + "0.33 | \n", + "-0.33 | \n", + "||
| HALLMARK_PEROXISOME-0 | \n", + "0.00 | \n", + "1.00 | \n", + "-1.00 | \n", + "||
| HALLMARK_PEROXISOME-1 | \n", + "0.50 | \n", + "0.20 | \n", + "0.30 | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "0.67 | \n", + "0.00 | \n", + "0.67 | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "0.67 | \n", + "1.00 | \n", + "-0.33 | \n", + "||
| HALLMARK_PROTEIN_SECRETION-0 | \n", + "0.67 | \n", + "0.50 | \n", + "0.17 | \n", + "||
| HALLMARK_PROTEIN_SECRETION-1 | \n", + "0.50 | \n", + "0.17 | \n", + "0.33 | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "0.20 | \n", + "0.33 | \n", + "-0.13 | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_SPERMATOGENESIS-0 | \n", + "0.12 | \n", + "0.00 | \n", + "0.12 | \n", + "||
| HALLMARK_SPERMATOGENESIS-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "NaN | \n", + "0.50 | \n", + "NaN | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "0.50 | \n", + "0.67 | \n", + "-0.17 | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "1.00 | \n", + "0.60 | \n", + "0.40 | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "0.40 | \n", + "1.00 | \n", + "-0.60 | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "0.60 | \n", + "0.50 | \n", + "0.10 | \n", + "||
| HALLMARK_UV_RESPONSE_DN-0 | \n", + "1.00 | \n", + "0.25 | \n", + "0.75 | \n", + "||
| HALLMARK_UV_RESPONSE_DN-1 | \n", + "0.33 | \n", + "0.50 | \n", + "-0.17 | \n", + "||
| HALLMARK_UV_RESPONSE_UP-0 | \n", + "0.00 | \n", + "1.00 | \n", + "-1.00 | \n", + "||
| HALLMARK_UV_RESPONSE_UP-1 | \n", + "0.33 | \n", + "0.00 | \n", + "0.33 | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "0.60 | \n", + "0.00 | \n", + "0.60 | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "0.00 | \n", + "0.20 | \n", + "-0.20 | \n", + "||
| T cell proliferation-0 | \n", + "0.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| T cell proliferation-1 | \n", + "0.67 | \n", + "0.20 | \n", + "0.47 | \n", + "||
| Yamanaka-TFs-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| Yamanaka-TFs-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| amigo-example-0 | \n", + "0.40 | \n", + "0.50 | \n", + "-0.10 | \n", + "||
| amigo-example-1 | \n", + "0.33 | \n", + "0.50 | \n", + "-0.17 | \n", + "||
| bicluster_RNAseqDB_0-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| bicluster_RNAseqDB_0-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| bicluster_RNAseqDB_1002-0 | \n", + "0.33 | \n", + "0.27 | \n", + "0.07 | \n", + "||
| bicluster_RNAseqDB_1002-1 | \n", + "0.00 | \n", + "0.57 | \n", + "-0.57 | \n", + "||
| endocytosis-0 | \n", + "0.50 | \n", + "0.25 | \n", + "0.25 | \n", + "||
| endocytosis-1 | \n", + "0.40 | \n", + "1.00 | \n", + "-0.60 | \n", + "||
| glycolysis-gocam-0 | \n", + "0.50 | \n", + "0.44 | \n", + "0.06 | \n", + "||
| glycolysis-gocam-1 | \n", + "0.50 | \n", + "0.50 | \n", + "0.00 | \n", + "||
| go-postsynapse-calcium-transmembrane-0 | \n", + "0.50 | \n", + "NaN | \n", + "NaN | \n", + "||
| go-postsynapse-calcium-transmembrane-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| go-reg-autophagy-pkra-0 | \n", + "0.50 | \n", + "0.40 | \n", + "0.10 | \n", + "||
| go-reg-autophagy-pkra-1 | \n", + "0.60 | \n", + "0.20 | \n", + "0.40 | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "0.40 | \n", + "NaN | \n", + "NaN | \n", + "||
| ig-receptor-binding-2022-0 | \n", + "0.50 | \n", + "0.00 | \n", + "0.50 | \n", + "||
| ig-receptor-binding-2022-1 | \n", + "0.50 | \n", + "0.50 | \n", + "0.00 | \n", + "||
| meiosis I-0 | \n", + "0.80 | \n", + "0.75 | \n", + "0.05 | \n", + "||
| meiosis I-1 | \n", + "0.67 | \n", + "0.75 | \n", + "-0.08 | \n", + "||
| molecular sequestering-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| molecular sequestering-1 | \n", + "0.20 | \n", + "0.00 | \n", + "0.20 | \n", + "||
| mtorc1-0 | \n", + "0.25 | \n", + "0.44 | \n", + "-0.19 | \n", + "||
| mtorc1-1 | \n", + "0.00 | \n", + "0.40 | \n", + "-0.40 | \n", + "||
| peroxisome-1 | \n", + "0.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| progeria-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| progeria-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| regulation of presynaptic membrane potential-1 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| sensory ataxia-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| sensory ataxia-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| term-GO:0007212-0 | \n", + "0.67 | \n", + "0.00 | \n", + "0.67 | \n", + "||
| term-GO:0007212-1 | \n", + "NaN | \n", + "0.25 | \n", + "NaN | \n", + "||
| tf-downreg-colorectal-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| tf-downreg-colorectal-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| no_synopsis | \n", + "EDS-0 | \n", + "1.00 | \n", + "0.00 | \n", + "1.00 | \n", + "|
| EDS-1 | \n", + "1.00 | \n", + "0.00 | \n", + "1.00 | \n", + "||
| FA-0 | \n", + "NaN | \n", + "0.50 | \n", + "NaN | \n", + "||
| FA-1 | \n", + "1.00 | \n", + "0.00 | \n", + "1.00 | \n", + "||
| HALLMARK_ADIPOGENESIS-0 | \n", + "0.25 | \n", + "0.00 | \n", + "0.25 | \n", + "||
| HALLMARK_ADIPOGENESIS-1 | \n", + "0.50 | \n", + "0.29 | \n", + "0.21 | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "1.00 | \n", + "0.00 | \n", + "1.00 | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "0.12 | \n", + "0.25 | \n", + "-0.12 | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "0.08 | \n", + "0.00 | \n", + "0.08 | \n", + "||
| HALLMARK_ANGIOGENESIS-0 | \n", + "NaN | \n", + "0.50 | \n", + "NaN | \n", + "||
| HALLMARK_ANGIOGENESIS-1 | \n", + "0.80 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_APICAL_JUNCTION-0 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| HALLMARK_APICAL_JUNCTION-1 | \n", + "0.50 | \n", + "1.00 | \n", + "-0.50 | \n", + "||
| HALLMARK_APICAL_SURFACE-0 | \n", + "0.20 | \n", + "0.25 | \n", + "-0.05 | \n", + "||
| HALLMARK_APICAL_SURFACE-1 | \n", + "0.50 | \n", + "1.00 | \n", + "-0.50 | \n", + "||
| HALLMARK_APOPTOSIS-0 | \n", + "1.00 | \n", + "0.50 | \n", + "0.50 | \n", + "||
| HALLMARK_APOPTOSIS-1 | \n", + "0.33 | \n", + "0.56 | \n", + "-0.22 | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "0.67 | \n", + "0.67 | \n", + "0.00 | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "0.33 | \n", + "0.33 | \n", + "0.00 | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "0.33 | \n", + "0.33 | \n", + "0.00 | \n", + "||
| HALLMARK_COAGULATION-1 | \n", + "0.60 | \n", + "0.67 | \n", + "-0.07 | \n", + "||
| HALLMARK_COMPLEMENT-0 | \n", + "0.00 | \n", + "0.75 | \n", + "-0.75 | \n", + "||
| HALLMARK_COMPLEMENT-1 | \n", + "0.40 | \n", + "0.36 | \n", + "0.04 | \n", + "||
| HALLMARK_DNA_REPAIR-0 | \n", + "0.60 | \n", + "0.43 | \n", + "0.17 | \n", + "||
| HALLMARK_DNA_REPAIR-1 | \n", + "0.33 | \n", + "0.29 | \n", + "0.05 | \n", + "||
| HALLMARK_E2F_TARGETS-0 | \n", + "0.50 | \n", + "0.50 | \n", + "0.00 | \n", + "||
| HALLMARK_E2F_TARGETS-1 | \n", + "0.55 | \n", + "0.75 | \n", + "-0.20 | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "NaN | \n", + "1.00 | \n", + "NaN | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "0.67 | \n", + "1.00 | \n", + "-0.33 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "NaN | \n", + "0.00 | \n", + "NaN | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "0.00 | \n", + "0.33 | \n", + "-0.33 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "0.25 | \n", + "0.12 | \n", + "0.12 | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "0.57 | \n", + "1.00 | \n", + "-0.43 | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "1.00 | \n", + "0.80 | \n", + "0.20 | \n", + "||
| HALLMARK_G2M_CHECKPOINT-0 | \n", + "1.00 | \n", + "0.57 | \n", + "0.43 | \n", + "||
| HALLMARK_G2M_CHECKPOINT-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_GLYCOLYSIS-0 | \n", + "0.40 | \n", + "1.00 | \n", + "-0.60 | \n", + "||
| HALLMARK_GLYCOLYSIS-1 | \n", + "0.33 | \n", + "0.60 | \n", + "-0.27 | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "0.86 | \n", + "1.00 | \n", + "-0.14 | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "0.71 | \n", + "1.00 | \n", + "-0.29 | \n", + "||
| HALLMARK_HEME_METABOLISM-0 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| HALLMARK_HEME_METABOLISM-1 | \n", + "0.00 | \n", + "0.10 | \n", + "-0.10 | \n", + "||
| HALLMARK_HYPOXIA-0 | \n", + "0.43 | \n", + "0.00 | \n", + "0.43 | \n", + "||
| HALLMARK_HYPOXIA-1 | \n", + "0.12 | \n", + "0.33 | \n", + "-0.21 | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "0.25 | \n", + "0.00 | \n", + "0.25 | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "0.75 | \n", + "0.00 | \n", + "0.75 | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "1.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "0.67 | \n", + "0.67 | \n", + "0.00 | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "0.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "0.00 | \n", + "0.33 | \n", + "-0.33 | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "1.00 | \n", + "0.67 | \n", + "0.33 | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "0.20 | \n", + "0.00 | \n", + "0.20 | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "1.00 | \n", + "0.00 | \n", + "1.00 | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "0.50 | \n", + "0.50 | \n", + "0.00 | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "0.80 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-0 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-1 | \n", + "0.50 | \n", + "0.75 | \n", + "-0.25 | \n", + "||
| HALLMARK_MTORC1_SIGNALING-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_MTORC1_SIGNALING-1 | \n", + "0.14 | \n", + "0.33 | \n", + "-0.19 | \n", + "||
| HALLMARK_MYC_TARGETS_V1-0 | \n", + "0.50 | \n", + "0.33 | \n", + "0.17 | \n", + "||
| HALLMARK_MYC_TARGETS_V1-1 | \n", + "0.50 | \n", + "1.00 | \n", + "-0.50 | \n", + "||
| HALLMARK_MYC_TARGETS_V2-0 | \n", + "NaN | \n", + "0.25 | \n", + "NaN | \n", + "||
| HALLMARK_MYC_TARGETS_V2-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_MYOGENESIS-0 | \n", + "NaN | \n", + "0.00 | \n", + "NaN | \n", + "||
| HALLMARK_MYOGENESIS-1 | \n", + "0.75 | \n", + "0.25 | \n", + "0.50 | \n", + "||
| HALLMARK_NOTCH_SIGNALING-0 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| HALLMARK_NOTCH_SIGNALING-1 | \n", + "0.33 | \n", + "0.50 | \n", + "-0.17 | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "1.00 | \n", + "0.50 | \n", + "0.50 | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_P53_PATHWAY-0 | \n", + "0.67 | \n", + "0.50 | \n", + "0.17 | \n", + "||
| HALLMARK_P53_PATHWAY-1 | \n", + "0.40 | \n", + "0.67 | \n", + "-0.27 | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "0.67 | \n", + "0.40 | \n", + "0.27 | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "0.00 | \n", + "0.33 | \n", + "-0.33 | \n", + "||
| HALLMARK_PEROXISOME-0 | \n", + "NaN | \n", + "0.25 | \n", + "NaN | \n", + "||
| HALLMARK_PEROXISOME-1 | \n", + "0.67 | \n", + "0.11 | \n", + "0.56 | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "0.40 | \n", + "0.57 | \n", + "-0.17 | \n", + "||
| HALLMARK_PROTEIN_SECRETION-0 | \n", + "NaN | \n", + "1.00 | \n", + "NaN | \n", + "||
| HALLMARK_PROTEIN_SECRETION-1 | \n", + "0.33 | \n", + "0.20 | \n", + "0.13 | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "NaN | \n", + "0.20 | \n", + "NaN | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_SPERMATOGENESIS-0 | \n", + "0.00 | \n", + "0.17 | \n", + "-0.17 | \n", + "||
| HALLMARK_SPERMATOGENESIS-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "0.33 | \n", + "0.00 | \n", + "0.33 | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "1.00 | \n", + "0.67 | \n", + "0.33 | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "1.00 | \n", + "0.40 | \n", + "0.60 | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "0.25 | \n", + "0.00 | \n", + "0.25 | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "0.67 | \n", + "0.50 | \n", + "0.17 | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "0.20 | \n", + "0.33 | \n", + "-0.13 | \n", + "||
| HALLMARK_UV_RESPONSE_DN-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| HALLMARK_UV_RESPONSE_DN-1 | \n", + "0.80 | \n", + "0.50 | \n", + "0.30 | \n", + "||
| HALLMARK_UV_RESPONSE_UP-0 | \n", + "0.33 | \n", + "0.40 | \n", + "-0.07 | \n", + "||
| HALLMARK_UV_RESPONSE_UP-1 | \n", + "0.17 | \n", + "0.33 | \n", + "-0.17 | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "1.00 | \n", + "0.50 | \n", + "0.50 | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "0.67 | \n", + "0.67 | \n", + "0.00 | \n", + "||
| T cell proliferation-0 | \n", + "0.50 | \n", + "1.00 | \n", + "-0.50 | \n", + "||
| T cell proliferation-1 | \n", + "0.50 | \n", + "0.67 | \n", + "-0.17 | \n", + "||
| Yamanaka-TFs-0 | \n", + "0.50 | \n", + "0.50 | \n", + "0.00 | \n", + "||
| Yamanaka-TFs-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| amigo-example-0 | \n", + "0.50 | \n", + "0.00 | \n", + "0.50 | \n", + "||
| amigo-example-1 | \n", + "0.00 | \n", + "0.33 | \n", + "-0.33 | \n", + "||
| bicluster_RNAseqDB_0-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| bicluster_RNAseqDB_0-1 | \n", + "0.50 | \n", + "0.00 | \n", + "0.50 | \n", + "||
| bicluster_RNAseqDB_1002-0 | \n", + "NaN | \n", + "0.33 | \n", + "NaN | \n", + "||
| bicluster_RNAseqDB_1002-1 | \n", + "0.20 | \n", + "0.00 | \n", + "0.20 | \n", + "||
| endocytosis-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| endocytosis-1 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| glycolysis-gocam-0 | \n", + "1.00 | \n", + "0.50 | \n", + "0.50 | \n", + "||
| glycolysis-gocam-1 | \n", + "0.50 | \n", + "0.50 | \n", + "0.00 | \n", + "||
| go-postsynapse-calcium-transmembrane-0 | \n", + "0.00 | \n", + "1.00 | \n", + "-1.00 | \n", + "||
| go-postsynapse-calcium-transmembrane-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| go-reg-autophagy-pkra-0 | \n", + "0.17 | \n", + "NaN | \n", + "NaN | \n", + "||
| go-reg-autophagy-pkra-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "0.00 | \n", + "1.00 | \n", + "-1.00 | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| ig-receptor-binding-2022-0 | \n", + "0.50 | \n", + "NaN | \n", + "NaN | \n", + "||
| ig-receptor-binding-2022-1 | \n", + "0.33 | \n", + "0.00 | \n", + "0.33 | \n", + "||
| meiosis I-0 | \n", + "1.00 | \n", + "0.75 | \n", + "0.25 | \n", + "||
| meiosis I-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| molecular sequestering-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| molecular sequestering-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| mtorc1-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| mtorc1-1 | \n", + "1.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| peroxisome-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| peroxisome-1 | \n", + "NaN | \n", + "1.00 | \n", + "NaN | \n", + "||
| progeria-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| progeria-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| regulation of presynaptic membrane potential-0 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| regulation of presynaptic membrane potential-1 | \n", + "0.75 | \n", + "1.00 | \n", + "-0.25 | \n", + "||
| sensory ataxia-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| sensory ataxia-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| term-GO:0007212-1 | \n", + "0.50 | \n", + "0.50 | \n", + "0.00 | \n", + "||
| tf-downreg-colorectal-0 | \n", + "0.50 | \n", + "1.00 | \n", + "-0.50 | \n", + "||
| tf-downreg-colorectal-1 | \n", + "0.00 | \n", + "0.40 | \n", + "-0.40 | \n", + "||
| ontological_synopsis | \n", + "EDS-0 | \n", + "0.18 | \n", + "0.17 | \n", + "0.02 | \n", + "|
| EDS-1 | \n", + "0.33 | \n", + "0.80 | \n", + "-0.47 | \n", + "||
| FA-0 | \n", + "NaN | \n", + "0.83 | \n", + "NaN | \n", + "||
| FA-1 | \n", + "0.38 | \n", + "0.23 | \n", + "0.15 | \n", + "||
| HALLMARK_ADIPOGENESIS-0 | \n", + "0.25 | \n", + "0.00 | \n", + "0.25 | \n", + "||
| HALLMARK_ADIPOGENESIS-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "0.75 | \n", + "0.40 | \n", + "0.35 | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "0.50 | \n", + "0.50 | \n", + "0.00 | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "0.00 | \n", + "0.09 | \n", + "-0.09 | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ANGIOGENESIS-0 | \n", + "0.20 | \n", + "0.00 | \n", + "0.20 | \n", + "||
| HALLMARK_ANGIOGENESIS-1 | \n", + "0.33 | \n", + "0.29 | \n", + "0.05 | \n", + "||
| HALLMARK_APICAL_JUNCTION-0 | \n", + "1.00 | \n", + "0.80 | \n", + "0.20 | \n", + "||
| HALLMARK_APICAL_JUNCTION-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_APICAL_SURFACE-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_APICAL_SURFACE-1 | \n", + "0.50 | \n", + "0.00 | \n", + "0.50 | \n", + "||
| HALLMARK_APOPTOSIS-0 | \n", + "0.50 | \n", + "0.60 | \n", + "-0.10 | \n", + "||
| HALLMARK_APOPTOSIS-1 | \n", + "1.00 | \n", + "0.33 | \n", + "0.67 | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "0.33 | \n", + "0.50 | \n", + "-0.17 | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "0.40 | \n", + "0.50 | \n", + "-0.10 | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "0.08 | \n", + "0.25 | \n", + "-0.17 | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "0.33 | \n", + "0.50 | \n", + "-0.17 | \n", + "||
| HALLMARK_COAGULATION-0 | \n", + "0.50 | \n", + "1.00 | \n", + "-0.50 | \n", + "||
| HALLMARK_COAGULATION-1 | \n", + "0.50 | \n", + "0.33 | \n", + "0.17 | \n", + "||
| HALLMARK_COMPLEMENT-0 | \n", + "0.33 | \n", + "0.50 | \n", + "-0.17 | \n", + "||
| HALLMARK_COMPLEMENT-1 | \n", + "0.56 | \n", + "0.70 | \n", + "-0.14 | \n", + "||
| HALLMARK_DNA_REPAIR-0 | \n", + "0.25 | \n", + "0.00 | \n", + "0.25 | \n", + "||
| HALLMARK_DNA_REPAIR-1 | \n", + "0.00 | \n", + "0.33 | \n", + "-0.33 | \n", + "||
| HALLMARK_E2F_TARGETS-0 | \n", + "0.83 | \n", + "0.50 | \n", + "0.33 | \n", + "||
| HALLMARK_E2F_TARGETS-1 | \n", + "0.40 | \n", + "0.86 | \n", + "-0.46 | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "1.00 | \n", + "0.00 | \n", + "1.00 | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "NaN | \n", + "0.05 | \n", + "NaN | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "0.26 | \n", + "0.20 | \n", + "0.06 | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "0.14 | \n", + "0.60 | \n", + "-0.46 | \n", + "||
| HALLMARK_G2M_CHECKPOINT-0 | \n", + "0.50 | \n", + "0.67 | \n", + "-0.17 | \n", + "||
| HALLMARK_G2M_CHECKPOINT-1 | \n", + "0.25 | \n", + "0.73 | \n", + "-0.48 | \n", + "||
| HALLMARK_GLYCOLYSIS-0 | \n", + "0.14 | \n", + "0.00 | \n", + "0.14 | \n", + "||
| HALLMARK_GLYCOLYSIS-1 | \n", + "0.00 | \n", + "0.11 | \n", + "-0.11 | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "0.60 | \n", + "0.11 | \n", + "0.49 | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "0.00 | \n", + "0.33 | \n", + "-0.33 | \n", + "||
| HALLMARK_HEME_METABOLISM-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_HEME_METABOLISM-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_HYPOXIA-0 | \n", + "0.00 | \n", + "0.50 | \n", + "-0.50 | \n", + "||
| HALLMARK_HYPOXIA-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "0.33 | \n", + "0.43 | \n", + "-0.10 | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "0.08 | \n", + "0.33 | \n", + "-0.25 | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "0.33 | \n", + "0.67 | \n", + "-0.33 | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "1.00 | \n", + "0.60 | \n", + "0.40 | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "0.75 | \n", + "0.43 | \n", + "0.32 | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "0.40 | \n", + "0.25 | \n", + "0.15 | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "0.00 | \n", + "0.25 | \n", + "-0.25 | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "0.82 | \n", + "0.25 | \n", + "0.57 | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "0.27 | \n", + "0.00 | \n", + "0.27 | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "0.00 | \n", + "0.20 | \n", + "-0.20 | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "0.33 | \n", + "0.00 | \n", + "0.33 | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "0.00 | \n", + "0.67 | \n", + "-0.67 | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-0 | \n", + "0.33 | \n", + "0.44 | \n", + "-0.11 | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-1 | \n", + "NaN | \n", + "0.29 | \n", + "NaN | \n", + "||
| HALLMARK_MTORC1_SIGNALING-0 | \n", + "0.20 | \n", + "0.12 | \n", + "0.08 | \n", + "||
| HALLMARK_MTORC1_SIGNALING-1 | \n", + "0.08 | \n", + "0.00 | \n", + "0.08 | \n", + "||
| HALLMARK_MYC_TARGETS_V1-0 | \n", + "0.40 | \n", + "0.71 | \n", + "-0.31 | \n", + "||
| HALLMARK_MYC_TARGETS_V1-1 | \n", + "0.33 | \n", + "0.10 | \n", + "0.23 | \n", + "||
| HALLMARK_MYC_TARGETS_V2-0 | \n", + "0.14 | \n", + "0.25 | \n", + "-0.11 | \n", + "||
| HALLMARK_MYC_TARGETS_V2-1 | \n", + "0.20 | \n", + "0.25 | \n", + "-0.05 | \n", + "||
| HALLMARK_MYOGENESIS-0 | \n", + "0.43 | \n", + "0.00 | \n", + "0.43 | \n", + "||
| HALLMARK_MYOGENESIS-1 | \n", + "0.33 | \n", + "0.00 | \n", + "0.33 | \n", + "||
| HALLMARK_NOTCH_SIGNALING-0 | \n", + "0.80 | \n", + "0.88 | \n", + "-0.07 | \n", + "||
| HALLMARK_NOTCH_SIGNALING-1 | \n", + "0.33 | \n", + "0.62 | \n", + "-0.29 | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "0.50 | \n", + "0.50 | \n", + "0.00 | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "0.27 | \n", + "0.33 | \n", + "-0.06 | \n", + "||
| HALLMARK_P53_PATHWAY-0 | \n", + "0.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_P53_PATHWAY-1 | \n", + "0.08 | \n", + "0.50 | \n", + "-0.42 | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "0.33 | \n", + "0.08 | \n", + "0.26 | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_PEROXISOME-0 | \n", + "0.50 | \n", + "0.43 | \n", + "0.07 | \n", + "||
| HALLMARK_PEROXISOME-1 | \n", + "NaN | \n", + "0.08 | \n", + "NaN | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "0.31 | \n", + "1.00 | \n", + "-0.69 | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "1.00 | \n", + "0.62 | \n", + "0.38 | \n", + "||
| HALLMARK_PROTEIN_SECRETION-0 | \n", + "0.40 | \n", + "0.00 | \n", + "0.40 | \n", + "||
| HALLMARK_PROTEIN_SECRETION-1 | \n", + "0.00 | \n", + "0.25 | \n", + "-0.25 | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "0.08 | \n", + "0.00 | \n", + "0.08 | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "0.55 | \n", + "0.64 | \n", + "-0.09 | \n", + "||
| HALLMARK_SPERMATOGENESIS-0 | \n", + "0.00 | \n", + "0.12 | \n", + "-0.12 | \n", + "||
| HALLMARK_SPERMATOGENESIS-1 | \n", + "0.11 | \n", + "0.00 | \n", + "0.11 | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "1.00 | \n", + "0.56 | \n", + "0.44 | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "0.00 | \n", + "0.70 | \n", + "-0.70 | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "1.00 | \n", + "0.00 | \n", + "1.00 | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "0.25 | \n", + "0.75 | \n", + "-0.50 | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "0.45 | \n", + "0.00 | \n", + "0.45 | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "0.00 | \n", + "0.17 | \n", + "-0.17 | \n", + "||
| HALLMARK_UV_RESPONSE_DN-0 | \n", + "0.00 | \n", + "NaN | \n", + "NaN | \n", + "||
| HALLMARK_UV_RESPONSE_DN-1 | \n", + "0.00 | \n", + "0.29 | \n", + "-0.29 | \n", + "||
| HALLMARK_UV_RESPONSE_UP-0 | \n", + "0.17 | \n", + "0.00 | \n", + "0.17 | \n", + "||
| HALLMARK_UV_RESPONSE_UP-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "0.17 | \n", + "0.17 | \n", + "0.00 | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "0.67 | \n", + "0.44 | \n", + "0.22 | \n", + "||
| T cell proliferation-0 | \n", + "0.25 | \n", + "0.43 | \n", + "-0.18 | \n", + "||
| T cell proliferation-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| Yamanaka-TFs-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| Yamanaka-TFs-1 | \n", + "0.08 | \n", + "0.11 | \n", + "-0.03 | \n", + "||
| amigo-example-0 | \n", + "0.25 | \n", + "0.44 | \n", + "-0.19 | \n", + "||
| amigo-example-1 | \n", + "0.40 | \n", + "0.30 | \n", + "0.10 | \n", + "||
| bicluster_RNAseqDB_0-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| bicluster_RNAseqDB_0-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| bicluster_RNAseqDB_1002-0 | \n", + "0.38 | \n", + "0.50 | \n", + "-0.12 | \n", + "||
| bicluster_RNAseqDB_1002-1 | \n", + "0.67 | \n", + "0.00 | \n", + "0.67 | \n", + "||
| endocytosis-0 | \n", + "0.33 | \n", + "0.20 | \n", + "0.13 | \n", + "||
| endocytosis-1 | \n", + "0.17 | \n", + "0.00 | \n", + "0.17 | \n", + "||
| glycolysis-gocam-0 | \n", + "0.00 | \n", + "0.33 | \n", + "-0.33 | \n", + "||
| glycolysis-gocam-1 | \n", + "0.26 | \n", + "0.19 | \n", + "0.08 | \n", + "||
| go-postsynapse-calcium-transmembrane-0 | \n", + "0.47 | \n", + "1.00 | \n", + "-0.53 | \n", + "||
| go-postsynapse-calcium-transmembrane-1 | \n", + "1.00 | \n", + "1.00 | \n", + "0.00 | \n", + "||
| go-reg-autophagy-pkra-0 | \n", + "0.00 | \n", + "0.25 | \n", + "-0.25 | \n", + "||
| go-reg-autophagy-pkra-1 | \n", + "0.33 | \n", + "1.00 | \n", + "-0.67 | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "0.62 | \n", + "0.75 | \n", + "-0.12 | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "0.35 | \n", + "0.70 | \n", + "-0.35 | \n", + "||
| ig-receptor-binding-2022-0 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| ig-receptor-binding-2022-1 | \n", + "0.14 | \n", + "0.11 | \n", + "0.03 | \n", + "||
| meiosis I-0 | \n", + "0.25 | \n", + "0.67 | \n", + "-0.42 | \n", + "||
| meiosis I-1 | \n", + "0.71 | \n", + "0.73 | \n", + "-0.01 | \n", + "||
| molecular sequestering-0 | \n", + "0.17 | \n", + "0.17 | \n", + "0.00 | \n", + "||
| molecular sequestering-1 | \n", + "0.33 | \n", + "0.14 | \n", + "0.19 | \n", + "||
| mtorc1-0 | \n", + "0.20 | \n", + "0.12 | \n", + "0.08 | \n", + "||
| mtorc1-1 | \n", + "1.00 | \n", + "0.22 | \n", + "0.78 | \n", + "||
| peroxisome-0 | \n", + "0.83 | \n", + "0.67 | \n", + "0.17 | \n", + "||
| peroxisome-1 | \n", + "0.43 | \n", + "0.14 | \n", + "0.29 | \n", + "||
| progeria-0 | \n", + "0.00 | \n", + "0.07 | \n", + "-0.07 | \n", + "||
| progeria-1 | \n", + "0.00 | \n", + "0.00 | \n", + "0.00 | \n", + "||
| regulation of presynaptic membrane potential-0 | \n", + "0.56 | \n", + "0.90 | \n", + "-0.34 | \n", + "||
| regulation of presynaptic membrane potential-1 | \n", + "1.00 | \n", + "0.60 | \n", + "0.40 | \n", + "||
| sensory ataxia-0 | \n", + "0.00 | \n", + "0.04 | \n", + "-0.04 | \n", + "||
| sensory ataxia-1 | \n", + "NaN | \n", + "0.11 | \n", + "NaN | \n", + "||
| term-GO:0007212-0 | \n", + "0.20 | \n", + "0.14 | \n", + "0.06 | \n", + "||
| term-GO:0007212-1 | \n", + "0.43 | \n", + "0.22 | \n", + "0.21 | \n", + "||
| tf-downreg-colorectal-0 | \n", + "0.57 | \n", + "0.33 | \n", + "0.24 | \n", + "||
| tf-downreg-colorectal-1 | \n", + "0.80 | \n", + "0.50 | \n", + "0.30 | \n", + "
| \n", + " | \n", + " | prompt_variant | \n", + "v1 | \n", + "v2 | \n", + "
|---|---|---|---|---|
| model | \n", + "method | \n", + "geneset | \n", + "\n", + " | \n", + " |
| gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "EDS-0 | \n", + "[[GO:0032964, GO:0030198, GO:0010712, GO:0043687, GO:0006493, GO:0006508, GO:0008270]] | \n", + "[[GO:0032964, matrix maturation, GO:0031012, MESH:D006023, MESH:D015238, zinc finger proteins, proteolytic subunits, MESH:D057057, MESH:M0465019]] | \n", + "
| EDS-1 | \n", + "[[GO:0032964, GO:0061448, GO:0030198, GO:0030166]] | \n", + "[[GO:0032964, GO:0030198, GO:0006457, GO:0006955]] | \n", + "||
| FA-0 | \n", + "[[GO:0006281, GO:0035825, GO:0006302, chromosome stability \\n\\nhypotheses: the enriched terms suggest that the common function of these genes is dna repair, specifically in the context of homologous recombination and double-strand break repair. the genes are part of a complex network involved in maintaining chromosome stability, which is critical for preventing mutations and malignant transformation. mutations in these genes have been linked to various forms of cancer and the fanconi anemia disorder. understanding the mechanisms by which these genes function in dna repair could provide insights into cancer development and potential therapeutic targets]] | \n", + "[[GO:0006281, GO:0035825, fanconi anemia pathway]] | \n", + "||
| FA-1 | \n", + "[[GO:0006281, fanconi anemia pathway, GO:0035825, MESH:M0443452, genome maintenance, GO:0006302]] | \n", + "[[GO:0006281, GO:0035825, MESH:D051856, rad51 family proteins, chromosome stability maintenance\\n\\nmechanism: these genes are involved in dna damage repair and maintenance of genome stability, particularly through homologous recombination and the formation of the fanconi anemia complementation group proteins. the rad51 family proteins and chromosomal stability maintenance are also important in these processes]] | \n", + "||
| HALLMARK_ADIPOGENESIS-0 | \n", + "[[GO:0005739, GO:0006119, GO:0022900, GO:0006091, MESH:M0496924, GO:0006631, GO:0006099, GO:0006635]] | \n", + "[[mitochondrial function, GO:0008152, GO:0006118, GO:0006631, redox reactions]] | \n", + "||
| HALLMARK_ADIPOGENESIS-1 | \n", + "[[mitochondrial function, GO:0070469, energy production, GO:0006629, GO:0006869, GO:0005515, GO:0016049, GO:0051301, antioxidant enzyme. \\n\\nmechanism/]] | \n", + "[[mitochondrial function; energy metabolism; lipid metabolism; electron transport chain. \\n\\nmechanism: these genes likely contribute to the production and regulation of energy in the form of atp through processes including beta-oxidation of lipids, GO:0006119, and electron transport chain activity. dysfunction or dysregulation of these genes may lead to mitochondrial dysfunction and impaired energy metabolism, which have been implicated in various diseases including neurodegenerative disorders, MONDO:0004995, MONDO:0005066]] | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[[chemokine signaling pathway, cytokine-cytokine receptor interaction, GO:0006955, GO:0042110, GO:0050776, GO:0006954, GO:0050900]] | \n", + "[[GO:0005125, GO:0042110, GO:0042379, GO:0002429, GO:0032623, GO:0032609, GO:0002504, GO:0050776, GO:0030217, GO:0050900, GO:0060333, GO:0001819, GO:0002685, GO:0070098, GO:0050852]] | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[[MESH:D018925, MESH:D016207, t cell-mediated immunity, interferon signaling, GO:0006954, tgf-beta signaling, toll-like receptor signaling, tnf signaling]] | \n", + "[[GO:0008009, cytokine signaling, GO:0019882]] | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[[protein kinase activity; membrane transport; enzyme catalysis\\n\\nmechanism: these genes are involved in signal transduction and cellular metabolism, with a focus on protein kinase activity, GO:0055085, and enzyme catalysis. they play roles in the transport of various molecules across biological membranes, including fatty acids, sugars, and ions. they are also important in regulating cellular responses to extracellular stimuli, such as growth factors, MESH:D006728, and cytokines. additionally, they catalyze metabolic reactions and contribute to various metabolic pathways]] | \n", + "[[GO:0004672, GO:0031344, GO:0008285, GO:0010468, regulation of cellular protein localization and movement]] | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[[GO:0004672, GO:0008134, GO:0005515, GO:0007165, GO:0003824]] | \n", + "[[GO:0004672, GO:0008134, GO:0006810, enzymatic activity, GO:0006511, GO:0061024, GO:0042445, GO:0016567]] | \n", + "||
| HALLMARK_ANGIOGENESIS-0 | \n", + "[[GO:0031012, GO:0007155, tissue development and regeneration, growth factor signaling, endothelial-specific signaling, cytokine signaling]] | \n", + "[[GO:0030198, GO:0007155, GO:0030199, GO:0006029, GO:0045765, GO:0009611]] | \n", + "||
| HALLMARK_ANGIOGENESIS-1 | \n", + "[[ecm organization, GO:0031589, GO:0016477]] | \n", + "[[GO:0030198, GO:0007155, GO:0007088, protein kinase activity regulation, GO:0070848, cellular response to transforming growth factor beta stimulus\\n\\nmechanism: the genes listed are involved in the organization of the extracellular matrix and cell adhesion. specifically, they play roles in binding to and regulating the spacing of collagen fibrils, inhibiting proteases, promoting cell-cell and cell-matrix interactions, and regulating mitosis and protein kinase activity. growth factors and transforming growth factor beta are also involved in signal transduction pathways that are regulated by these genes]] | \n", + "||
| HALLMARK_APICAL_JUNCTION-0 | \n", + "[[GO:0005884, GO:0007155, GO:0007010, GO:0008360, GO:0007165]] | \n", + "[[GO:0007155, GO:0007010, GO:0005925, GO:0070160]] | \n", + "||
| HALLMARK_APICAL_JUNCTION-1 | \n", + "[[GO:0070160, GO:0031012, GO:0005604, GO:0007155, adhesion junction, GO:0007160]] | \n", + "[[GO:0070160, GO:0007155, GO:0008014, integrin, GO:0007165, adhesion g-protein coupled receptor (gpcr), GO:0015629, UBERON:4000022, protein tyrosine kinase (ptk), GO:0016303, map kinase, MESH:D016212]] | \n", + "||
| HALLMARK_APICAL_SURFACE-0 | \n", + "[[GO:0007155, GO:0007165, GO:0061024, GO:0015031]] | \n", + "[[GO:0007166, GO:0007169, GO:1901796, GO:0019048, GO:0045785, GO:0043408, GO:2000145, GO:0032956, GO:0051897, GO:0048015, GO:0010810, GO:0030334, regulation of cell growth\\n\\nmechanism and hypotheses: the enriched terms suggest a common mechanism involving transmembrane signaling pathways, with a focus on cell adhesion, migration, and growth regulation. several of the genes are involved in the regulation of the mapk signaling pathway, which is known to play a central role in cellular processes such as proliferation, differentiation, and apoptosis. pathway analysis of these genes may further elucidate the specific regulatory mechanisms at play]] | \n", + "||
| HALLMARK_APICAL_SURFACE-1 | \n", + "[[GO:0007155, GO:0007165, GO:0007154]] | \n", + "[[GO:0007160, GO:0006811, GO:0007165, GO:0098631, insulin regulation, GO:0016485]] | \n", + "||
| HALLMARK_APOPTOSIS-0 | \n", + "[[GO:0006915, GO:0008219, GO:0043067, GO:0097153, binding of proteins involved in cell death.\\n\\nmechanism: the majority of the genes on the list are involved in apoptotic processes or regulate cell death. many of these genes belong to the bcl-2 protein family, which regulate apoptosis by either inhibiting or promoting cell death. other gene products, such as the caspases, also play a crucial role in the apoptotic process by cleaving proteins involved in cell death, ultimately leading to cell death. the enrichment of this theme in the gene list suggests that the regulation of apoptosis and programmed cell death is a significant biological mechanism that the genes in the list are involved in]] | \n", + "[[GO:0006915, GO:0008219, GO:0007165]] | \n", + "||
| HALLMARK_APOPTOSIS-1 | \n", + "[[apoptosis regulation, cytokine signaling, growth factor regulation]] | \n", + "[[GO:0097153, GO:0042981, positive regulation of dna fragmentation, GO:0043067, GO:0010941, GO:1901796, GO:0006974, GO:0070613]] | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[[GO:0140359, long-chain fatty-acid metabolism, GO:0008203, GO:0006629, GO:0006637]] | \n", + "[[GO:0006869, GO:0008203, GO:0006631, peroxisomal biogenesis, GO:0004448, GO:0008146]] | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[[peroxisome biogenesis, GO:0006631, GO:0006699, GO:0008203, GO:0140359, GO:0016491, atp-binding cassette, GO:0005490]] | \n", + "[[GO:0007031, GO:0001676, GO:0006699, GO:0008202, GO:0008203, GO:0001523, GO:0006635, alpha-oxidation, GO:0006720, lipid metabolic process \\n\\nmechanism: these genes function in a variety of processes involved in lipid metabolism and peroxisome biogenesis. peroxisomes are intracellular organelles involved in many metabolic pathways, including fatty acid beta-oxidation, which our enriched terms suggest is a common theme among these genes. additionally, these genes are involved in the synthesis of bile acids, steroid hormones, and retinoids, highlighting the importance of lipid metabolism in cellular function]] | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[[GO:0006695, GO:0006633, GO:0006629, regulation of cholesterol levels, transport across cell membranes]] | \n", + "[[GO:0006629, GO:0006869, GO:0008610]] | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[[GO:0006695, GO:0006629, GO:0007165]] | \n", + "[[GO:0006695, GO:0006644, GO:0006633, GO:0016125]] | \n", + "||
| HALLMARK_COAGULATION-0 | \n", + "[[GO:0006956, GO:0007596, GO:0006508, GO:0030198]] | \n", + "[[GO:0007596, extracellular matrix remodeling, GO:0030449]] | \n", + "||
| HALLMARK_COAGULATION-1 | \n", + "[[blood coagulation cascade; complement activation, classical pathway; extracellular matrix disassembly; calcium ion binding. \\n\\nmechanism: these genes are involved in the regulation and activation of different pathways implicated in blood coagulation, GO:0006956, and extracellular matrix remodelling. blood coagulation involves the conversion of prothrombin to thrombin by coagulation factors, which leads to the formation of a fibrin clot. complement activation is a cascade resulting in the removal of damaged cells and pathogens. extracellular matrix disassembly and remodelling are implicated in cellular processes such as tissue repair, GO:0001525, metastasis. calcium-binding proteins play a vital role in signalling pathways regulation of enzymatic activities]] | \n", + "[[extracellular matrix breakdown, GO:0007596, protein inhibition]] | \n", + "||
| HALLMARK_COMPLEMENT-0 | \n", + "[[GO:0006956, GO:0006955, GO:0030162, GO:0030168]] | \n", + "[[GO:0008233, GO:0007596, GO:0006956]] | \n", + "||
| HALLMARK_COMPLEMENT-1 | \n", + "[[GO:0006956, GO:0007596, cytokine signaling, GO:0006468, GO:0006955, GO:0006954]] | \n", + "[[GO:0006956, GO:0007596, GO:0006955, GO:0030168, cytokine signaling, GO:0002685, response to virus.\\n\\nmechanism: these genes are involved in regulating different aspects of immune response, including complement activation, platelet activation, cytokine signaling, and leukocyte migration. they are also involved in blood coagulation, which can be activated during an immune response to prevent pathogen spread. the over-representation of these genes suggests that immune activation and regulation are key to the identified biological process]] | \n", + "||
| HALLMARK_DNA_REPAIR-0 | \n", + "[[GO:0006281, transcription initiation, GO:0006396, GO:0009117]] | \n", + "[[GO:0006281, transcription initiation, GO:0009117]] | \n", + "||
| HALLMARK_DNA_REPAIR-1 | \n", + "[[GO:0006270, GO:0006261, GO:0006297, transcription, dna-template-dependent, GO:0045893, GO:0000122, GO:0006281, GO:0000723, GO:0065004]] | \n", + "[[GO:0006281, transcription regulation]] | \n", + "||
| HALLMARK_E2F_TARGETS-0 | \n", + "[[GO:0006260, GO:0006281, GO:0051726]] | \n", + "[[GO:0006260, GO:0006281, GO:0051276]] | \n", + "||
| HALLMARK_E2F_TARGETS-1 | \n", + "[[GO:0006260, GO:0006281, dna polymerase, GO:0009117, GO:0006298, chromatin structure\\n\\nmechanism: the genes on this list primarily function in dna replication and repair. many of them are involved in dna polymerase activity, nucleotide metabolism, mismatch repair, and chromatin structure. it is likely that these genes work together in a coordinated manner to ensure accurate dna replication and repair, and that defects in these processes can lead to genetic instability and cancer development]] | \n", + "[[GO:0006260, GO:0006281, cell-cycle checkpoint regulation]] | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[[GO:0030198, GO:0030199, GO:0048251, GO:0071711, regulation of protein localization to extracellular matrix, GO:0043236, GO:0001968, GO:0005518]] | \n", + "[[GO:0030198, GO:0007155, GO:0005518, actin binding activity, GO:0007229, GO:0001501, GO:0005201, GO:0006936, GO:0005604, GO:0031012, GO:0008009, GO:0008083, GO:0016860, GO:0006508, GO:0005125]] | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[[GO:0030198, GO:0005518, GO:0051015, GO:0005125, GO:0007155, GO:0016477]] | \n", + "[[GO:0030198, GO:0006936, GO:0007155]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[[membrane-bound proteins, MESH:D004798, GO:0000981]] | \n", + "[[MESH:D002352, MESH:D004798, MESH:D008565, GO:0000981, receptors, MESH:D003598]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[[GO:0055085, cell signaling, GO:0004672, GO:1904659, GO:0006811]] | \n", + "[[GO:0006631, GO:0006811, GO:0010468]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[[membrane-associated protein complex, GO:0019899, GO:0034220, transcriptional regulation]] | \n", + "[[GO:0005515, GO:0007165, GO:0019899, GO:0005737, GO:0043687, GO:0006355, GO:0006915, GO:0045860, positive regulation of cell proliferation.\\n\\nmechanism/]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[[GO:0005515, GO:0003824, GO:0008134, GO:0006355, GO:0007165, cytokine signaling pathway, regulation of cell growth and differentiation]] | \n", + "[[GO:0007165, GO:0004672, g-protein coupled receptor signaling pathway, GO:0055085, GO:0035556, GO:0004721, GO:0006468, zinc ion binding. \\n\\nhypotheses: the enriched terms suggest that the genes in this list are involved in regulatory mechanisms that help to control intracellular signaling cascades and protein expression through phosphorylation and dephosphorylation of proteins, and zinc ion binding. additionally, these genes may play a role in transmembrane transport and regulation of ion channels]] | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[[GO:0006629, mitochondrial function, GO:0003824, GO:0006631, oxidation-reduction process, metabolism of carboxylic acid, GO:0006118, GO:0006082]] | \n", + "[[GO:0006631, GO:0005975, amino acid metabolism, mitochondrial function, oxidative stress response]] | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[[GO:0006629, oxidation-reduction process, energy production, metabolism of fatty acids, mitochondrial function, GO:0045333]] | \n", + "[[GO:0006631, energy production, mitochondrial function, GO:0006629, oxidation-reduction process, GO:0006637, GO:0006099, MESH:D014451, GO:0019752, GO:0015936, GO:0006084, GO:0022900]] | \n", + "||
| HALLMARK_G2M_CHECKPOINT-0 | \n", + "[[GO:0051301, GO:0006260, GO:0007059, GO:0000910]] | \n", + "[[GO:0051726, GO:0006260, GO:0006281]] | \n", + "||
| HALLMARK_G2M_CHECKPOINT-1 | \n", + "[[GO:0006270, GO:0007059, GO:0000075, GO:0007052, GO:0007346, GO:0065004]] | \n", + "[[GO:0006260, GO:0051726, GO:0006281, GO:0007059, GO:0000910]] | \n", + "||
| HALLMARK_GLYCOLYSIS-0 | \n", + "[[GO:0070085, GO:0005975, fructose-bisphosphate metabolism, GO:0006098, GO:0006006, GO:0006012, GO:0006090, GO:0006089, GO:0019319, GO:0006011, GO:0052573, GO:0004332]] | \n", + "[[GO:0006096, GO:0005975]] | \n", + "||
| HALLMARK_GLYCOLYSIS-1 | \n", + "[[GO:0006096, GO:0005975, GO:0007165, GO:1904659, GO:0033554]] | \n", + "[[GO:0052574, GO:0006006, protein kinase binding activity, GO:0006090, GO:0006024, GO:0015012, GO:0006098, GO:0006096, rna polymerase iii transcription initiation, GO:0051287, GO:0022618, GO:0030199, GO:0008408, GO:0042803, atp-binding cassette transporter activity]] | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[[GO:0007411, GO:0007155, transcriptional regulation, cell communication. \\n\\nhypotheses: \\nthese genes may be involved in regulating the formation of neural circuits and maintaining neural plasticity through dynamic regulation of gene expression and protein signaling. the enriched terms suggest that the neural development process involves complex regulation of cell-cell communication and adhesion, as well as transcriptional control of gene expression. axon guidance is critical for the proper formation of neural circuits, and dysregulation of this process may lead to neural disorders]] | \n", + "[[neuronal development, GO:0007155, GO:0007165, GO:0016477, GO:0010977, GO:0001525, MESH:D018121, transcriptional regulation]] | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[[GO:0007411, GO:0007155, transcription regulation, neuro-endocrine signaling, protein cleavage, cell migration.\\n\\nmechanism: these genes are involved in various aspects of neuronal development and signaling, including axon guidance, neuron migration, cell adhesion and communication, transcription regulation, and protein cleavage. these processes are critical for proper central nervous system development and function]] | \n", + "[[GO:0007155, GO:0007411, neuronal proliferation and differentiation, GO:0007165, GO:0001525]] | \n", + "||
| HALLMARK_HEME_METABOLISM-0 | \n", + "[[GO:0006811, GO:0010468, protein turnover, GO:0061024]] | \n", + "[[GO:0006810, GO:0005488, MESH:D008565, MONDO:0018815, solute carrier (slc) family of transporters]] | \n", + "||
| HALLMARK_HEME_METABOLISM-1 | \n", + "[[GO:0005515, GO:0003824, GO:0008152, GO:0006082, GO:0006810, GO:0006811, GO:0006820, GO:0044281, GO:0019538, GO:0006357, GO:0003924, GO:0016740, GO:0000166, GO:0003677, GO:0000988, GO:0006163, GO:0008643, GO:0050801, GO:0003723, GO:0019899]] | \n", + "[[GO:1904659, GO:0003723, GO:0003677, GO:0000988, GO:0006811, GO:0019899, GO:0042826, GO:0140657, GO:0003824, GO:0008270]] | \n", + "||
| HALLMARK_HYPOXIA-0 | \n", + "[[GO:0006096, GO:0006006, GO:0006000, GO:0005975, MESH:D004734, GO:0045333, GO:0019318, GO:0019682, triose-phosphate metabolic process, GO:0006090, GO:0006754]] | \n", + "[[GO:0006096, GO:0006006, GO:0005515, transcription regulation]] | \n", + "||
| HALLMARK_HYPOXIA-1 | \n", + "[[GO:0006006, insulin signaling pathway, GO:0051726, transcriptional regulation]] | \n", + "[[GO:0006096, GO:0016310, GO:0006006, GO:0051726, GO:0007165, transcriptional regulation, heparan sulfate biosynthesis]] | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[[cytokine, receptor, t-cell, GO:0006955, GO:0065007]] | \n", + "[[cytokine signaling, GO:0042110, GO:0042113, GO:0007159, GO:0030593, GO:0050900]] | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[[GO:0004896, GO:0002224, GO:0002685, GO:0002521, GO:0002682, GO:0046649, GO:0019221, GO:0007159, GO:0051249, positive regulation of leukocyte proliferation\\n\\nmechanism: these genes are involved in the immune system response and regulation, specifically in the activation, differentiation, and migration of leukocytes. they are also involved in cytokine-mediated signaling pathways and toll-like receptor signaling pathways. the enriched terms suggest that these genes are involved in the regulation of various aspects of immune system processes, including leukocyte proliferation and adhesion]] | \n", + "[[GO:0004896, GO:0007166, GO:0045321, GO:0050900, GO:0006955, GO:0006954, GO:0002250, GO:0070663, GO:0002521, GO:0042110, GO:0042113, GO:0046649]] | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[[cytokine receptor activity; signal transduction; jak-stat cascade; cytokine-mediated signaling pathway\\n\\nmechanism: the enriched terms suggest that the commonality in gene function is the involvement of cytokine receptors and signaling pathways, particularly the jak-stat cascade, in cytokine-mediated signaling. this pathway is activated by cytokine binding to their respective receptors, leading to activation of the jak family of tyrosine kinases, which then phosphorylate and activate stat transcription factors to induce gene expression changes and cellular responses. the presence of these genes in the list suggests a potential role in regulating immune responses and inflammation through cytokine signaling]] | \n", + "[[GO:0004896, GO:0050778, GO:0007155, GO:0019221, GO:0002687]] | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[[GO:0005126, GO:0002376, GO:0001817, GO:0050776, cytokine-mediated signaling pathway\\n\\nmechanism]] | \n", + "[[GO:0004896, GO:0019221, GO:0050776, GO:0050900, apoptosis regulation, GO:0006954, antimicrobial response]] | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[[cytokine signaling, GO:0004950, GO:0004930, GO:0050900, GO:0004908, GO:0002224, GO:0005164]] | \n", + "[[GO:0005125, GO:0008009, GO:0004930, GO:0050900, inflammation\\n\\nmechanism]] | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[[GO:0004896, GO:0004930, GO:0042379, GO:0006955, GO:0006954, GO:0019221, GO:0050900, GO:0002694, GO:0002682, GO:0001819, GO:0009617, GO:0032496, GO:0070555, GO:0034612, GO:0042110]] | \n", + "[[GO:0004896, GO:0004930, GO:0004950, GO:0004888, GO:0004896]] | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[[interferon-induced protein, GO:0051607, GO:0006955, nucleotide-binding domain, leucine-rich repeat-containing receptor signaling, GO:0005764, GO:0019882, cytokine]] | \n", + "[[interferon response, GO:0051607, GO:0006955]] | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[[GO:0140888, cytokine signaling pathway, GO:0045087, GO:0009615, GO:0006952]] | \n", + "[[GO:0140888, GO:0045087, GO:0051607, cytokine signaling, GO:0019882, ubiquitin-mediated proteolysis\\n\\nmechanism: these genes are involved in the innate immune response and antiviral activity, particularly in the interferon signaling pathway. they encode proteins that regulate cytokine signaling, antigen processing and presentation, and ubiquitin-mediated proteolysis. the functions of these genes suggest a coordinated response to viral infection, with the interferon signaling pathway acting as a central mediator of the antiviral response]] | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[[interferon signaling, immune response regulation, cytokine signaling, tnf-receptor superfamily, protein tyrosine phosphatase, ubiquitin-proteasome system, MONDO:0007435]] | \n", + "[[GO:0006955, GO:0019221, chemokine signaling pathway, GO:0019882]] | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[[GO:0006955, cytokine signaling, GO:0030163, GO:0000502, ubiquitin system, viral rna sensing, MESH:D018925, GO:0019882]] | \n", + "[[GO:0045087, GO:0051607, GO:0005125, GO:0009615, GO:0001817, GO:0051607, GO:0032481, type i interferon signaling pathway. \\n\\nmechanism/]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[[GO:0005509, GO:0055085, GO:0007155, GO:0004672, GO:0007186]] | \n", + "[[GO:0005509, GO:0005245, GO:0006811, GO:0015085, GO:0005388, GO:0019722, GO:0055074, GO:0048306]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[[cytokine signaling, g-protein coupled receptor signaling, GO:0019722, protein metabolism and processing]] | \n", + "[[GO:0005509, GO:0042981, GO:0055085, GO:0006811, GO:0006468]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[[receptor signaling pathway, GO:0006468, negative regulation of transcription, GO:0031396, GO:0071345, GO:0032880, GO:0070374]] | \n", + "[[GO:0044425, GO:0007165, GO:0003824]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[[signal transduction; cytokine activity; coagulation; ion transport; extracellular matrix organization. \\n\\nmechanism: the enriched terms suggest that the commonality in the function of these genes is related to signal transduction and regulation of various biological processes, such as coagulation, GO:0005125, GO:0030198, and ion transport. specifically, these genes are involved in regulating signaling pathways that are critical for these biological processes. there are several pathways known to contribute to these enriched terms, including the jak/stat, MESH:D016328, mapk/erk, and pi3k pathways. these pathways play important roles in cell signaling, GO:0006954, GO:0006955, other cellular processes]] | \n", + "[[cytokine signaling, growth factor signaling, coagulation and complement activation, enzymatic activity regulation]] | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[[GO:0008017, GO:0007010, regulation of protein activity, GO:0051301, GO:0019894, GO:0003779]] | \n", + "[[microtubule organization, GO:0007098, GO:0030036, GO:0051726, GO:0071539]] | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[[microtubule organization, GO:0140014, GO:0051301]] | \n", + "[[GO:0008017, GO:0008574, GO:0007098, GO:0051225, GO:0003774, GO:0007010]] | \n", + "||
| HALLMARK_MTORC1_SIGNALING-0 | \n", + "[[GO:0046034, GO:0006629, GO:0006006, GO:0006457, GO:0046907]] | \n", + "[[GO:0006457, GO:0006006, microtubule organization and biogenesis, GO:0000502, GO:0043043, GO:0042254]] | \n", + "||
| HALLMARK_MTORC1_SIGNALING-1 | \n", + "[[GO:0051087, GO:0005515, GO:0006457, GO:0043161]] | \n", + "[[GO:0008152, GO:0009117, GO:0006629, GO:0005975, GO:0006457, GO:0030163, GO:0010468, GO:0000988, GO:0003682]] | \n", + "||
| HALLMARK_MYC_TARGETS_V1-0 | \n", + "[[GO:0006413, GO:0042254, GO:0006260, GO:0006281, GO:0008380, GO:0009117]] | \n", + "[[GO:0042254, GO:0000394, GO:0006412, GO:0006412, GO:0006457, chaperonin-mediated protein folding]] | \n", + "||
| HALLMARK_MYC_TARGETS_V1-1 | \n", + "[[GO:0006413, GO:0006412, GO:0042254]] | \n", + "[[GO:0042254, GO:0006413, GO:0006414, GO:0006397]] | \n", + "||
| HALLMARK_MYC_TARGETS_V2-0 | \n", + "[[GO:0006396, GO:0042254, rrna maturation]] | \n", + "[[GO:0006364, ribosomal subunit biogenesis, GO:0003723, nucleolar function, GO:0006412]] | \n", + "||
| HALLMARK_MYC_TARGETS_V2-1 | \n", + "[[GO:0006364, nucleolar rna processing, GO:0042273, GO:0003723]] | \n", + "[[GO:0006364, GO:0005730, GO:0003723, ribosomal biogenesis, GO:0051726]] | \n", + "||
| HALLMARK_MYOGENESIS-0 | \n", + "[[GO:0003779, GO:0006936, sarcomere assembly, GO:0005509, GO:0005861, GO:0005523, MESH:D024510, GO:0005524, GO:0004672, GO:0005515, GO:0032982]] | \n", + "[[GO:0006936, muscle metabolism, GO:0007010]] | \n", + "||
| HALLMARK_MYOGENESIS-1 | \n", + "[[GO:0006936, GO:0005861, GO:0005509, GO:0003779, sarcomere organization and biogenesis]] | \n", + "[[GO:0005861, MESH:M0013780, MESH:D018995, GO:0006936, GO:0005509, sarcomere assembly, MESH:D024510]] | \n", + "||
| HALLMARK_NOTCH_SIGNALING-0 | \n", + "[[GO:0007219, GO:0016567, GO:0001709, GO:0016055]] | \n", + "[[GO:0007219, basic helix-loop-helix transcription factor activity, GO:0016567, GO:0016563, GO:0005102, GO:0097153, GO:0006468]] | \n", + "||
| HALLMARK_NOTCH_SIGNALING-1 | \n", + "[[GO:0007219, GO:0016567]] | \n", + "[[GO:0007219, GO:0016567, transcriptional regulation, GO:0001709]] | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[[GO:0006754, GO:0022900, GO:0005746, GO:0006119]] | \n", + "[[GO:0005739, GO:0006119, GO:0022900, MESH:D004734, GO:0031966, MESH:D024101]] | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[[GO:0005746, GO:0006119, mitochondrial metabolism, complex i-v, energy production]] | \n", + "[[GO:0005746, GO:0006754, GO:0022900, GO:0006119]] | \n", + "||
| HALLMARK_P53_PATHWAY-0 | \n", + "[[GO:0006281, GO:0010468, GO:0008083]] | \n", + "[[cyclin family, GO:0006281, GO:0008083, GO:0004672, GO:0000988, zinc finger protein]] | \n", + "||
| HALLMARK_P53_PATHWAY-1 | \n", + "[[GO:0006281, GO:0051726, GO:0007165, GO:0006915, MESH:D016207]] | \n", + "[[GO:0008083, transcriptional regulation, GO:0006915, GO:0006281]] | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[[GO:0006006, insulin signaling, pancreatic development, neuroendocrine regulation]] | \n", + "[[GO:0006006, insulin regulation, GO:0031016, GO:0006096, GO:0006094, GO:0030073, hormone regulation]] | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[[GO:0006006, pancreatic islet development, neuroendocrine differentiation, GO:0007269, MESH:D009473]] | \n", + "[[GO:0006006, GO:0030073, pancreatic islet development, neuroendocrine differentiation]] | \n", + "||
| HALLMARK_PEROXISOME-0 | \n", + "[[atp binding cassette transporter activity, GO:0006631, GO:0042445, GO:0008289, GO:0043574, GO:0005502]] | \n", + "[[GO:0140359, GO:0055085, atp-binding cassette, GO:0043574, GO:0006631, GO:0006839]] | \n", + "||
| HALLMARK_PEROXISOME-1 | \n", + "[[GO:0005777, GO:0006635, antioxidant response, mitochondrial carrier protein]] | \n", + "[[GO:0005777, GO:0006631, beta-oxidation, MESH:D018384, antioxidant defense mechanism, coenzyme a ligase, aldehyde dehydrogenase family, MESH:D009195]] | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[[GO:0004672, GO:0035556, GO:1902531, GO:0050794, GO:0003824, cytoskeletal regulation]] | \n", + "[[GO:0004672, intracellular signaling, GO:0050794]] | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[[GO:0004672, GO:0007165, GO:0006468, GO:0035556]] | \n", + "[[GO:0016301, GO:0006468, GO:0007165]] | \n", + "||
| HALLMARK_PROTEIN_SECRETION-0 | \n", + "[[GO:0005794, GO:0005480, GO:0005764]] | \n", + "[[GO:0005794, membrane trafficking, GO:0016192, GO:0015031, GO:0006906, GO:0035493, GO:0005793]] | \n", + "||
| HALLMARK_PROTEIN_SECRETION-1 | \n", + "[[golgi transport, GO:0016192, GO:0015031, GO:0008104, GO:0032880, GO:0006886, GO:0016197]] | \n", + "[[GO:0007030, GO:0006888, GO:0016192, GO:0007040, sorting nexin-containing complex, GO:0030665, GO:0032880]] | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[[GO:0016209, GO:0006749, GO:0016491]] | \n", + "[[antioxidant activity; redox regulation; catalytic activity, UBERON:0035930, such as water and oxygen. the over-representation of terms related to antioxidant activity, redox regulation, and responding to oxidative stress suggest that these genes are involved in maintaining the balance between oxidants and antioxidants in the body, help protect against oxidative damage]] | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[[GO:0016209, redox regulation, MESH:D018384]] | \n", + "[[oxidative stress response, antioxidant defense, regulation of reactive oxygen species, GO:0006749, superoxide anion radical metabolism, peroxiredoxin-mediated detoxification]] | \n", + "||
| HALLMARK_SPERMATOGENESIS-0 | \n", + "[[GO:0051726, GO:0003677, GO:0003723, GO:0016301, transcription regulation, chromatin organization and modification]] | \n", + "[[GO:0008584, GO:0007283, GO:0097722, GO:0007340, GO:0048232, testicular germ cell proliferation\\n\\nmechanism and]] | \n", + "||
| HALLMARK_SPERMATOGENESIS-1 | \n", + "[[GO:0005515, enzymatic activity, GO:0006811]] | \n", + "[[GO:0006811, GO:0006468, MESH:D054875, GO:0007283, receptor signaling]] | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[[growth factor signaling, transcriptional regulation, smad/tgf-beta signaling pathway, cellular differentiation]] | \n", + "[[tgf-beta signaling pathway, transcriptional regulation, GO:0007165, cell growth and differentiation]] | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[[GO:0005024, GO:0060395, GO:0030509]] | \n", + "[[tgf-beta signaling pathway, GO:0030509, GO:0071141, GO:0004674, GO:0008134, GO:0006468, GO:0030154, GO:0060348, GO:0042981, GO:0034436]] | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[[GO:0006955, cytokine signaling pathway, transcription regulation. \\n\\nmechanism: these genes are primarily involved in regulating the immune response through the cytokine signaling pathway. they also play a role in transcriptional regulation of genes involved in these pathways. overall, these genes are important in regulating the response to pathogens and maintaining immune homeostasis]] | \n", + "[[GO:0004950, GO:0005125, GO:0006955, GO:0006954, GO:0050900, GO:0007165]] | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[[cytokine signaling pathway, GO:0002682, GO:0006351, GO:0006355, GO:0050900, GO:0006954, GO:0050727, GO:0032496, GO:0002237, GO:0009615, GO:0045893, GO:0045892]] | \n", + "[[interleukin signaling, GO:0032602, GO:0006955]] | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[[GO:0044183, GO:0006457, GO:0006396, cellular stress response, GO:0006401]] | \n", + "[[endoplasmic reticulum stress response, GO:0006457, GO:0008380, GO:0006402, mrna localization, translation regulation, stress response]] | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[[GO:0006457, GO:0006396, GO:0006413, endoplasmic reticulum stress response, GO:0042254]] | \n", + "[[GO:0006457, GO:0061077, GO:0015031, GO:0006413, GO:0003723, MESH:D020365, GO:0042254, aminoacyl-trna synthesis, GO:0005783, MESH:D005786]] | \n", + "||
| HALLMARK_UV_RESPONSE_DN-0 | \n", + "[[GO:0006816, cytoskeletal organization, cell signaling, protein regulation]] | \n", + "[[GO:0030198, GO:0007155, GO:0006811, GO:0004672, transcription regulation, receptor signaling pathway]] | \n", + "||
| HALLMARK_UV_RESPONSE_DN-1 | \n", + "[[GO:0030198, GO:0007165, GO:0006811]] | \n", + "[[GO:0030198, GO:0030155, GO:0006468, positive regulation of cellular signaling pathway activity, GO:0022604, GO:0072659]] | \n", + "||
| HALLMARK_UV_RESPONSE_UP-0 | \n", + "[[GO:0006810, GO:0003824, regulation of transcription, GO:0016310, GO:0005515, GO:0006950, GO:0006915, GO:0006811, GO:0005524, GO:0007165, GO:0005975]] | \n", + "[[GO:0006810, GO:0008152, GO:0003824]] | \n", + "||
| HALLMARK_UV_RESPONSE_UP-1 | \n", + "[[GO:0008152, GO:0005515, GO:0007165, GO:0009165, GO:0006468, transcription factor activity\\n\\nmechanism: these enriched terms suggest that the commonality between these genes is their involvement in fundamental biological processes required for normal cell function. these include metabolism, signal transduction, and protein biosynthesis and regulation. the transcription factor activity term suggests that some of these genes may be transcriptional regulators, controlling the expression of other genes involved in these processes. overall, these genes likely work together to maintain cellular homeostasis and respond to internal and external cues]] | \n", + "[[GO:0003723, GO:0003677, GO:0000166, GO:0006396, GO:0006260]] | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[[wnt signaling pathway regulation, transcriptional regulation, GO:0051726]] | \n", + "[[GO:0016055, transcriptional regulation, cell cycle progression]] | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[[GO:0016055, GO:0008013, transcription regulation]] | \n", + "[[GO:0016055, GO:0051726, transcriptional regulation]] | \n", + "||
| T cell proliferation-0 | \n", + "[[GO:0006955, GO:0007165, GO:0001816, cell proliferation and differentiation, GO:0042981]] | \n", + "[[cytokine, MESH:D007378, MESH:D011948, GO:0005530, GO:0008180, GO:0000502, protein tyrosine phosphatase, MESH:D010770, GO:0000981]] | \n", + "||
| T cell proliferation-1 | \n", + "[[cytokine, GO:0006955, GO:0023052, receptor, t cell]] | \n", + "[[cytokine signaling, tnf-receptor superfamily, GO:0006955, GO:0007165, GO:0019882, cell proliferation and survival, protein phosphorylation and kinase activity]] | \n", + "||
| Yamanaka-TFs-0 | \n", + "[[MESH:D047108, stem cell pluripotency, MESH:D063646, cell cycle progression]] | \n", + "[[MESH:D047108, GO:0001709, cell cycle progression]] | \n", + "||
| Yamanaka-TFs-1 | \n", + "[[MESH:D047108, stem cell maintenance, GO:0010468]] | \n", + "[[MESH:D047108, GO:0048863, pluripotent stem cell, transcription factor regulation, homeobox protein]] | \n", + "||
| amigo-example-0 | \n", + "[[GO:0030198, GO:0007155, GO:0007229, GO:0051495, GO:0002576]] | \n", + "[[GO:0031012, GO:0007155, MESH:D011509, GO:0005202, integrin]] | \n", + "||
| amigo-example-1 | \n", + "[[GO:0030198, GO:0007155, GO:0006029, GO:0042339, GO:0007229, GO:0030168]] | \n", + "[[GO:0030198, GO:0007155, GO:0016477, GO:0009888, GO:0042246, signaling pathway regulation, GO:0030168]] | \n", + "||
| bicluster_RNAseqDB_0-0 | \n", + "[[GO:0055085, GO:0006811, GO:0005524, zinc finger domain binding, GO:0007186, GO:0000988]] | \n", + "[[GO:0006351, GO:0005515, MESH:D016335, GO:0005509, MESH:D008565]] | \n", + "||
| bicluster_RNAseqDB_0-1 | \n", + "[[GO:0019722, GO:0000988, GO:0055085]] | \n", + "[[calcium binding, receptor protein activity, GO:0000988, GO:0005515]] | \n", + "||
| bicluster_RNAseqDB_1002-0 | \n", + "[[GO:0006936, GO:0007015, GO:0032972, GO:0005509, GO:0005861, GO:0005865, GO:0003779, GO:0045214, GO:0005523, GO:0017022, GO:0045932, skeletal muscle thin filament, cardiac muscle thin filament]] | \n", + "[[GO:0006936, GO:0005509, GO:0043269, GO:0032516, GO:0051015]] | \n", + "||
| bicluster_RNAseqDB_1002-1 | \n", + "[[GO:0006936, GO:0051015, GO:0005523, calcium binding, myofibril assembly.\\n\\nmechanism: these genes are involved in the regulation and maintenance of muscle structure and the contraction cycle. they act through the interaction of actin and myosin filaments, with the regulation of calcium ions controlling muscle contraction. the proteins encoded by these genes are involved in ion channel regulation, protein binding and modification, and energy metabolism]] | \n", + "[[GO:0006936, GO:0005509, GO:0051015, GO:0043462, GO:0097009, GO:0006811]] | \n", + "||
| endocytosis-0 | \n", + "[[GO:0006897, intracellular trafficking, cytoskeleton reorganization]] | \n", + "[[GO:0006897, GO:0007010, GO:0007165, GO:0006629, GO:0060348, brain development. \\n\\nhypotheses: these genes may be involved in common pathways related to endocytic vesicle trafficking, cytoskeletal organization, and signal transduction. some of the genes are associated with lipid metabolism and bone and brain development, suggesting their potential roles in cellular processes related to these functions]] | \n", + "||
| endocytosis-1 | \n", + "[[GO:0006897, GO:0016192, intracellular signaling, GO:0015031, cytoskeletal organization]] | \n", + "[[GO:0006897, intracellular trafficking, cytoskeletal reorganization]] | \n", + "||
| glycolysis-gocam-0 | \n", + "[[glucose metabolism; glycolysis\\n\\nmechanism: these genes play a role in converting glucose to produce energy in the form of atp. hexokinase (hk1) and glucose phosphate isomerase (gpi) are involved in the initial steps of glucose metabolism, while phosphofructokinase (pfkm), MESH:D005634, and pyruvate kinase (pkm) are involved in glycolysis. triosephosphate isomerase (tpi1) and glyceraldehyde-3-phosphate dehydrogenase (gapdh) are also involved in glycolysis and produce atp by oxidizing glucose. phosphoglycerate mutase (pgam2) and enolase (eno3) are also involved in glycolysis and help convert glucose to pyruvate, which can then be converted to atp]] | \n", + "[[GO:0006096, GO:0006006, MESH:D004734]] | \n", + "||
| glycolysis-gocam-1 | \n", + "[[GO:0006096, GO:0005975, energy pathway]] | \n", + "[[GO:0006096, GO:0006006, GO:0004743, GO:0019682, GO:0006000, phosphoenolpyruvate metabolic process]] | \n", + "||
| go-postsynapse-calcium-transmembrane-0 | \n", + "[[GO:0006816, GO:0004970, n-methyl-d-aspartate receptor complex, GO:0043269, GO:0014069, GO:0007165]] | \n", + "[[GO:0006816, intracellular calcium homeostasis, ionotropic glutamate receptor regulation, nmda receptor subunits, sodium/calcium exchanger proteins, trp ion channel family]] | \n", + "||
| go-postsynapse-calcium-transmembrane-1 | \n", + "[[GO:0006816, GO:0005509, GO:0005216, GO:0005102, GO:0007268, GO:0030594]] | \n", + "[[GO:0005509, GO:0005262, GO:0004970, calcium-mediated signaling pathway, GO:0007268, GO:0031175, GO:0005216]] | \n", + "||
| go-reg-autophagy-pkra-0 | \n", + "[[summary: regulation of cellular processes, including cell growth and metabolism, GO:0006915, GO:0006955, and regulation of chromatin remodeling and transcription.\\n\\nmechanism: these genes function in various pathways involved in the regulation of cellular processes. akt1 and pik3ca are involved in the pi3k/akt/mtor signaling pathway, which regulates cell growth, MESH:D013534, and metabolism. casp3 is a protease involved in the execution-phase of cell apoptosis. ccny and cdk5r1 are involved in the regulation of cell division cycles and the development of the central nervous system. hspb1 plays an important role in cell differentiation, but its overexpression may promote cancer cell proliferation and metastasis while protecting cancer cells from apoptosis. irgm regulates autophagy formation in response to intracellular pathogens. kat5 is a histone acetylase that has a role in dna repair and apoptosis and is thought to play an important role in signal transduction. mlst8, rptor, and smcr8 are involved in the torc1 signaling pathway, which regulates protein synthesis and cell growth in response to nutrient and insulin levels. nod2 is a pattern recognition receptor that detects cytosolic nucleic acids and trans]] | \n", + "[[MESH:D002470, GO:0016301, GO:0009966, GO:0001558, GO:0042981, GO:0010506, GO:0032006]] | \n", + "||
| go-reg-autophagy-pkra-1 | \n", + "[[GO:0038202, GO:0032006, GO:0010605, activation of map3k7/tak1]] | \n", + "[[GO:0016049, GO:0004672, GO:0006955, GO:0007165, GO:0000988, neuronal development, GO:0006468]] | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[[GO:0005764, glycoside hydrolase activity, GO:0005975, GO:0016787, GO:0006027, GO:0005980, GO:0006689, GO:0015929, acid hydrolase activity, chitin catabolic process\\n\\nmechanism: these genes participate in the lysosomal degradation of various carbohydrate molecules, breaking them down into their component parts for further processing by the cell]] | \n", + "[[glycosyl hydrolase activity, degradation of carbohydrates, GO:0006032, GO:0030211, GO:0003796, GO:0030214]] | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[[GO:0004559, GO:0004415, lysosomal enzyme activity, GO:0016798, GO:0006487]] | \n", + "[[GO:0016787, GO:0044248, GO:0006027, GO:0005764]] | \n", + "||
| ig-receptor-binding-2022-0 | \n", + "[[immunoglobulin receptor binding activity, GO:0002253, GO:0098542, GO:0002922, b cell-mediated immunity]] | \n", + "[[GO:0019731, GO:0098542, GO:0002253, immunoglobulin receptor binding activity]] | \n", + "||
| ig-receptor-binding-2022-1 | \n", + "[[GO:0002250, GO:0002376, antigen binding activity, immunoglobulin receptor binding activity. \\n\\nmechanism: the enriched terms suggest that these genes are involved in the recognition and response to specific foreign antigens encountered by the immune system. antigen binding activity enables the binding of specific antigens, while immunoglobulin receptor binding activity allows for the activation and signaling of immune cells. together, these genes contribute to the adaptive immune response and immune system processes by recognizing and responding to diverse foreign antigens]] | \n", + "[[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253]] | \n", + "||
| meiosis I-0 | \n", + "[[meiotic recombination; homologous recombination; chromosome segregation during meiosis; double-strand break repair via homologous recombination.\\n\\nmechanism: these genes are all involved in the meiotic cell cycle process, specifically in events related to recombination, repair, and segregation of chromosomes during meiosis. the proteins encoded by these genes interact with each other to form protein complexes that are essential for proper meiotic division. the enriched terms indicate a strong association with meiotic recombination and double-strand break repair via homologous recombination. additionally, they suggest a role in chromosome segregation during meiosis]] | \n", + "[[GO:0140013, GO:0035825, GO:0007059, GO:0006281, GO:0000795]] | \n", + "||
| meiosis I-1 | \n", + "[[meiotic recombination, GO:0006281, GO:0035825, GO:0007059, GO:0006302, holliday junction, rad51, GO:0007127]] | \n", + "[[meiotic recombination, GO:0006281, GO:0007059, GO:0035825, holliday junction resolution, double-strand dna binding, GO:0007276, GO:0007130]] | \n", + "||
| molecular sequestering-0 | \n", + "[[GO:0005515, GO:0006955, intracellular transport\\n\\nmechanism/]] | \n", + "[[GO:0006955, GO:0051726, GO:0046907]] | \n", + "||
| molecular sequestering-1 | \n", + "[[GO:0006810, regulation of cell growth and survival, GO:0010468, GO:0006915]] | \n", + "[[GO:0051726, GO:0006955, GO:0005515]] | \n", + "||
| mtorc1-0 | \n", + "[[GO:0046034, GO:0006629, GO:0006006, GO:0006457, GO:0046907]] | \n", + "[[GO:0006457, GO:0006006, microtubule organization and biogenesis, GO:0000502, GO:0043043, GO:0042254]] | \n", + "||
| mtorc1-1 | \n", + "[[GO:0000502, GO:0030163]] | \n", + "[[GO:0000502, GO:1904659, GO:0008152, GO:0003676, GO:0044183, GO:0005524, GO:0005783, GO:0005739, GO:0006096, GO:0006631]] | \n", + "||
| peroxisome-0 | \n", + "[[peroxisome biogenesis, GO:0016558, peroxin]] | \n", + "[[peroxisome biogenesis, peroxisomal protein import, peroxin proteins, MONDO:0019234, neonatal adrenoleukodystrophy, MONDO:0019609, MONDO:0009959, MONDO:0008972, MONDO:0009958]] | \n", + "||
| peroxisome-1 | \n", + "[[peroxisome biogenesis, matrix protein import, MONDO:0009279, peroxin (pex) family]] | \n", + "[[peroxisome biogenesis, GO:0005777, GO:0017038]] | \n", + "||
| progeria-0 | \n", + "[[GO:0006998, chromatin organization and maintenance, dna repair and recombination]] | \n", + "[[GO:0005652, GO:0005635, GO:0006281]] | \n", + "||
| progeria-1 | \n", + "[[GO:0006325, GO:0006281, nuclear stability]] | \n", + "[[GO:0006997, GO:0006281, chromatin structure organization, GO:0000723]] | \n", + "||
| regulation of presynaptic membrane potential-0 | \n", + "[[GO:0007268, GO:0005216, neurological function]] | \n", + "[[GO:0005216, GO:0031175, GO:0007268, GO:0042391]] | \n", + "||
| regulation of presynaptic membrane potential-1 | \n", + "[[GO:0005216, GO:0048666, GO:0007268]] | \n", + "[[GO:0005267, chloride ion transmembrane transport, GO:0042391, GO:0034220, GO:0030594]] | \n", + "||
| sensory ataxia-0 | \n", + "[[MONDO:0015626, MONDO:0005244, MONDO:0007790, GO:0043209, GO:0006264, tetratricopeptide repeat, transporter protein\\n\\nmechanism: these genes are involved in myelin upkeep and various neurological diseases associated with defects in myelin sheath synthesis and functions. they play roles in mitochondrial dna replication and transport, as well as protein transportation across the nuclear membrane. the presence of tetratricopeptide repeat motifs in these genes suggests their roles in protein-protein interactions and chaperone functions]] | \n", + "[[MONDO:0015626, MONDO:0007790, MONDO:0005244, myelin sheath maintenance, GO:0006264]] | \n", + "||
| sensory ataxia-1 | \n", + "[[MONDO:0011890, MONDO:0007790, MONDO:0011527, GO:0043217, peripheral myelin sheath, n-acetyl-d-glucosamine residue degradation, MESH:D008565, GO:0007399, nervous system myelination, GO:0006260]] | \n", + "[[GO:0042552, GO:0007422, GO:0016567, er-associated protein degradation.\\n\\nmechanism/]] | \n", + "||
| term-GO:0007212-0 | \n", + "[[GO:0007186, GO:0007189, regulation of cyclic nucleotide metabolic process, regulation of camp metabolic process]] | \n", + "[[g-protein signaling, GO:0007165, neurotransmitter activity]] | \n", + "||
| term-GO:0007212-1 | \n", + "[[GO:0007186, GO:0019932, GO:0007212]] | \n", + "[[g-protein signaling pathway, GO:0030594, GO:1902531]] | \n", + "||
| tf-downreg-colorectal-0 | \n", + "[[transcriptional regulation, GO:0006338, GO:0000988, GO:0003700, rna polymerase ii regulatory region sequence-specific dna binding, zinc finger domain, GO:0042393, nucleosome binding.\\n\\nmechanism: the enriched functions suggest that the given set of genes are involved in transcriptional regulation and chromatin remodeling. transcription factors bind to specific dna sequences and regulate gene expression, while chromatin remodeling alters the structure of chromatin to allow or prevent access to the dna by transcriptional machinery. zinc finger domain-containing proteins are involved in dna binding, and histone binding proteins facilitate the formation of transcriptionally active or inactive chromatin structures. the enriched functions suggest the potential involvement of these genes in both gene activation and repression, which may have important implications in cellular differentiation, development, and disease]] | \n", + "[[transcription regulation, GO:0006338, GO:0003700]] | \n", + "||
| tf-downreg-colorectal-1 | \n", + "[[transcription regulation, chromatin structure alteration, cell cycle progression, GO:0003682]] | \n", + "[[GO:0003700, GO:0006355, GO:0006325, GO:0010468, transcription factor complex\\n\\nmechanism: these genes all play a role in regulating transcription, primarily at the level of dna binding and chromatin organization. they are involved in the regulation of gene expression and the formation of transcription factor complexes]] | \n", + "||
| no_synopsis | \n", + "EDS-0 | \n", + "[[GO:0030198, GO:0030199, GO:0006024]] | \n", + "[[GO:0030198, GO:0043062, GO:0030199, GO:0006486, GO:0008233, GO:0008270]] | \n", + "|
| EDS-1 | \n", + "[[GO:0030199, GO:0030198, GO:0032964]] | \n", + "[[GO:0032963, GO:0030198, GO:0031012]] | \n", + "||
| FA-0 | \n", + "[[fanconi anemia pathway, homologous recombination repair pathway, dna double-strand break repair]] | \n", + "[[GO:0006281, GO:0006325, GO:0006312, GO:0006302, GO:0035825, GO:0006260]] | \n", + "||
| FA-1 | \n", + "[[GO:0006281, GO:0006302, GO:0035825, mitotic cell-cycle checkpoint, GO:0006974]] | \n", + "[[fanconi anemia pathway, GO:0035825, GO:0006302]] | \n", + "||
| HALLMARK_ADIPOGENESIS-0 | \n", + "[[GO:0006631, GO:0006869, GO:0005746, GO:0006637, GO:0032000, GO:0016042, GO:0019216, GO:0033108, GO:0035336, GO:0033539, GO:0051791]] | \n", + "[[GO:0006629, GO:0006631, mitochondrial function, GO:0006119, GO:0006099, beta-oxidation of fatty acids, GO:0006084, GO:0006637, GO:0015980, GO:0005975]] | \n", + "||
| HALLMARK_ADIPOGENESIS-1 | \n", + "[[GO:0006119, GO:0006631, GO:0006457, GO:0030301, GO:0019915, stress response, GO:0045333, mitochondrial metabolism, energy generation, GO:0006986, GO:0046890, GO:0032368, GO:0033344, GO:0007517, GO:0006979, GO:0001666, regulation of fatty acid catabolic process, GO:0019216]] | \n", + "[[GO:0005740, GO:0006122]] | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[[GO:0042110, GO:0030098, GO:0019221, GO:0002682, GO:0050776]] | \n", + "[[GO:0002376, GO:0042110, GO:0019221, GO:0019882, GO:0030098, GO:0050900, GO:0050778, GO:0050777, GO:0001817]] | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[[GO:0005125, GO:0008009, GO:0034341, GO:0042110, GO:0050727]] | \n", + "[[GO:0042110, cytokine signaling, GO:0019882, GO:0006955, chemokine signaling, interferon signaling, GO:0030183, GO:0050900]] | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[[GO:0006351, regulation of transcription, GO:0006629, GO:0030163]] | \n", + "[[GO:0016567, GO:0036211, GO:0008134, GO:0045892, GO:0071535, GO:0031647, GO:0043161]] | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[[GO:0006508, GO:0004672, GO:0007010, GO:0006695, GO:0045944, GO:0043066]] | \n", + "[[regulation of transcription, GO:0005515, GO:0007155, GO:0007165, GO:0016126]] | \n", + "||
| HALLMARK_ANGIOGENESIS-0 | \n", + "[[GO:0030198, GO:0007267, GO:0043405, GO:0042127, GO:0030155, GO:0002576]] | \n", + "[[GO:0030198, GO:0070848, GO:1903010, GO:0042060]] | \n", + "||
| HALLMARK_ANGIOGENESIS-1 | \n", + "[[GO:0030198, GO:0001525, vascular development, GO:0030335, GO:0001938, GO:0017015, GO:0007155]] | \n", + "[[GO:0030198, GO:0001525, GO:0007155]] | \n", + "||
| HALLMARK_APICAL_JUNCTION-0 | \n", + "[[GO:0098609, GO:0034332, GO:0002159, GO:0030198]] | \n", + "[[GO:0007155, GO:0007010, GO:0048041, regulation of actin cytoskeleton, GO:0051017, GO:0046847, GO:0035023]] | \n", + "||
| HALLMARK_APICAL_JUNCTION-1 | \n", + "[[GO:0070160, GO:0007155, GO:0007154, GO:0022407, GO:0043542, GO:0030198, cell junction organization and biogenesis, GO:0032956, GO:0001525, GO:0010810]] | \n", + "[[GO:0007155, GO:0016477, GO:0048870, GO:0007229, GO:0008360, focal adhesion\\n\\nmechanism: the enriched terms suggest that the common function of these genes is involved in cell adhesion and migration. these processes are essential for various biological functions such as wound healing, inflammation, and embryonic development. integrin-mediated signaling pathway and focal adhesion are two crucial pathways in cell adhesion and migration, which are perturbed in many types of cancer and autoimmune diseases. these findings may shed light on the underlying mechanism and potential targets for drug development]] | \n", + "||
| HALLMARK_APICAL_SURFACE-0 | \n", + "[[GO:0051716, GO:0005515, GO:0035556, GO:0007155, GO:0055085, GO:0061024, GO:0015031]] | \n", + "[[GO:0007155, GO:0023052, GO:0006810]] | \n", + "||
| HALLMARK_APICAL_SURFACE-1 | \n", + "[[GO:0007155, GO:0016477, GO:0007165, GO:0038023, GO:0006468, GO:0008104, GO:0055085, GO:0003824]] | \n", + "[[GO:0007155, GO:0007186, GO:0010906, GO:0050796, GO:0070528, GO:0043406, GO:0050731, GO:0051897, GO:0061024, GO:0043066]] | \n", + "||
| HALLMARK_APOPTOSIS-0 | \n", + "[[GO:0006915, GO:0043123, GO:0050855, GO:0001817, GO:0002697, GO:0050670, GO:0051249, GO:0050856, GO:0034097, GO:0032496]] | \n", + "[[GO:0006915, GO:0012501, regulation of cell death\\n\\nmechanism: these genes are involved in various processes that regulate cell death. they participate in the apoptotic process, the programmed cell death that occurs in multicellular organisms. apoptosis is a complex physiological process that is essential for development and homeostasis in healthy adult tissues. these genes also contribute to the regulation of cell death, preventing or promoting apoptosis under specific conditions]] | \n", + "||
| HALLMARK_APOPTOSIS-1 | \n", + "[[cellular stress response, GO:0006915, GO:0006954, GO:0043067, negative regulation of nf-kappab transcription factor, GO:0043280]] | \n", + "[[GO:0097153, GO:0006915, GO:0006954, GO:0008285, GO:0050871, GO:0001819, GO:0045944, GO:0004672, GO:0046328, GO:0010803]] | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[[GO:0006695, GO:0006699, peroxisome biogenesis]] | \n", + "[[peroxisome organization; steroid metabolic process; cholesterol metabolic process; fatty acid metabolic process; lipid metabolic process\\n\\nmechanism: \\n\\nthese genes are involved in various metabolic pathways, especially those related to lipid and sterol metabolism. many of these genes are involved in the transport of lipids and cholesterol, including the abc transporters abca1, abca2, abca3, abca4, abca5, abca6, abca8, abca9, and abcg4. other genes such as cat, ch25h, crot, cyp7a1, GO:0033783, MESH:D013253, dhcr24, and hsd17b6 are involved in the synthesis, GO:0009056, and modification of cholesterol and sterols. \\n\\nadditionally, these genes are also involved in peroxisome biogenesis and function, with genes such as pex1, pex11a, pex11g, pex12, pex13, pex16, pex19, pex26, MESH:D010758]] | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[[GO:0006629, GO:0006869, GO:0005777, mitochondrial function]] | \n", + "[[GO:0006695, GO:0006629, GO:0007031, peroxisome biogenesis, GO:0008202, GO:0006635, GO:0006699, GO:0015908, GO:0006886]] | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[[GO:0016126, GO:0006695, GO:0030301, GO:0006629, GO:0008202, GO:0042632]] | \n", + "[[GO:0006695, GO:0006629, GO:0045540, GO:0019216, GO:0016126]] | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[[GO:0006695, GO:0006629, GO:0008203, GO:0016126, GO:0008299, GO:0042632, GO:0045540, GO:0019216]] | \n", + "[[GO:0006695, GO:0006694, GO:0006629]] | \n", + "||
| HALLMARK_COAGULATION-0 | \n", + "[[GO:0007596, GO:0006956, GO:0030168, GO:0042730, GO:0042060]] | \n", + "[[GO:0030198, GO:0030574, GO:0007596, GO:0042730, GO:0002576, GO:0052547, GO:0045055, GO:0045862]] | \n", + "||
| HALLMARK_COAGULATION-1 | \n", + "[[GO:0030198, GO:0007596, GO:0006508, GO:0006955]] | \n", + "[[GO:0007596, GO:0006955]] | \n", + "||
| HALLMARK_COMPLEMENT-0 | \n", + "[[c1q binding, GO:0006958, GO:0010951, GO:0043154, GO:2001237, GO:1903051]] | \n", + "[[GO:0006956, GO:0002576, GO:0050776, GO:0009611, blood coagulation\\n\\nmechanism: genes involved in complement activation, platelet degranulation, regulation of immune response, response to wounding, and blood coagulation are enriched in this gene set. these functions are related to the prevention of thrombosis and regulation of the immune system]] | \n", + "||
| HALLMARK_COMPLEMENT-1 | \n", + "[[GO:0006955, GO:0007596, GO:0030163, GO:0006508, GO:0010951, GO:0071345, GO:0010952, GO:0030194, GO:0030449]] | \n", + "[[GO:0006955, GO:0007596, GO:0006508, GO:0030168, GO:0006954, GO:0010952]] | \n", + "||
| HALLMARK_DNA_REPAIR-0 | \n", + "[[GO:0006260, GO:0006281, GO:0006397, GO:0006351, GO:0042278]] | \n", + "[[GO:0006260, GO:0006281, dna binding and packaging, GO:0009117, GO:0006338]] | \n", + "||
| HALLMARK_DNA_REPAIR-1 | \n", + "[[GO:0097747, GO:0003677, GO:0006397, GO:0006281]] | \n", + "[[GO:0006260, GO:0006281, transcription elongation, GO:0006396, GO:0009117, GO:0003682]] | \n", + "||
| HALLMARK_E2F_TARGETS-0 | \n", + "[[GO:0006260, GO:0007049, GO:0051301, GO:0140014, GO:0006281]] | \n", + "[[GO:0006260, GO:0007049, GO:0007052, GO:0007059, GO:0007346, GO:0006281, GO:0006334]] | \n", + "||
| HALLMARK_E2F_TARGETS-1 | \n", + "[[GO:0006260, GO:0006281, GO:0071897, GO:0006302, GO:0022616, GO:0006974, GO:0000075, dna damage recognition and signaling]] | \n", + "[[GO:0006260, GO:0006281, GO:0051726, GO:0007059]] | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[[GO:0030198, GO:0043062, GO:0042277, GO:0030199, GO:0007155, GO:0007229, GO:0043410, GO:0005125, GO:0043498, GO:0010646, GO:0071711, GO:0007166, GO:0008285, GO:0070374, GO:0043236, GO:0005509, GO:0030335]] | \n", + "[[GO:0030198, GO:0030199, GO:0032964, GO:0071711, regulation of growth factor signaling, regulation of bmp signaling, regulation of tgf-beta signaling]] | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[[GO:0030198, GO:0007155, GO:0005604, GO:0005581, GO:0007229, GO:0005925, GO:0005515, ecm-receptor interaction, GO:0030334, GO:0007010]] | \n", + "[[GO:0030198, GO:0007155, GO:0007229, GO:0030574, GO:0009888, GO:0016477, GO:0071711]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[[GO:0006811, GO:0006631, GO:0006006, GO:0032870, GO:0008203, drug binding]] | \n", + "[[GO:0005509, GO:0006816, GO:0005516, GO:0010857, GO:0055074, GO:0005262, GO:0030899]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[[GO:0006629, GO:0007165, transcriptional regulation]] | \n", + "[[GO:0006811, GO:0023051, transport of small molecules, GO:0072657, GO:0009966, GO:0008202, GO:0010817, GO:0048522, GO:0010468, GO:0043066, GO:0051246, GO:0071363]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[[GO:0006351, GO:0008152, GO:0008283, GO:0006955, GO:0007165]] | \n", + "[[GO:0005509, GO:0051302, GO:0042981, GO:0006816]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[[GO:0008152, GO:0007165, GO:0032502, GO:0006955, GO:0006351, GO:0019538, GO:0006810, GO:0001558, GO:0042981, GO:0006811]] | \n", + "[[GO:0051726, GO:0008283, GO:0006260, GO:0051301, cancer progression]] | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[[1. metabolic process \\n2. oxidation-reduction process \\n3. response to oxidative stress \\n4. lipid metabolic process \\n5. carbohydrate metabolic process \\n6. amino acid metabolic process \\n7. detoxification \\n8. fatty acid beta-oxidation \\n9. tca cycle \\n10. electron transport chain \\n11. glucose homeostasis \\n12. protein folding and stabilization \\n13. ion homeostasis]] | \n", + "[[GO:0006635, mitochondrial beta-oxidation of fatty acids, GO:0015980, GO:0008152, GO:0044255, GO:0006084, coenzyme metabolic process, GO:0001676, GO:0019752, GO:0006099]] | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[[GO:0006629, oxidative stress response, energy production]] | \n", + "[[GO:0006631, MESH:D004734, mitochondrial function, GO:0016042, oxidative stress response]] | \n", + "||
| HALLMARK_G2M_CHECKPOINT-0 | \n", + "[[GO:0022402, GO:0140014, GO:0007059, GO:0007052, GO:0000226, GO:0006260]] | \n", + "[[cdc20, cdc25a, cdc25b, cdc27, cdc45, cdc6, cdc7, cdk1, cenpa, cenpe, cenpf, chek1, cks1b, cks2, dbf4, e2f1, e2f2, e2f3, e2f4, espl1, exo1, fbxo5, gins2, h2ax, h2az1, h2az2, h2bc12, hmmr, hus1, ilf3, incenp, katna1, kif11, kif15, kif20b, kif22, kif23, kif2c, kif4a, kif5b, kpna2, kpnb1, lig3, mad2l1, map3k20, mcm2, mcm3, mcm5, mcm6, ne]] | \n", + "||
| HALLMARK_G2M_CHECKPOINT-1 | \n", + "[[GO:0006260, GO:0007049, GO:0006281, GO:0140014, GO:0007059]] | \n", + "[[GO:0051726, GO:0006260, chromosomal segregation, GO:0051276, GO:0006281]] | \n", + "||
| HALLMARK_GLYCOLYSIS-0 | \n", + "[[1. glycosylation\\n2. glycolysis\\n3. pentose phosphate pathway]] | \n", + "[[GO:0006096, GO:0005978, glycosylation pathway]] | \n", + "||
| HALLMARK_GLYCOLYSIS-1 | \n", + "[[GO:0006006, energy generation, GO:0016052, GO:0006096, GO:0006090, GO:0006099, GO:0022900, GO:0006119, GO:0006754]] | \n", + "[[GO:0008152, GO:0006796, molecular function regulation, GO:0033554, GO:0031323, GO:0019538, GO:0050794, GO:0044281]] | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[[GO:0030182, GO:0007411, GO:0016477, GO:0007155, GO:0008283]] | \n", + "[[GO:0007399, nervous system neuron differentiation, nervous system development and angiogenesis, GO:0045765, GO:0023056, GO:0048598]] | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[[GO:0007399, GO:0007165, GO:0007155]] | \n", + "[[GO:0031175, GO:0007411, GO:0051960, GO:0007165, GO:0007267]] | \n", + "||
| HALLMARK_HEME_METABOLISM-0 | \n", + "[[GO:0006811, GO:0005515, GO:0008152]] | \n", + "[[GO:0015886, GO:0051536, [2fe-2s] cluster binding]] | \n", + "||
| HALLMARK_HEME_METABOLISM-1 | \n", + "[[GO:0048821, GO:0045646, GO:0042541, GO:0015671, GO:0020037, GO:0005506, GO:0043496, GO:0046982]] | \n", + "[[gene expression regulation; metabolism; transport\\n\\nmechanism and hypotheses:\\nthe genes in this list are involved in various cellular processes, including gene expression regulation, GO:0008152, and transport. gene expression regulation may be a mechanism by which these genes function, possibly through the involvement of transcription factors such as foxo3 and klf3. metabolism may also be a key mechanism, as many of these genes are involved in metabolic pathways, such as fech and alas2 in heme synthesis, and gclc and gclm in glutathione metabolism. transport may also be a contributing mechanism, as several genes in this list, such as slc2a1 and slc6a9, are involved in membrane transport of various molecules. overall, the commonality in function among these genes may be attributed to their roles in regulating cellular metabolism and transporting molecules across various membranes]] | \n", + "||
| HALLMARK_HYPOXIA-0 | \n", + "[[GO:0008152, GO:0006096, GO:0006979, GO:0080135, GO:1901031, GO:0046324, GO:0006006, GO:0005975, GO:0006974]] | \n", + "[[GO:0006110, GO:0051246, GO:0010628, GO:0030198, GO:0006006, GO:0009749, GO:0001558, GO:0008284, GO:0051094]] | \n", + "||
| HALLMARK_HYPOXIA-1 | \n", + "[[glycolysis; gluconeogenesis; citrate cycle; pyruvate metabolism; atp production\\n\\nmechanism: these genes are enriched in functions related to energy metabolism, including glycolysis, GO:0006094, the citrate cycle, GO:0006090, and atp production. they are involved in various aspects of energy metabolism, such as glucose uptake and metabolism, GO:0005980, atp synthesis. the over-representation of these functions suggests that these genes may play a role in the regulation of energy metabolism at the cellular organismal level]] | \n", + "[[hk1, hk2, pfkl, pfkfb3, gys1, pklr, pgk1, tpi1, aldoa, eno2, pgam2, pgm2, fbp1, eno1, ndst1, ndst2]] | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[[il10ra, tnfrsf18, il18r1, il1r2, il1rl1, il2ra, il2rb, il4r, MESH:D016753, MESH:D018793, tnfrsf1b, tnfrsf21, tnfrsf4, tnfrsf8, tnfrsf9, tnfsf11, tnfsf10, ifngr1, ccr4, ctla4, cxcl10, icos, irf4, irf6, irf8, socs1, socs2, ager, cish, gata1, gbp4, spp1, bcl2, bcl2l1, bmpr2, ccnd2, ccne1, cd79b, galm, glipr2, gpx4, hk2, MESH:D016753, itga6, itgae, itih5, klf6, lif, lrig1, ltb, mxd1, myc]] | \n", + "[[il2ra, il1r2, il2rb, il10ra, ctla4, cd44, MESH:D016753, il1rl1, il18r1, icos, tnfrsf4, tnfrsf18, tnfrsf8, tnfrsf21, tnfsf11, tnfrsf9, tnfsf10, tnfrsf1b, cd48, tnfrsf4, cxcl10, MESH:D018793, selp, ccne1, MESH:D047990, socs1, socs2]] | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[[cytokine signaling pathway, GO:0006955, GO:0002682, GO:0006954, leukocyte migration and chemotaxis, GO:0002694, GO:0071347, GO:0032680]] | \n", + "[[GO:0006955, cell signaling, GO:0005125, GO:0008009, GO:0008083, GO:0007166, GO:0002250, GO:0030595, GO:0050900, GO:0006954]] | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[[GO:0006955, cytokine signaling pathway, GO:0060333, positive regulation of interleukin production, GO:0032729]] | \n", + "[[GO:0019221, GO:0002757, GO:0007259, GO:0002694, regulation of leukocyte migration and chemotaxis, GO:0035456, GO:0034341, GO:0070555, GO:0070671, GO:0070741, response to tumor necrosis factor. \\n\\nhypotheses: these genes are involved in activating immune responses and cytokine-mediated signaling pathways. the enrichment of terms related to leukocyte activation and chemotaxis suggests an increased focus on the recruitment of immune cells to sites of infection and inflammation. the involvement of genes related to cytokine signaling, such as jak-stat cascade, suggests that the activation of immune responses may be regulated by cytokines released in response to infection or inflammation. overall, these genes are likely involved in the regulation of immune system activation and inflammation]] | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[[GO:0005126, GO:0006955, GO:0050900, jak-stat signaling pathway, GO:0034341, GO:0002690, GO:0051249, GO:0001817, GO:0050863, GO:0019221, GO:1902105]] | \n", + "[[cytokine signaling, GO:0006954, GO:0006955, interleukin signaling, GO:0008009, jak-stat signaling, toll-like receptor signaling]] | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[[GO:0050900, cytokine signaling, GO:0002224, GO:0006954, GO:0032729, GO:0045087, GO:0032733, GO:0030595]] | \n", + "[[cytokine signaling, GO:0006955, GO:0006954]] | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[[cytokine signaling, chemokine signaling, GO:0050900, GO:0002250, GO:0045087]] | \n", + "[[GO:0004896, GO:0042379, GO:0050900, GO:0002694, GO:0050778, GO:0045088, GO:0005149, GO:0042110, GO:0006952, GO:0006954, GO:0002685, GO:0034097]] | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[[interferon signaling, GO:0045087, antiviral defense]] | \n", + "[[GO:0051607, GO:0045087, interferon signaling, type i interferon response, viral defense]] | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[[GO:0034341, GO:0002718, GO:0060333, GO:0045070, GO:0032897, innate immune response-activating signal transduction, GO:0060337, GO:0035457, antiviral mechanism by interferon-stimulated genes (isg)]] | \n", + "[[GO:0051607, GO:0002376, GO:0140888]] | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[[GO:0051607, GO:0035458, GO:0071357, GO:0045071, GO:0031323, GO:0002682, GO:0034097, GO:0034340]] | \n", + "[[GO:0060337, GO:0006955, GO:0002579, GO:0051607, GO:0046596, GO:0032481, GO:0045087, GO:0034341, GO:0032727, GO:0002504, GO:0002479, GO:0032728, GO:0071357, GO:0043331, GO:0016032, GO:0045859, GO:0006954, GO:0060333, GO:0038187]] | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[[interferon signaling, GO:0019882, GO:0045321]] | \n", + "[[GO:0019882, interferon response, GO:0001816, GO:0006954, GO:0002376, GO:0050776, GO:0006952, GO:0009615, response to interferon]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[[GO:0005509, contractile fiber part, GO:0006936]] | \n", + "[[GO:0005509, GO:0070588, GO:0051924, GO:0051899, GO:0042391, GO:0071277]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[[GO:0043167, GO:0007165, GO:0019222, GO:0050794, g protein-coupled receptor signaling, GO:0035556, GO:0031325, GO:0043066, metabolic process regulation, GO:0005509, GO:0034765, GO:0001932, GO:0043169, GO:0045859, GO:0051716]] | \n", + "[[GO:0006811, neurological signaling, tissue development.\\n\\nmechanism]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[[GO:0006955, GO:0007165, GO:0050794, cytokine signaling, GO:0006954, GO:0006935, GO:0008284, GO:0043066]] | \n", + "[[GO:0006955, cellular signaling, GO:0001525]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[[GO:0006955, GO:0006954, GO:0002694, GO:0001817, interleukin-10 signaling, tumor necrosis factor (tnf) signaling, GO:0006956, platelet activation and aggregation, eicosanoid synthesis]] | \n", + "[[1. immune response\\n2. inflammatory response\\n3. coagulation\\n4. positive regulation of endothelial cell migration \\n5. cell adhesion\\n6. positive regulation of cell migration \\n7. signal transduction \\n8. negative regulation of apoptotic process \\n9. regulation of angiogenesis \\n10. positive regulation of protein serine/threonine kinase activity \\n11. positive regulation of transcription from rna polymerase ii promoter \\n\\nmechanism: the enriched functions suggest that these genes play an important role in innate and adaptive immune responses, inflammatory processes, GO:0007596, cell adhesion and migration, GO:0001525, and signal transduction pathways. they could be involved in regulating the expression and activity of various immune cells, MESH:D016207, chemokines to modulate immunity inflammation. the coagulation-related genes may contribute to thrombotic disorders cardiovascular diseases by affecting blood clot formation fibrinolysis. the cell adhesion migration-related genes are potentially involved in tumor metastasis progression through facilitating cell invasion motility. the signal]] | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[[GO:0007018, GO:0007052, cell division, chromosome separation]] | \n", + "[[GO:0007052, GO:0007017, GO:0051301, GO:0007010, GO:0030029]] | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[[kinesin family members, microtubule formation and stabilization, spindle formation and assembly, GO:0000910, GO:0051726, gene expression and chromosome segregation]] | \n", + "[[GO:0007051, GO:0031023, GO:0007059, GO:0071173, GO:0051382, GO:0007052, GO:0000226, GO:0007098, GO:0007020, GO:0000075, GO:0007018, GO:0007346, GO:0000070, GO:0001578, GO:0008017, GO:0000910, GO:0030953]] | \n", + "||
| HALLMARK_MTORC1_SIGNALING-0 | \n", + "[[GO:0006457, GO:0050776, GO:0009117, GO:0006629, gluconeogenesis and glycolysis, mrna processing and splicing]] | \n", + "[[glycolysis; tca cycle; cholesterol biosynthesis; pentose phosphate pathway\\n\\nmechanism and hypotheses:\\nthe enriched terms suggest that these genes are involved in various aspects of cellular metabolism. glycolysis is the central pathway for glucose metabolism, converting glucose into pyruvate. the tca cycle is responsible for generating energy from the breakdown of carbohydrates, MESH:D005227, and amino acids. the cholesterol biosynthesis pathway is responsible for producing cholesterol, which is involved in membrane structure, steroid hormone synthesis, and bile salt production. the pentose phosphate pathway is involved in the production of nadph, which is critical for many cellular processes, including antioxidant defense and biosynthesis.\\n\\noverall, these genes are likely involved in regulating various aspects of cellular metabolism, including energy production, biosynthesis of important molecules like cholesterol and nadph, mediating the cellular response to oxidative stress]] | \n", + "||
| HALLMARK_MTORC1_SIGNALING-1 | \n", + "[[GO:0044237, protein regulation, transcriptional regulation, translation regulation, GO:0006281, stress response.\\n\\nmechanism: these enriched terms suggest that the identified genes are involved in several pathways, including maintaining cellular metabolism and homeostasis, regulating transcription and translation of proteins, repairing dna in response to damage, and responding to cellular stress]] | \n", + "[[GO:0051087, GO:0006457, co-factor binding, GO:0008152, GO:0005524]] | \n", + "||
| HALLMARK_MYC_TARGETS_V1-0 | \n", + "[[GO:0006412, GO:0006457, GO:1990904, u4/u6.u5 tri-snrnp, chaperone-mediated protein folding.\\n\\nmechanism: these genes are involved in protein synthesis and processing, including translation and ribosome biogenesis. many of them are also involved in protein folding and chaperone-mediated protein folding. the u4/u6.u5 tri-snrnp is also highly represented, indicating these genes may be involved in splicing]] | \n", + "[[GO:0006397, GO:0006413, GO:0042254]] | \n", + "||
| HALLMARK_MYC_TARGETS_V1-1 | \n", + "[[GO:0006396, GO:0006413, GO:0006446, GO:0042254, GO:0008380, GO:0006397]] | \n", + "[[GO:0006396, GO:0006412, GO:0042254, GO:0006402, GO:0043488, regulation of mrna splicing, GO:0043393, GO:0008380, GO:0006417, GO:0003723]] | \n", + "||
| HALLMARK_MYC_TARGETS_V2-0 | \n", + "[[GO:0042254, GO:0008033, GO:0006364, GO:0016072, GO:0009451, GO:0022613]] | \n", + "[[GO:0042254, GO:0006364, GO:0003723, GO:0005681, GO:0006413]] | \n", + "||
| HALLMARK_MYC_TARGETS_V2-1 | \n", + "[[GO:0042254, GO:0006364, GO:0000394, rna polymerase ii regulation, rna processing and modification]] | \n", + "[[GO:0006396, GO:0022613, GO:0042254, GO:0000166, GO:0003723, GO:0090304, GO:0042273, GO:0006364, GO:0065004]] | \n", + "||
| HALLMARK_MYOGENESIS-0 | \n", + "[[GO:0006936, GO:0006816, z-disc, UBERON:0002036, GO:0030017, MESH:D014335, GO:0005861, GO:0071689]] | \n", + "[[muscle filament sliding; sarcomere organization; muscle system process\\n\\nmechanism: the majority of the listed genes are involved in muscle contraction and development, specifically in the organization and structure of the sarcomere. the enriched terms - muscle filament sliding, GO:0045214, muscle system process - all relate to the mechanisms of muscle contraction the intricate process of sarcomere formation]] | \n", + "||
| HALLMARK_MYOGENESIS-1 | \n", + "[[UBERON:0001630, MESH:D009218, MESH:D000199, MESH:D014336, filament]] | \n", + "[[GO:0003012, GO:0006936, GO:0045214, GO:0030029]] | \n", + "||
| HALLMARK_NOTCH_SIGNALING-0 | \n", + "[[GO:0007219, GO:0045165, GO:0022008, GO:0030154, GO:0045893, GO:0043066, GO:0008285, GO:0043065, GO:0045747, GO:0016055, GO:0007268]] | \n", + "[[GO:0007219, GO:0008593, GO:0016055, GO:0030111, GO:0045944, GO:0045596, GO:0045597]] | \n", + "||
| HALLMARK_NOTCH_SIGNALING-1 | \n", + "[[GO:0051726, GO:0030154, GO:0001709, transcriptional regulation, GO:0016567]] | \n", + "[[GO:0007219, GO:0005515, GO:0000122, GO:0000988]] | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[[GO:0022900, GO:0045333, GO:0002082]] | \n", + "[[GO:0042773, mitochondrial atp synthesis coupled electron transport in respiratory chain, GO:0033108, GO:0006979]] | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[[GO:0006119, GO:0005746, GO:0070469, GO:0005739, MESH:D004734, GO:0031966, GO:0006099, GO:0006635, citrate cycle, GO:0098798, GO:0006754, GO:0051536]] | \n", + "[[GO:0003954, GO:0022900, GO:0042773, GO:0005743, GO:0007005, GO:0006119, GO:0033108, respiratory chain complex i, ii, iii, iv, v, vi, GO:0006743, GO:0006631]] | \n", + "||
| HALLMARK_P53_PATHWAY-0 | \n", + "[[GO:0006974, GO:0051726, cell growth and proliferation]] | \n", + "[[GO:0051726, GO:0006915, GO:0008285, GO:0006974, negative regulation of cellular process.\\n\\nmechanism: the genes in this list are enriched in functions that regulate the cell cycle and cell death. specifically, they are involved in cell cycle arrest, apoptosis, negative regulation of cell proliferation, and response to dna damage stimulus]] | \n", + "||
| HALLMARK_P53_PATHWAY-1 | \n", + "[[GO:0051726, GO:0006281, GO:0030330, GO:0000082, response to dna damage]] | \n", + "[[GO:0006974, GO:0051726, GO:0006915, GO:0006281, MESH:D002470, p53 signaling, checkpoint regulation, transcriptional regulation, GO:0006338]] | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[[pancreatic development, beta cell differentiation, GO:0030073, GO:0042593, GO:0006006]] | \n", + "[[GO:0030073, GO:0042593, GO:0003309, GO:0003323, pancreatic beta cell function, pancreatic islet cell development]] | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[[GO:0003323, GO:0030073, glucose regulation, diabetes-related pathways]] | \n", + "[[GO:0003323, GO:0030073, GO:0042593, GO:0031018, GO:0050796, GO:0006006, positive regulation of pancreatic beta cell differentiation, GO:0010827, regulation of insulin secretion by glucose]] | \n", + "||
| HALLMARK_PEROXISOME-0 | \n", + "[[GO:0006631, GO:0006805, steroid hormone biosynthesis]] | \n", + "[[GO:0140359, GO:0006631, GO:0006695, GO:0035357, GO:0005777]] | \n", + "||
| HALLMARK_PEROXISOME-1 | \n", + "[[GO:0006631, GO:0007031, GO:0015721, GO:0006282]] | \n", + "[[GO:0006631, GO:0006629, GO:0008202, GO:0030301, GO:0006641, GO:0008206, GO:0005777]] | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[[mapk cascade; pi3k-akt signaling pathway; regulation of cell proliferation\\n\\nmechanism: the enriched terms suggest that the common function of the listed genes is to regulate cellular processes related to signal transduction and cell cycle/apoptosis. the mapk cascade is a crucial signaling pathway that controls the expression of genes required for cellular proliferation, differentiation, and survival. pi3k-akt signaling pathway controls cell survival, GO:0040007, and metabolism. the enriched term \"regulation of cell proliferation\" suggests that the listed genes contribute to regulating the balance between cell growth and division. these genes could affect the rate of cellular proliferation, arresting or promoting the cell cycle or modulating apoptotic signal transduction]] | \n", + "[[GO:0016301, GO:0006468, GO:0010646, GO:0035556, regulation of map kinase activity\\n\\nmechanism: these genes are involved in several signaling pathways and primarily regulate protein kinase activity and phosphorylation. they are involved in the regulation of cell communication and intracellular signaling cascades, including the map kinase cascade]] | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[[GO:0033554, GO:0035556, GO:0006468, GO:0042981, GO:0080135]] | \n", + "[[GO:0007165, GO:0006468, GO:0008152, GO:0001558, GO:0042127, GO:0042981, GO:0045859, GO:0043408, GO:0032024, GO:0005975, GO:0010906, GO:0010604]] | \n", + "||
| HALLMARK_PROTEIN_SECRETION-0 | \n", + "[[GO:0016192, GO:0046907, GO:0006897, GO:0061024, GO:0008104, GO:0048193]] | \n", + "[[GO:0016192, endosome to golgi transport, GO:0006886, GO:0008104, GO:0015031, regulation of membrane organization and biogenesis]] | \n", + "||
| HALLMARK_PROTEIN_SECRETION-1 | \n", + "[[GO:0048193, GO:0005768, GO:0005764, GO:0006612, GO:0006886, GO:0042391, GO:0034765, GO:0005773]] | \n", + "[[GO:0006886, GO:0006891, GO:0007030, GO:0072583]] | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[[GO:0016209, GO:0051920, GO:0006749, GO:0006979, GO:0070301]] | \n", + "[[GO:0016209, redox regulation, GO:0006749, oxidation-reduction process, GO:0006979]] | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[[GO:0016209, regulation of iron ion binding, GO:0006979, GO:0048821, GO:2000378, GO:0006282, GO:0070301, GO:0050790, GO:0032092, regulation of thiol-dependent ubiquitinyl hydrolase activity, GO:0034599]] | \n", + "[[oxidative stress response, redox regulation, GO:0006749, GO:0016209, GO:0000302]] | \n", + "||
| HALLMARK_SPERMATOGENESIS-0 | \n", + "[[GO:0007283, GO:0140013, GO:0007130, GO:0007281, GO:0097722, oocyte meiosis]] | \n", + "[[GO:0140013, GO:0007283, GO:0007059, GO:0051301, GO:0140014]] | \n", + "||
| HALLMARK_SPERMATOGENESIS-1 | \n", + "[[GO:1903047, GO:0010971, regulation of spindle assembly checkpoint, GO:0034501, GO:0090234, GO:0051985, GO:0110028]] | \n", + "[[GO:0007052, GO:0007059, GO:0007094]] | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[[tgf-beta signaling pathway, GO:0030514, GO:0090287, GO:0030513, GO:0006351, GO:0006355, GO:0045893, GO:0000122]] | \n", + "[[GO:0030509, GO:0000122, GO:0045944, GO:0048705, GO:0007183, GO:0007179]] | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[[tgf-beta signaling pathway, GO:0030509, GO:0030513, GO:0030198, GO:0060391]] | \n", + "[[GO:0007179, GO:0030514, GO:0010990]] | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[[ccl2, ccl20, ccl4, ccl5, ccn1, ccnd1, ccrl2, cd44, cd69, cd80, cd83, cdkn1a, icam1, icoslg, ifih1, ifit2, ifngr2, GO:0043514, il15ra, MESH:D020382, il1a, il1b, GO:0070743, MESH:D015850, il6st, il7r, inhba, irf1, jag1, nfkb1, nfkb2, nfkbia, nfkbie, nr4a1, nr4a2, nr4a3, ptger4, MESH:D051546, rel, rela, relb, ripk2, stat5a, tlr2, tnf, tnfaip2, tnfaip3, tnfaip6, tnfaip8, tnfrsf9, tnfsf9, tnip1, tnip]] | \n", + "[[GO:0006955, GO:0006954, GO:0034097, GO:0050865, GO:0071624, GO:0032855, GO:0010552, GO:0051092, GO:0043406, GO:0007259, GO:0043065, GO:0004672]] | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[[cytokine signaling, GO:0000988, stress response, GO:0050776, GO:0006954]] | \n", + "[[GO:0006955, GO:0006954, GO:0032680, GO:0001816, GO:0032496, negative regulation of nf-kappab transcription factor activity.\\n\\nmechanism and]] | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[[GO:0006457, GO:0036503, upr signaling pathway]] | \n", + "[[GO:0006457, MESH:M0354322, ubiquitin-mediated proteolysis, GO:0034976, GO:0006986, GO:0006397, GO:0008380]] | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[[GO:0006457, GO:0006605, GO:0006396, GO:0006950, GO:0006417, GO:0016481, GO:0006986, GO:0006913, GO:0008380, GO:1903021, GO:0016032, GO:0032496, GO:0072659, GO:0017148, GO:0022613, negative regulation of transcription by rna polymerase]] | \n", + "[[GO:0006457, chaperone-mediated protein processing, GO:0015031, GO:0007029, GO:0006986]] | \n", + "||
| HALLMARK_UV_RESPONSE_DN-0 | \n", + "[[tgf-beta signaling pathway, GO:0030198, GO:0007155, GO:0030334, GO:0042127]] | \n", + "[[GO:0004672, GO:0003700, GO:0006355, GO:0035556, cytoplasmic membrane-bounded vesicle, receptor protein signaling pathway, GO:0007155, GO:0001932, GO:0007399, GO:0007498, GO:0045666]] | \n", + "||
| HALLMARK_UV_RESPONSE_DN-1 | \n", + "[[GO:0030198, GO:0030036, GO:0030155, GO:0007160, GO:0016477, GO:0007229, GO:0030199, GO:0035023, GO:0030178, basement membrane formation, GO:0014909]] | \n", + "[[GO:0030198, GO:0007165, GO:0008083, neural development, GO:0022008]] | \n", + "||
| HALLMARK_UV_RESPONSE_UP-0 | \n", + "[[GO:0006355, regulation of transcription, dna-templated; go:0044267, cellular protein metabolic process; go:0009968, GO:0009968]] | \n", + "[[GO:0033554, GO:0031323, GO:0051050, GO:0009966]] | \n", + "||
| HALLMARK_UV_RESPONSE_UP-1 | \n", + "[[GO:0006955, GO:0008104, GO:0051726]] | \n", + "[[GO:0008104, GO:0006950, GO:0042981, GO:0008283, GO:0006979, regulation of transcription, GO:0006974, GO:0007049, response to hypoxia.\\n\\nmechanism]] | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[[GO:0016055, GO:0007219, transcriptional regulation, GO:0030154, GO:0008283]] | \n", + "[[cellular response to wnt stimulus, GO:0090263, GO:0045746]] | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[[GO:0007219, GO:0045747, GO:0045746, GO:0045165]] | \n", + "[[GO:0016055, GO:0007219, GO:0005515, GO:0008134]] | \n", + "||
| T cell proliferation-0 | \n", + "[[cd28 co-stimulation, il-2 signaling, GO:0042110]] | \n", + "[[GO:0002376, GO:0042110, GO:0001816, GO:0046649, GO:0006955, GO:0007166]] | \n", + "||
| T cell proliferation-1 | \n", + "[[GO:0042110, GO:0051247, GO:0001817]] | \n", + "[[t cell activation; cytokine signaling; lymphocyte proliferation; immune response\\n\\nmechanism: these genes are all involved in the regulation and function of the immune system, specifically in t cell activation, GO:0046651, and cytokine signaling pathways. they play a role in immune responses to pathogens, MONDO:0007179, MONDO:0004992]] | \n", + "||
| Yamanaka-TFs-0 | \n", + "[[GO:0000988, transcriptional regulation, GO:0030154, GO:0008283, stem cell maintenance, MESH:D047108]] | \n", + "[[GO:0000988, GO:0003677, GO:0048863]] | \n", + "||
| Yamanaka-TFs-1 | \n", + "[[MESH:D047108, regulation of transcription, GO:0048863]] | \n", + "[[pluripotency, self-renewal, GO:0048863]] | \n", + "||
| amigo-example-0 | \n", + "[[GO:0030198, GO:0030199, GO:0001525, GO:0001568, GO:0030168, GO:0001666, GO:0001936]] | \n", + "[[extracellular matrix organization; angiogenesis; positive regulation of cell migration; positive regulation of endothelial cell migration; positive regulation of sprouting angiogenesis; positive regulation of angiogenesis; positive regulation of vascular endothelial cell migration; positive regulation of smooth muscle cell migration; positive regulation of vascular smooth muscle cell migration; positive regulation of tube formation; positive regulation of endothelial cell proliferation; positive regulation of vascular endothelial growth factor production. \\n\\nhypotheses: several of the genes in the list encode for extracellular matrix components or regulators of matrix organization, including col3a1, col5a2, lum, postn, and vcan. others, such as cxcl6, pdgfa, pf4, and vegfa, encode for angiogenic growth factors. itgav is a common denominator and is associated with integrin-mediated signaling that regulates cell adhesion, migration, angiogenesis. fgfr1 has also been shown to play a critical role in angiogenesis extracellular matrix organization by regulating downstream signaling pathways such as pi3k mapk]] | \n", + "||
| amigo-example-1 | \n", + "[[GO:0030198, GO:0030155, regulation of cell substrate adhesion, GO:0045785, GO:0043062]] | \n", + "[[GO:0030198, GO:0007155, GO:0001525, GO:0016477, GO:0030334, GO:0008284, GO:0043410]] | \n", + "||
| bicluster_RNAseqDB_0-0 | \n", + "[[GO:0005509, GO:0050804, transcriptional regulation, GO:0050808]] | \n", + "[[GO:0030182, GO:0006811, GO:0000988, GO:0005509, GO:0007399, GO:0007267, synapse assembly and organization, g protein-coupled receptor signaling, GO:0003723, GO:0005515]] | \n", + "||
| bicluster_RNAseqDB_0-1 | \n", + "[[GO:0007186, GO:0010468, GO:0007154, GO:0006355, GO:0005515, GO:0007155, GO:0001932, GO:0016055, GO:0030334, GO:0007165, GO:0043408, GO:0003677, GO:0006357, GO:0005543, GO:0051493, GO:0006811]] | \n", + "[[GO:0006396, GO:0008134, GO:0006355, GO:0003682, GO:0005634, GO:0003723, GO:0006397, transcriptional regulation, GO:0061629]] | \n", + "||
| bicluster_RNAseqDB_1002-0 | \n", + "[[atp hydrolysis coupled calcium ion transport, GO:0030036, GO:0006936, GO:0033365, GO:0051147, GO:0014743, GO:0045214]] | \n", + "[[GO:0006936, GO:0045214, GO:0006941, GO:0060048]] | \n", + "||
| bicluster_RNAseqDB_1002-1 | \n", + "[[GO:0006936, MESH:D024510, GO:0007519, GO:0055001, GO:0030239, GO:0007517]] | \n", + "[[GO:0006936, GO:0033275, GO:0031034, GO:0005509, GO:0045214, MESH:D024510]] | \n", + "||
| endocytosis-0 | \n", + "[[GO:0006897, GO:0016192, GO:0007041, GO:0007032, GO:0030163]] | \n", + "[[GO:0030301, GO:0006629, GO:0006897, GO:0030163]] | \n", + "||
| endocytosis-1 | \n", + "[[GO:0006897, GO:0006898, GO:0016197, GO:0015031, GO:0006886, GO:0007032, GO:0016192, endosomal sorting]] | \n", + "[[GO:0006897, GO:0007032, GO:0036010, GO:0006898, GO:0016192]] | \n", + "||
| glycolysis-gocam-0 | \n", + "[[GO:0006096, GO:0005975, GO:0006006, GO:0019318]] | \n", + "[[GO:0006006, GO:0006096]] | \n", + "||
| glycolysis-gocam-1 | \n", + "[[GO:0006096, GO:0006006, GO:0006007]] | \n", + "[[GO:0005975, GO:0006006, GO:0006096, GO:0006754]] | \n", + "||
| go-postsynapse-calcium-transmembrane-0 | \n", + "[[GO:0005509, GO:0005262, GO:0019722, GO:0006874, GO:0034765]] | \n", + "[[GO:0006816, GO:0015075, GO:0099601, GO:0007268, GO:0034765]] | \n", + "||
| go-postsynapse-calcium-transmembrane-1 | \n", + "[[GO:0005509, GO:0004970, GO:0051966, GO:0046928, GO:0005216, GO:0034765, GO:0004672, GO:0051924, GO:0051247]] | \n", + "[[GO:0005216, neurotransmitter signaling, GO:0050804, GO:0005509, GO:0008066]] | \n", + "||
| go-reg-autophagy-pkra-0 | \n", + "[[GO:0033554, GO:0010506, GO:0007165]] | \n", + "[[GO:0006950, GO:0006915, GO:0042981, GO:0043123, GO:0046330]] | \n", + "||
| go-reg-autophagy-pkra-1 | \n", + "[[GO:0097190, GO:0016485, GO:0031323]] | \n", + "[[autophagy regulation, GO:0033554, GO:0006915]] | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[[glycoside hydrolase activity, GO:0005975, GO:0006027, GO:0009311, GO:0005764, GO:0005783, catabolism of carbohydrate, MONDO:0019249]] | \n", + "[[GO:0005975, GO:0005764, GO:0016798, glycoside hydrolase activity, GO:0004556, GO:0008422, acid alpha-glucosidase activity, GO:0004565, GO:0015929, GO:0015923, n-acetylglucosaminidase activity, GO:0004308, GO:0015926, GO:0005980, GO:0006027, mucopolysaccharide catabolic process, GO:0016266, GO:0006491]] | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[[GO:0006096, metabolism of carbohydrates, GO:0019318, GO:0006013, GO:0009311, chitin catabolic/metabolic process, hyaluronan catabolic/metabolic process, glycosphingolipid metabolic/catabolic process, sialic acid catabolic/metabolic process]] | \n", + "[[GO:0005975, GO:0070085, GO:0000272, GO:0004553, GO:0015929, GO:0004556, GO:0004565]] | \n", + "||
| ig-receptor-binding-2022-0 | \n", + "[[GO:0002377, t cell receptor signaling, GO:0042113, t cell activation. \\n\\nhypotheses: this list of genes is heavily enriched in those involved in the function and development of b cells and t cells. specifically, they play a role in the production and function of immunoglobulins and t cell receptors, as well as the activation of these cell types. this suggests that these genes are integral to the proper functioning of the immune system]] | \n", + "[[GO:0002376, GO:0046649, GO:0002250, GO:0042113, GO:0003823, antibody-mediated immunity\\n\\nmechanism]] | \n", + "||
| ig-receptor-binding-2022-1 | \n", + "[[GO:0006955, GO:0046649, GO:0030098]] | \n", + "[[GO:0002377, GO:0042113, GO:0016064]] | \n", + "||
| meiosis I-0 | \n", + "[[meiotic recombination, crossover formation, GO:0007130, GO:0006281, GO:0035825]] | \n", + "[[GO:0006281, GO:0035825, GO:0140013, GO:0007059, GO:0007129, GO:0006974, m phase of meiosis, dna replication-independent nucleosome assembly, crossover junction formation, GO:0007281, GO:0036093, GO:0009994, GO:0007283, GO:0071173, GO:0006298, GO:0033554]] | \n", + "||
| meiosis I-1 | \n", + "[[GO:0007059, GO:0051321, GO:0006310, synapsis of chromosomes, GO:0051276, GO:0051177]] | \n", + "[[GO:0140013, GO:0006281, GO:0007059, MESH:D011995, GO:0035825, GO:0006302, GO:0007129, crossing-over, GO:0051276]] | \n", + "||
| molecular sequestering-0 | \n", + "[[GO:0002376, GO:0006950, GO:0006457, GO:0051641, GO:0006396, GO:0006829, GO:0010467, GO:0007165]] | \n", + "[[GO:0034599, GO:0001558, GO:0032088, GO:0043066, GO:0051726, GO:0010468, GO:0008285]] | \n", + "||
| molecular sequestering-1 | \n", + "[[GO:0006979, GO:0032088, GO:0055072, GO:0016567, GO:0043066]] | \n", + "[[GO:0006979, GO:0006974, GO:0080135, regulation of protein localization to organelles, GO:0043065, GO:0043066, GO:0008285, GO:0050821]] | \n", + "||
| mtorc1-0 | \n", + "[[GO:0006457, GO:0050776, GO:0009117, GO:0006629, gluconeogenesis and glycolysis, mrna processing and splicing]] | \n", + "[[glycolysis; tca cycle; cholesterol biosynthesis; pentose phosphate pathway\\n\\nmechanism and hypotheses:\\nthe enriched terms suggest that these genes are involved in various aspects of cellular metabolism. glycolysis is the central pathway for glucose metabolism, converting glucose into pyruvate. the tca cycle is responsible for generating energy from the breakdown of carbohydrates, MESH:D005227, and amino acids. the cholesterol biosynthesis pathway is responsible for producing cholesterol, which is involved in membrane structure, steroid hormone synthesis, and bile salt production. the pentose phosphate pathway is involved in the production of nadph, which is critical for many cellular processes, including antioxidant defense and biosynthesis.\\n\\noverall, these genes are likely involved in regulating various aspects of cellular metabolism, including energy production, biosynthesis of important molecules like cholesterol and nadph, mediating the cellular response to oxidative stress]] | \n", + "||
| mtorc1-1 | \n", + "[[GO:0006457, GO:0015031, GO:0042254]] | \n", + "[[GO:0006810, GO:0008152, GO:0006457]] | \n", + "||
| peroxisome-0 | \n", + "[[GO:0005778, peroxisome targeting, GO:0007031]] | \n", + "[[GO:0007031, peroxisome biogenesis, protein import into peroxisome, peroxisome membrane organization, peroxisomal matrix organization]] | \n", + "||
| peroxisome-1 | \n", + "[[peroxisome biogenesis, peroxisome membrane organization, GO:0016559]] | \n", + "[[GO:0007031, peroxisome biogenesis, GO:0016559]] | \n", + "||
| progeria-0 | \n", + "[[GO:0006281, GO:0051276, regulation of transcription]] | \n", + "[[GO:0006281, GO:0006997, GO:0010467, GO:0007568]] | \n", + "||
| progeria-1 | \n", + "[[GO:0006281, GO:0006325, GO:0090398]] | \n", + "[[GO:0006325, GO:0006281, GO:0000723, nuclear localization, nuclear lamina organization, genome stability regulation]] | \n", + "||
| regulation of presynaptic membrane potential-0 | \n", + "[[GO:0004970, GO:0099536, GO:0001505, GO:0007268, GO:0043269, GO:0005244, GO:0042391]] | \n", + "[[GO:0006811, GO:0048666, GO:0007268, GO:0042391, GO:0034765]] | \n", + "||
| regulation of presynaptic membrane potential-1 | \n", + "[[GO:0005216, GO:0007268, GO:0005261, GO:0007215, GO:0019228, GO:0006813, GO:0060080, MESH:D005680, sodium ion transport. \\n\\nhypotheses: \\n1. the enrichment of ion channel activity-related terms suggests that the genes play a crucial role in regulating ion transport during neuronal signaling, which in turn influences synaptic plasticity and memory formation.\\n2. the enrichment of synaptic transmission-related terms points towards the involvement of the genes in various aspects of synaptic signaling, including the glutamate and gaba receptor signaling pathways, inhibition of neuronal activity, and modulation of action potential generation. \\n3. overall, the enrichment of these terms hints at a potential interaction between the listed genes in regulating various aspects of neural signal processing, synaptic transmission, and plasticity]] | \n", + "[[GO:0005216, GO:0042803, GO:0008066, GO:0016917, GO:0005261]] | \n", + "||
| sensory ataxia-0 | \n", + "[[mitochondrial function, GO:0006457, GO:0030163, GO:0055085]] | \n", + "[[GO:0042552, GO:0007411, GO:0007399, GO:0008104, GO:0031175]] | \n", + "||
| sensory ataxia-1 | \n", + "[[\"nervous system development\", \"axon guidance\", \"myelination\", \"neuron projection\", \"synaptic transmission\"]] | \n", + "[[GO:0044237, neurological development, myelin sheath formation]] | \n", + "||
| term-GO:0007212-0 | \n", + "[[GO:0030594, GO:0007186, GO:0046928, GO:0007212, GO:0007188]] | \n", + "[[GO:0007186, GO:0007188, GO:0046928, GO:0032225, positive regulation of camp biosynthetic process, GO:0007194, GO:0007212, prostaglandin receptor signaling pathway]] | \n", + "||
| term-GO:0007212-1 | \n", + "[[g protein coupled receptor signaling pathway, g protein beta/gamma subunit complex binding]] | \n", + "[[GO:0007186, dopamine receptor activity, GO:0007188, GO:0004952, GO:0099528, d1 dopamine receptor signaling pathway]] | \n", + "||
| tf-downreg-colorectal-0 | \n", + "[[transcriptional regulation, GO:0006325]] | \n", + "[[transcription regulation, GO:0016569, GO:0032502, GO:0065004, GO:0006950]] | \n", + "||
| tf-downreg-colorectal-1 | \n", + "[[GO:0003677, regulation of transcription, GO:0003682, GO:0008134, GO:0003713, negative regulation of transcription]] | \n", + "[[GO:0003677, transcriptional regulation, GO:0010468, GO:0000988, GO:0003682, GO:0006357, GO:0006355, GO:0000977, GO:0043565, GO:0051090]] | \n", + "||
| ontological_synopsis | \n", + "EDS-0 | \n", + "[[GO:0030199, GO:0030198, GO:0006024, GO:0061448]] | \n", + "[[GO:0030199, GO:0061448, GO:0062023, GO:0030198, GO:0006024]] | \n", + "|
| EDS-1 | \n", + "[[GO:0030199, GO:0030198, GO:0030166, GO:0061448]] | \n", + "[[GO:0030198, GO:0030199, GO:0030166, GO:0006024, GO:0061448]] | \n", + "||
| FA-0 | \n", + "[[GO:0006281, GO:0000724, GO:0006513, fanconi anemia complementation group]] | \n", + "[[GO:0006281, GO:0006513]] | \n", + "||
| FA-1 | \n", + "[[GO:0006281, GO:0006513, GO:0000724, fanconi anemia complementation group, GO:0000785, GO:0005654, GO:0140513]] | \n", + "[[GO:0006281, GO:0006513]] | \n", + "||
| HALLMARK_ADIPOGENESIS-0 | \n", + "[[fad binding activity, GO:0016407, lipid binding activity, coenzyme binding, identical protein binding activity, citrate biosynthetic process]] | \n", + "[[mitochondrial function, GO:0006754, GO:0006629, GO:0005515, GO:0023052]] | \n", + "||
| HALLMARK_ADIPOGENESIS-1 | \n", + "[[mitochondrial respiration, mitochondrial function, GO:0008152, energy production, GO:0022900, GO:0006629, GO:0006631, GO:0006637]] | \n", + "[[GO:0005746, GO:0022900, GO:0006754, GO:0006631, GO:0015746, GO:0016746, dehydrogenase activity, GO:0016491, GO:0022857]] | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[[GO:0005125, GO:0004896, integrin binding activity, GO:0004672, GO:0000988, t-cell receptor binding activity, abc-type peptide antigen transporter activity.\\n\\nmechanism: these genes are involved in various aspects of immune response, including cytokine activity, cytokine receptor activity, and t-cell receptor binding activity. they also play a role in antigen processing and presentation through the abc-type peptide antigen transporter activity. the integrin binding activity reflects the involvement of integrins in leukocyte adhesion and migration. finally, the transcription factor activity reflects the importance of transcriptional regulation in immune responses]] | \n", + "[[GO:0005125, chemokine receptor binding activity, interleukin receptor binding activity, mhc class protein complex binding activity, identical protein binding activity\\n\\nmechanism: these genes are involved in the regulation of the immune response, including the production of cytokines and chemokines, binding to immune receptors, and mhc class protein complex binding. their common function is likely related to the regulation of the immune system and the activation of the immune response against foreign invaders]] | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[[GO:0005125, GO:0008009, mhc class ii protein complex binding activity, signaling receptor binding activity, protein kinase binding activity, integrin binding activity, identical protein binding activity, sh2 domain binding activity, GO:0004252, rna binding activity, GO:0046982, GO:0008083]] | \n", + "[[GO:0005125, chemokine receptor binding activity, GO:0004672, GO:0004896, identical protein binding activity, integrin binding activity, GO:0002376, GO:0005840, GO:0042803, GO:0042110, transcription activator activity, rna polymerase ii-specific. \\n\\nmechanism and hypotheses: these enriched terms suggest that the identified genes are involved in immune system processes such as cytokine signaling, chemokine receptor binding, and t cell activation. protein kinase activity may be involved in signaling pathways downstream of cytokine receptors or chemokine receptors. the presence of ribosome-related terms suggests these genes may play a role in protein synthesis in immune cells. the identified enriched terms point to a central role of the immune system in the functions of these genes, with potential impacts on inflammation, infection, and other immune-related diseases]] | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[[binding activity, GO:0008152, GO:0043167, nucleic acid binding. \\n\\nmechanism: the enriched terms suggest that the listed genes have a common function in binding and metabolic processes. it is possible that these genes are involved in regulating the flow and utilization of energy and molecules within cells]] | \n", + "[[GO:0006468, GO:0035556, GO:0010604]] | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[[GO:0004672, GO:0035556, GO:0000079, GO:0007166]] | \n", + "[[1. binding of metal ions \\n2. protein kinase activity \\n3. positive regulation of protein kinase activity \\n4. cytoskeletal protein binding activity \\n5. signal transduction \\n\\nmechanism: these enriched terms indicate that the genes have a role in signal transduction pathways and cytoskeletal organization. the genes are involved in the binding of metal ions and protein kinases, which are important components of these pathways. additionally, the positive regulation of protein kinase activity suggests that these genes have a role in the amplification of signal transduction through cascade-like pathways]] | \n", + "||
| HALLMARK_ANGIOGENESIS-0 | \n", + "[[extracellular matrix organization; cell adhesion; protein binding; signaling pathway; regulation of cell proliferation.\\n\\nmechanism: the enriched terms suggest that these genes are involved in extracellular matrix organization and cell signaling pathways that regulate cell proliferation and adhesion. many of the genes are structural constituents of the extracellular matrix and influence cell-matrix interactions. others are involved in cell signaling pathways, such as the notch and fibroblast growth factor pathways, that play critical roles in cell proliferation and differentiation. some of the genes have also been implicated in diseases involving abnormal extracellular matrix formation or cell signaling dysregulation, such as ehlers-danlos syndrome, MONDO:0004975, MONDO:0004992]] | \n", + "[[extracellular matrix organization; cell signaling; blood coagulation; lipid metabolism; immunity.\\n\\nmechanism and hypotheses: these genes appear to be involved in a variety of pathways related to extracellular matrix organization, cell signaling, and intercellular communication. specifically, several genes encode proteins that are structural components of the extracellular matrix or interact with extracellular matrix proteins, suggesting a role in tissue development, remodeling, or repair. many of these genes also participate in signaling pathways that control cell proliferation, differentiation, and migration. additionally, several genes are involved in blood coagulation and lipid metabolism, which may be related to their roles in cardiovascular disease. finally, some genes have roles in immunity and host defense against infectious pathogens, possibly contributing to susceptibility or resistance to infectious diseases. overall, these common functions may point to a greater role for extracellular matrix and signaling pathways in disease pathogenesis]] | \n", + "||
| HALLMARK_ANGIOGENESIS-1 | \n", + "[[UBERON:4000022, binding activity]] | \n", + "[[GO:0030198, cell signaling, protein binding activity, GO:1902533, GO:0062023]] | \n", + "||
| HALLMARK_APICAL_JUNCTION-0 | \n", + "[[GO:0007010, GO:0007155, GO:0005102, kinase activity.\\n\\nmechanism: these genes are involved in the maintenance of cell structure and organization through regulation of the cytoskeleton. they also contribute to cell-cell interactions and signaling through receptor binding and kinase activity. a biological pathway that might be involved is the rho gtpase signaling pathway, which regulates actin cytoskeleton dynamics and cell adhesion]] | \n", + "[[actin filament binding activity, integrin binding activity, protein kinase binding activity, sh2 domain binding activity, cell adhesion molecule binding activity, identical protein binding activity, GO:0005096, atp binding activity, cadherin binding activity, collagen binding activity, GO:0051219, GO:0042803]] | \n", + "||
| HALLMARK_APICAL_JUNCTION-1 | \n", + "[[cell adhesion: cdh3, cdh4, cdh6, cdh11, cdh15, cd276, cd209, icam5, icam2, icam1, itga3, itga9, itga10, itgb1, cldn4, cldn5, cldn6, cldn7, cldn8, cldn9, cldn11, cldn14, cldn18, cldn19\\n- protein kinase activity: cdk8, ptk2, syk, taok2, vav2, src\\n- actin filament binding: actn1, actn3, lima1, nexn, calb2, pfn1\\n- metalloendopeptidase activity: adamts5, adam23, mmp2, mmp9\\n- integrin binding: jup, vcam1, slit2]] | \n", + "[[integrin binding activity, cell adhesion molecule binding activity, sh3 domain binding activity, identical protein binding activity, actin filament binding activity, protein kinase binding activity]] | \n", + "||
| HALLMARK_APICAL_SURFACE-0 | \n", + "[[GO:0007165, cell surface receptor activity, protein binding activity]] | \n", + "[[GO:0005886, GO:0005615, signaling receptor binding activity, protein domain specific binding activity, protein kinase binding activity, GO:0006811, GO:0051247, GO:0010468, GO:0007155, GO:1902531]] | \n", + "||
| HALLMARK_APICAL_SURFACE-1 | \n", + "[[GO:0005886, GO:0009986, GO:0055085, GO:0038023, positive regulation of transcription, GO:0010468, GO:0006468, GO:0005615]] | \n", + "[[GO:0010468, signaling receptor binding activity, GO:0045944, GO:2001234, GO:0006811, GO:0060244, GO:0051965, carbohydrate binding activity, GO:1902531, GO:1904054]] | \n", + "||
| HALLMARK_APOPTOSIS-0 | \n", + "[[GO:0006915, GO:0005125, transcription factor binding activity. \\n\\nmechanism/]] | \n", + "[[GO:0097190, GO:0006955, GO:0005125, identical protein binding activity, protease binding activity, enzyme binding activity, GO:0000988, dna binding activity]] | \n", + "||
| HALLMARK_APOPTOSIS-1 | \n", + "[[GO:0006915, GO:0005125, GO:0010941, GO:2001233, GO:0001819, GO:0042981, GO:0043067, positive regulation of apoptotic process.\\n\\nmechanism: these genes are involved in apoptotic signaling and cytokine activity, which suggests that they play a role in regulating cell death and programmed cell death. the enriched terms suggest that these genes may be regulated by shared signaling pathways or transcriptional programs that control apoptosis and cytokine production. one potential underlying mechanism could involve the activation of pro-apoptotic proteins in response to cellular stress or damage, leading to the release of cytokines that further promote cell death. alternatively, these genes may be involved in controlling the balance between cell survival and death in response to external cues such as cytokine signaling or nutrient availability. further research is needed to fully elucidate the molecular mechanisms underlying these gene functions]] | \n", + "[[apoptotic process; cytokine activity; protein binding activity.\\n\\nmechanism: the genes in this list are involved in processes related to cell death, GO:0006955, and molecular interactions. the enriched terms suggest that these genes may be involved in pathways related to apoptosis, cytokine signaling, protein interactions. it is possible that these genes contribute to the regulation of cell death through cytokine-mediated signaling pathways protein-protein interactions]] | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[[GO:0006629, GO:0030301, GO:0006633]] | \n", + "[[cholesterol binding activity, GO:0016887, GO:0005319, GO:0008559, atp binding activity, GO:0007031, vitamin d receptor binding activity, GO:0042626]] | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[[GO:0030301, GO:0015908, GO:0007031, GO:0004467, GO:0008123, atp binding activity, ubiquitin-dependent protein binding activity. \\n\\nmechanism: these genes are likely involved in the regulation and transport of lipids, particularly cholesterol and long-chain fatty acids, in cells and tissues. peroxisomal proteins and functions may also play a role in this process, including in the regulation of lipid metabolism]] | \n", + "[[GO:0008610, GO:0006631, GO:0008203, GO:0007031, GO:0015908, peroxisome matrix targeting, abc-type transporter activity. \\n\\nmechanism]] | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[[GO:0042632, GO:0008610, GO:0010883, phospholipid binding activity, fatty acid binding activity, low-density lipoprotein particle binding activity, more]] | \n", + "[[GO:0006695, GO:0008610, GO:0019216, GO:0042632, GO:0090181]] | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[[GO:0006695, GO:0008299, GO:0055088, GO:0006646, GO:0000122, GO:0045944, GO:0070458, GO:0001676]] | \n", + "[[GO:0006695, GO:0008299, GO:0006633]] | \n", + "||
| HALLMARK_COAGULATION-0 | \n", + "[[GO:0006508, complement pathways, GO:0007596, GO:0007155]] | \n", + "[[GO:0006956, GO:0050817, GO:0008237]] | \n", + "||
| HALLMARK_COAGULATION-1 | \n", + "[[GO:0006508, GO:0007596, GO:0006956, negative regulation of proteolysis. \\n\\nmechanism: the enriched terms suggest that these genes are involved in the regulation of proteolytic activity in several biological processes, including blood coagulation and immune response]] | \n", + "[[metalloendopeptidase activity; serine-type endopeptidase activity; protease binding activity; identical protein binding activity; complement binding activity \\n\\nmechanism and hypotheses: these enriched terms suggest that the common mechanism or pathway involves the regulation of proteolysis and immune response, particularly the complement system. metalloendopeptidase and serine-type endopeptidase activity are involved in the proteolytic degradation of various extracellular matrix components including collagen, GO:0005577, and proteoglycan, as well as destruction of pathogenic microorganisms during immune response. protease binding activity, identical protein binding activity, and complement binding activity are involved in protein-protein interactions that regulate proteolysis and activation of complement components. therefore, the hypothesis is that the common mechanism of these genes is related to the regulation of proteolysis and complement system activity]] | \n", + "||
| HALLMARK_COMPLEMENT-0 | \n", + "[[GO:0004867, protease binding activity, enzyme binding activity, calcium ion binding activity]] | \n", + "[[GO:0005515, GO:0046872, GO:0019899, GO:0042802, GO:0005524, GO:0003677, calcium ion binding. \\n\\nmechanism]] | \n", + "||
| HALLMARK_COMPLEMENT-1 | \n", + "[[GO:0005515, GO:0019899, GO:0005488, GO:0004175, metal ion binding.\\n\\nmechanism: the enriched terms suggest that these genes play a role in protein-protein interactions and enzymatic reactions involving metal ions]] | \n", + "[[GO:0004222, GO:0004252, complement binding activity, heparin binding activity, GO:0008234, GO:0004869, GO:0005201, serine-type endopeptidase inhibitor activity involved in apoptotic process, GO:0004722, MESH:D011809]] | \n", + "||
| HALLMARK_DNA_REPAIR-0 | \n", + "[[GO:0006281, GO:0097747, nucleotide metabolism. \\n\\nmechanism: these genes are predominantly involved in regulating dna replication, transcription, and repair. they may also play roles in the metabolism of nucleotides and nucleotide analogs that target dna synthesis. the enrichment of terms related to rna polymerase may reflect the closely intertwined nature of dna and rna synthesis]] | \n", + "[[dna binding activity, transcription initiation, rna binding activity, GO:0009117, rna splicing. \\n\\nmechanism: these genes are likely involved in regulating dna replication, transcription, and various steps in rna processing, including splicing and export from the nucleus. they could also be involved in nucleotide metabolism and/or maintaining genomic stability]] | \n", + "||
| HALLMARK_DNA_REPAIR-1 | \n", + "[[GO:0006260, GO:0006281, rna transcription]] | \n", + "[[GO:0003677, GO:0003723, GO:0009117, GO:0006281, transcription initiation, protein-macromolecule adaptor activity.\\n\\nmechanism: these genes work together to maintain the integrity and expression of genetic information, with a focus on dna-related processes]] | \n", + "||
| HALLMARK_E2F_TARGETS-0 | \n", + "[[GO:0006260, GO:0051726, GO:0006325]] | \n", + "[[GO:0006260, GO:0006281, GO:0051726, GO:0003682, GO:0005524, GO:0019899, GO:0042393, GO:0043130]] | \n", + "||
| HALLMARK_E2F_TARGETS-1 | \n", + "[[dna binding activity, protein binding activity, enzyme binding activity, chromatin binding activity, atp binding activity, histone binding activity, rna binding activity, identical protein binding activity]] | \n", + "[[dna binding activity, chromatin binding activity, rna binding activity, enzyme binding activity, GO:0042803, single-stranded dna binding activity, identical protein binding activity, histone binding activity, atp binding activity, cyclin binding activity, nucleic acid binding activity]] | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[[GO:0005201, integrin binding activity, collagen binding activity, identical protein binding activity, fibrinogen binding activity, protease binding activity]] | \n", + "[[GO:0005201, collagen binding activity, heparin binding activity, GO:0005125, GO:0008083, signaling receptor binding activity, wnt-protein binding activity]] | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[[GO:0005201, collagen binding activity, integrin binding activity, heparin binding activity, GO:0008237, signaling receptor binding activity.\\n\\nmechanism: these genes are involved in the maintenance and formation of the extracellular matrix, which provides structural support to cells and tissues. they play a role in cell adhesion, signaling, and migration through interactions with the extracellular matrix. the enriched binding activities suggest that these genes are involved in extracellular matrix remodeling and regulation of growth factor signaling. metallopeptidase activity may be involved in the degradation of extracellular matrix components]] | \n", + "[[collagen binding activity, integrin binding activity, heparin binding activity, GO:0005201, GO:0008237, platelet-derived growth factor binding activity, GO:0008009, fibronectin binding activity, GO:0004867]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[[GO:0005509, GO:0000166, enzyme binding activity, MESH:D048788, gene transcription, GO:0006811]] | \n", + "[[GO:0004888, GO:0022857, GO:0001216]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[[GO:0005515, GO:0000988, transmembrane transporter activity.\\n\\nmechanism: the enriched terms suggest that the genes on the list are involved in various cellular processes that require protein-protein interaction, transcriptional regulation, and transmembrane transport of substances. a possible hypothesis is that these genes play a role in signal transduction and regulation of gene expression]] | \n", + "[[GO:0007165, transcriptional regulation, GO:0003824, GO:0038023, GO:0003676, GO:0007154, GO:0042445, protein-protein interaction\\n\\nhypotheses: the enriched terms suggest that the genes in this list are involved in various aspects of signaling and transcriptional regulation. they may function in pathways such as cell signaling, hormone metabolism, and protein-protein interaction. this list includes genes encoding enzymes with specific activities, as well as receptor and nucleic acid binding proteins that are crucial for signaling and transcriptional regulation]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[[GO:0022857, protein binding activity]] | \n", + "[[enzyme binding activity, identical protein binding activity, calcium ion binding activity, GO:0005215, phosphorylation-dependent protein binding activity, atpase binding activity, GO:0004930, GO:0004712, nucleotide binding activity, ubiquitin protein ligase binding activity, transcription factor binding activity, histone deacetylase binding activity, GO:0016787, GO:0016491]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[[(1) enzymatic activity; (2) binding activity; (3) transcription regulation. \\n\\nmechanism: these genes likely play roles in various biological pathways, such as metabolism, cell signaling, and gene expression regulation. given the enrichment in enzymatic activity, it is possible that some of these genes are involved in metabolic pathways, such as lipid metabolism. the enrichment in binding activity may reflect the importance of protein-protein interactions and signaling cascades in cellular processes. the enrichment in transcription regulation suggests that many of these genes may be key players in regulating gene expression and ultimately cell fate]] | \n", + "[[binding activity, GO:0005215, enzyme binding activity, identical protein binding activity, protein kinase binding activity, GO:0004930]] | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[[GO:0047617, GO:0006631, GO:0120227, GO:0008289, GO:0004467, GO:0006099, GO:0046356]] | \n", + "[[fatty acid-coa ligase activity, GO:0003995, long-chain fatty acid binding activity, GO:0003985, GO:0016615, GO:0000104, GO:0016616]] | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[[GO:0016491, binding activity, GO:0006631, GO:0006084, heme-binding activity]] | \n", + "[[GO:0003824, GO:0016491, GO:0006631, GO:0006629, metabolic pathways. \\n\\nmechanism: these genes may be involved in the regulation of lipid and fatty acid metabolism, potentially through oxidation-reduction processes and metabolic pathways]] | \n", + "||
| HALLMARK_G2M_CHECKPOINT-0 | \n", + "[[dna binding activity, chromatin binding activity, protein binding activity, enzyme binding activity, histone binding activity, GO:0003714]] | \n", + "[[dna binding activity, transcription regulation, GO:0004672, protein binding activity, GO:0016570]] | \n", + "||
| HALLMARK_G2M_CHECKPOINT-1 | \n", + "[[dna-binding transcription factor activity; protein kinase activity; microtubule binding activity. \\n\\nmechanism: these genes are likely involved in the regulation of gene expression, cell cycle progression, and cytoskeletal dynamics through the binding and modification of dna, MESH:D011506, and microtubules. specifically, they may be involved in processes such as transcriptional regulation, dna replication and repair, GO:0007059, GO:0051301]] | \n", + "[[dna-binding transcription factor, GO:0004672, protein binding activity, GO:0140014, GO:0006260, GO:0010467]] | \n", + "||
| HALLMARK_GLYCOLYSIS-0 | \n", + "[[GO:0008378, GO:0015020, n-acetylglucosamine sulfotransferase activity, GO:0035250, glucosaminyl-proteoglycan 3-beta-glucosyltransferase activity, GO:0016758, GO:0045130, GO:0016779]] | \n", + "[[GO:0008194, GO:0008146, GO:0008378, GO:0015020, GO:0004553, heparan sulfate binding activity, several others]] | \n", + "||
| HALLMARK_GLYCOLYSIS-1 | \n", + "[[GO:0005975, GO:0006024, GO:0006493]] | \n", + "[[enzyme binding activity, GO:0008194, atp binding activity, GO:0008378, GO:0004340, fructose binding activity, heme binding activity, GO:0016787, rna binding activity, identical protein binding activity, GO:0046983, nucleoside triphosphate activity]] | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[[GO:0006357, GO:0016525, GO:0007155, GO:0030036, GO:0010604, GO:0007411, GO:0030336]] | \n", + "[[GO:0032502, GO:0007165, MESH:D005786]] | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[[GO:0007165, GO:0007155, GO:0007399, transcription regulation]] | \n", + "[[GO:0007155, transcription regulation, GO:0007165, negative regulation, positive regulation]] | \n", + "||
| HALLMARK_HEME_METABOLISM-0 | \n", + "[[GO:0020037, GO:0015075, protein binding activity, GO:0000988]] | \n", + "[[GO:0005215, binding activity, GO:0003824]] | \n", + "||
| HALLMARK_HEME_METABOLISM-1 | \n", + "[[transmembrane transport; protein binding activity; metal ion binding activity; dna-binding transcription activator activity\\n\\nmechanism: these genes are involved in various transport and binding activities, especially transmembrane transport, indicating a possible importance in cellular trafficking and signaling pathways. additionally, they exhibit a significant enrichment in protein and metal ion binding activities, which may suggest a role in protein-protein interactions and redox reactions, respectively. finally, dna-binding transcription activator activity is found to be enriched, indicating that these genes may regulate gene expression]] | \n", + "[[enzyme binding activity, protein domain specific binding activity, GO:0046982, identical protein binding activity, GO:0042803]] | \n", + "||
| HALLMARK_HYPOXIA-0 | \n", + "[[enzyme binding activity, GO:0005515, GO:0003700, carbohydrate binding activity, signaling receptor binding activity, identical protein binding activity, atp binding activity, nad binding activity, phosphoprotein binding activity, metal ion binding activity, GO:0003924, GO:0008083, GO:0008194, phospholipid binding activity, platelet-derived growth factor binding activity]] | \n", + "[[enzyme binding activity, protein kinase binding activity, identical protein binding activity, GO:0003700, GO:0004674, calcium ion binding activity, nucleic acid binding activity, atp binding activity, GO:0060422, gtp binding activity, GO:0004340, GO:0005353, GO:0008459, heparin binding activity, apolipoprotein binding activity]] | \n", + "||
| HALLMARK_HYPOXIA-1 | \n", + "[[GO:0006006, GO:0016301, transcriptional regulation, GO:0023052]] | \n", + "[[GO:0042802, GO:0019899, GO:0005524, GO:0019901, GO:0005509, GO:0005102, GO:0015035, GO:0016538, GO:0008083, GO:0005353, GO:0004347, nadph binding activity, GO:0042803, MESH:D013213]] | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[[GO:0005125, interleukin receptor binding activity, cytokine binding activity, GO:0031295, GO:0051250, GO:0006952, GO:0006955, interleukin binding activity]] | \n", + "[[GO:0042802, GO:0003700, GO:0005125, GO:0005096, interleukin receptor binding activity, ubiquitin protein ligase activity.\\n\\nmechanism: these genes likely play a role in regulating various cell signaling pathways, including cytokine and growth factor signaling, as well as intracellular protein degradation via ubiquitin-proteasome system]] | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[[GO:0004896, interleukin binding activity, identical protein binding activity, gtp binding activity, GO:0001216, protein kinase binding activity, atp binding activity, GO:0016787, collagen binding activity, small gtpase binding activity, GO:0061630, GO:0004197, GO:0005215, rna binding activity, calcium ion binding activity, signaling receptor binding activity, GO:0005125, GO:0008083, enzyme binding activity, several others.\\n\\nmechanism: these genes are involved in immune response cytokine activity. many of them encode for cytokine receptors, transcription factors, enzymes involved in immune system pathways processes. the enrichment of terms related to protein binding, including dna binding identical protein binding, may suggest that many of these genes act as transcriptional regulators in immune cells, coordinating the expression of genes involved in immune function. the enrichment of transporter activity may indicate that some of these genes are involved in cell migration or trafficking of immune cells to sites of inflammation or infection. additionally, the enrichment of terms related to enzyme activity may suggest that some of]] | \n", + "[[GO:0004896, protein binding activity, GO:0003824, dna binding activity, rna binding activity, apoptosis. \\n\\nmechanism: these genes are involved in various cellular processes such as signaling and cytokine receptor activity, where they play a role in transmitting signals from the outside to the inside of the cell, as well as in regulating the immune system. they are also involved in enzyme activity, dna and rna binding activity, and apoptosis, playing a role in various pathways such as the regulation of gene expression and programmed cell death]] | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[[GO:0005125, GO:0004896, protein kinase binding activity, GO:0006954, GO:0006955, GO:0007165]] | \n", + "[[GO:0004896, GO:0004896, growth factor receptor binding activity]] | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[[GO:0004896, interleukin binding activity, GO:0008009, GO:0001819, GO:0050778, GO:0098542, GO:0010604]] | \n", + "[[GO:0005125, signaling receptor binding activity, GO:0001819, GO:0019221, GO:0009967, GO:0004896, GO:0050776]] | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[[GO:0005125, GO:0008009, identical protein binding activity, GO:0038023, GO:0006811]] | \n", + "[[GO:0005125, GO:0004896, GO:0004930, GO:0002376, GO:0006954, GO:0008009]] | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[[GO:0004930, GO:0004896, enzyme binding activity, identical protein binding activity, GO:0007165, calcium ion binding activity, protease binding activity, transporter activity.\\n\\nmechanism: these genes are involved in various mechanisms related to cell signaling and transport. one hypothesis is that these genes may collectively contribute to the regulation of calcium levels and calcium-dependent signaling pathways, as well as cytokine-mediated signaling pathways involved in immune response]] | \n", + "[[GO:0004896, GO:0004930, signaling receptor binding activity, identical protein binding activity, enzyme binding activity]] | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[[GO:0005125, GO:0098542, GO:0046597, rna binding activity, identical protein binding activity]] | \n", + "[[GO:0006955, GO:0019882, cytokines/chemokines, interferon-related genes, rna processing/editing]] | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[[GO:0098542, GO:0050709, GO:0046597, GO:0045071, GO:0030501, GO:0002688, regulation of transcription]] | \n", + "[[GO:0098542, GO:0045071, GO:0035458, GO:0071345, GO:0042590, GO:0006469, GO:0010604, GO:0046597, GO:0019221, GO:0045669, GO:0052548]] | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[[GO:0004896, GO:0000981, identical protein binding activity, enzyme binding activity, GO:0042110, cell adhesion molecule binding activity, positive regulation of activated cd8-positive t cell proliferation, GO:0038187, GO:0061630, GO:0000166, GO:0004930, protein kinase binding activity, calcium ion binding activity, complement binding activity, GO:0004867, GO:0008009, integrin binding activity.\\n\\nmechanism: these genes predominantly function in the immune system and are related to the activation and proliferation of t cells, cytokine signaling, pattern recognition, and complement cascades. the enriched terms suggest an association with signaling cascades, receptor binding, enzyme activity, and immune response to pathogens]] | \n", + "[[GO:0005125, GO:0008009, GO:0001216, enzyme binding activity, identical protein binding activity, protease binding activity, GO:0042803, rna binding activity, GO:0050852, GO:0061630]] | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[[GO:0019882, GO:0045087, cytokine signaling, GO:0045321, antiviral defense]] | \n", + "[[GO:0019882, cytokine signaling, antiviral defense]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[[calcium ion binding activity, atp binding activity, GO:0008511, GO:0004930, GO:0004888, GO:0016887, identical protein binding activity, protein kinase binding activity]] | \n", + "[[GO:0003824, protein binding activity, GO:0000988, identical protein binding activity, ion binding activity.\\n\\nmechanism]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[[protein binding activity, calcium ion binding activity, atp binding activity, identical protein binding activity, GO:0008507, GO:0005337, GO:0043273, GO:0003924, GO:0015432]] | \n", + "[[GO:0005488, GO:0003824, GO:0004930, GO:0000988, GO:0005509, GO:0005524, protein homodimerization activity.\\n\\nmechanism: the enriched terms suggest that these genes are involved in cellular regulation and signaling processes through binding and enzymatic activities, particularly involving calcium ions and atp. many genes also have transcription factor activity, indicating a role in gene expression regulation. g protein-coupled receptor activity is also overrepresented, suggesting a role in cellular signaling processes]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[[binding activity; enzyme activity; transcription activator activity. \\n\\nmechanism: these enriched terms suggest that the commonality among these genes is that they are involved in various types of binding and enzymatic activities, as well as regulating transcription. it is possible that these genes work together in regulatory pathways to bind to specific targets, catalyze reactions, modulate transcriptional activity in the cell]] | \n", + "[[GO:0005515, enzyme binding activity, transcriptional regulation, ion binding activity, dna binding activity, GO:0004930, GO:0005125, identical protein binding activity]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[[GO:0005178, GO:0005515, GO:0005524, GO:0071345, GO:0043167, ubiquitin protein ligase binding. \\n\\nmechanism: the shared function of binding among the enriched terms suggests that these genes may play a role in mediating protein regulation and signal transduction pathways through protein-protein or protein-ligand interactions. the involvement in cellular response to cytokine stimulus may suggest a potential role in modulating immune responses]] | \n", + "[[enzymatic activity, GO:0019901, binding activity\\n\\nmechanism: the enriched functions suggest that these genes may be involved in the regulation of cellular processes through protein-protein interactions, including enzymatic activities and binding activities. this could involve pathways such as signal transduction or gene expression regulation]] | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[[microtubule binding activity, GO:0005096, actin filament binding activity, microtubule plus-end binding activity, identical protein binding activity, protein kinase binding activity, kinetochore binding activity, cytoskeletal protein binding activity, gamma-tubulin binding activity]] | \n", + "[[microtubule binding activity, actin binding activity, GO:0005096]] | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[[microtubule binding activity, GO:0007052, GO:0000226]] | \n", + "[[GO:0008017, mitotic processes, GO:0000910, GO:0007018, spindle organization. \\n\\nmechanism: these genes play important roles in the regulation and organization of microtubules, which are key components of the cytoskeleton involved in cell division processes such as mitosis and cytokinesis. the enrichment of terms related to microtubule binding and regulation suggest that these genes may function together in a pathway that regulates the dynamics and organization of microtubules during these cellular processes. they may also be involved in microtubule-based movement, which is crucial for various cellular activities such as intracellular transport and cell migration]] | \n", + "||
| HALLMARK_MTORC1_SIGNALING-0 | \n", + "[[binding activity, enzymatic activity, GO:0006412, GO:0023052, GO:0008152]] | \n", + "[[GO:0005515, GO:0003723, enzymatic activity, structural constituent of cytoskeleton. \\n\\nmechanism: these genes likely play a role in cellular processes such as transcription, translation, protein folding, and cytoskeletal organization]] | \n", + "||
| HALLMARK_MTORC1_SIGNALING-1 | \n", + "[[GO:0005515, enzyme activity. \\n\\nmechanism: the enriched terms suggest that these genes play a role in protein-protein interactions and enzymatic reactions, potentially involved in metabolic pathways or signal transduction cascades]] | \n", + "[[GO:0006457, GO:0005783, ubiquitin-proteasome system, GO:0015031, GO:0030163]] | \n", + "||
| HALLMARK_MYC_TARGETS_V1-0 | \n", + "[[ribosome binding activity; rna binding activity; translation initiation factor activity; protein folding chaperone activity\\n\\nmechanism: these genes are involved in different aspects of protein synthesis, such as ribosome binding, GO:0006413, and rna binding. they also contribute to protein folding processes as chaperones. the enrichment of these terms suggests that these genes function together to ensure proper protein synthesis and folding, which are vital to numerous cellular processes]] | \n", + "[[GO:0003743, ribosome binding activity, rna binding activity, GO:0003735, protein folding chaperone activity, GO:0140713]] | \n", + "||
| HALLMARK_MYC_TARGETS_V1-1 | \n", + "[[GO:0006396, GO:0003676, GO:0006457, ribosomal structural activity. \\n\\nmechanism: these genes likely function together in the post-transcriptional regulation of gene expression, from rna splicing to translation initiation and ribosome assembly]] | \n", + "[[GO:0000394, GO:0006413, GO:0003723, GO:0003676, GO:0006457, ribosome structure\\n\\nmechanism: these genes are involved in rna processing, including mrna splicing and translation initiation, as well as binding to rna and nucleic acids. some genes also play roles in protein folding and ribosome structure. the underlying biological mechanism or pathway is likely related to rna processing and regulation of gene expression]] | \n", + "||
| HALLMARK_MYC_TARGETS_V2-0 | \n", + "[[GO:0006364, rna binding activity, GO:0046982, mitochondrial function, GO:0051726]] | \n", + "[[GO:0006364, GO:0042273, snorna binding activity, GO:0005730, rna binding activity]] | \n", + "||
| HALLMARK_MYC_TARGETS_V2-1 | \n", + "[[GO:0006364, snorna binding activity, GO:0042273, rna binding activity, GO:0005730]] | \n", + "[[GO:0006364, ribosomal biogenesis, rna binding activity, GO:0005730]] | \n", + "||
| HALLMARK_MYOGENESIS-0 | \n", + "[[cytoskeletal protein binding activity, actin binding activity, atp binding activity, calcium ion binding activity, identical protein binding activity, enzyme binding activity, GO:0042803]] | \n", + "[[actin binding activity, calcium ion binding activity, atp binding activity, identical protein binding activity, cytoskeletal protein binding activity, enzyme binding activity, UBERON:0005090]] | \n", + "||
| HALLMARK_MYOGENESIS-1 | \n", + "[[actin binding activity, cytoskeletal protein binding activity, calcium ion binding activity, myosin binding activity, atp binding activity, kinase binding activity, muscle structure development. \\n\\nmechanism: these genes are involved in muscle structure and function as they encode proteins that bind to actin, myosin, and other cytoskeletal proteins to form the muscle fibers. they also bind to calcium ions and atp, which are necessary for muscle contraction, and contribute to the development of muscle structure]] | \n", + "[[GO:0006936, GO:0030036, GO:0006600, GO:0032956, regulation of muscle contraction.\\n\\nmechanism: these genes are involved in the regulation of muscle contraction and actin cytoskeleton organization, likely through their roles in calcium ion binding, myosin light chain kinase activity, and actin filament binding. several of the genes are also involved in creatine metabolism, which is important for energy generation in muscle tissues]] | \n", + "||
| HALLMARK_NOTCH_SIGNALING-0 | \n", + "[[GO:0007219, GO:0016567]] | \n", + "[[GO:0007219, GO:0016567, GO:0006357, GO:0051247, GO:0016055, scf-dependent proteasomal ubiquitin-dependent protein catabolic process, cyclin-dependent protein kinase holoenzyme complex]] | \n", + "||
| HALLMARK_NOTCH_SIGNALING-1 | \n", + "[[\"notch signaling pathway,\" \"protein ubiquitination,\" \"negative regulation of cell differentiation,\" \"regulation of dna-templated transcription.\"]] | \n", + "[[GO:0007219, GO:0016567]] | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[[GO:0022900, GO:0006119, mitochondrial metabolism, GO:0006637, ketone body metabolism.\\n\\nmechanism and]] | \n", + "[[GO:0009055, ubiquitin protein ligase binding activity, MESH:D014451, rna binding activity, GO:0042803, metal ion binding activity.\\n\\nmechanism and]] | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[[GO:0005746, GO:0006118, GO:0006754, MESH:D009245, MESH:D003576, GO:0016467, flavin adenine dinucleotide]] | \n", + "[[mitochondria\\n- atp synthesis\\n- respiratory chain complex\\n- electron transfer\\n- oxidoreductase activity\\n- iron-sulfur cluster binding\\n\\nmechanism: these genes are involved in the regulation of metabolic processes and energy production in the mitochondria. they play important roles in cellular respiration, which involves the conversion of nutrients into energy necessary for cellular activities. the enriched terms suggest that these genes are closely related to the function of the mitochondrial respiratory chain complex and atp synthase, both of which are necessary for energy production in the form of atp. additionally, several of these genes are involved in electron transfer and oxidoreductase activity, which are also important in metabolic processes that lead to energy production. finally, there is a common theme of iron-sulfur cluster binding, which suggests a common mechanism in the regulation of metabolic processes and energy production]] | \n", + "||
| HALLMARK_P53_PATHWAY-0 | \n", + "[[GO:0042981, protein binding activity, GO:0003700]] | \n", + "[[GO:0003677, GO:0005515, GO:0003824, GO:0000988, growth factor activity. \\n\\nmechanism: these genes likely play roles in regulating transcription, protein-protein interactions, metabolism, and growth factor signaling pathways]] | \n", + "||
| HALLMARK_P53_PATHWAY-1 | \n", + "[[GO:0000988, rna binding activity, enzyme binding activity, identical protein binding activity, dna binding activity, histone binding activity]] | \n", + "[[GO:0005515, dna binding activity, GO:0016301]] | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[[GO:0006006, GO:0030073, GO:0006357]] | \n", + "[[GO:0042593, GO:0050796, GO:0046326, GO:0006006]] | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[[GO:0006006, GO:0030073, glucose homeostasis.\\n\\nmechanism]] | \n", + "[[GO:0030073, GO:0006006, transcriptional regulation, transcription factor binding activity, rna polymerase ii-specific dna binding activity, GO:0000122, positive regulation of transcription by rna polymerase ii. \\n\\nmechanism and]] | \n", + "||
| HALLMARK_PEROXISOME-0 | \n", + "[[GO:0006629, GO:0006631, GO:0006810, GO:0003824, GO:0005501, steroid binding.\\n\\nmechanism and]] | \n", + "[[GO:0001676, GO:0043574, GO:0008203, GO:0006633, lipid binding activity, atp binding activity, GO:0016491]] | \n", + "||
| HALLMARK_PEROXISOME-1 | \n", + "[[GO:0004467, GO:0016401, GO:0047676, GO:0031957, peroxisome targeting sequence binding activity, GO:0006633]] | \n", + "[[GO:0006629, mitochondrial function, GO:0006281]] | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[[GO:0004672, cytoskeleton structure, GO:0006629, protein binding activity]] | \n", + "[[GO:0004672, g protein-coupled receptor binding activity, transcription factor binding activity, enzyme binding activity, GO:0007166, GO:0035556, GO:0032007, GO:0010971, negative regulation of vasc, negative regulation of nitrogen com, actin filament binding activity, cytoskeletal protein binding activity]] | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[[GO:0006468, intracellular signaling, GO:0016301, GO:0016791, enzyme binding activity. \\n\\nmechanism: the enriched terms suggest that many of the genes are involved in regulatory processes related to protein modification through phosphorylation and dephosphorylation. this could implicate several signaling pathways, such as mapk, pi3k/akt, and nf-kappab pathways]] | \n", + "[[GO:0006468, GO:0035556, GO:0016301, enzyme binding activity, GO:0004672, identical protein binding activity, scaffold protein binding activity]] | \n", + "||
| HALLMARK_PROTEIN_SECRETION-0 | \n", + "[[GO:0007030, GO:0006888, retrograde transport, vesicle recycling, GO:0090110, GO:0006891, GO:0008333, GO:0006893, GO:0048488, GO:0016192, vesicle recycling]] | \n", + "[[GO:0007030, GO:0048193, GO:0090110, GO:0006888, retrograde transport, vesicle recycling, GO:0034260, negative regulation of autophagosome formation and maturation, GO:1905604, GO:1905280, GO:0002091, GO:0009967]] | \n", + "||
| HALLMARK_PROTEIN_SECRETION-1 | \n", + "[[GO:0048193, GO:0032456, GO:0035493, GO:0006891, GO:0070836]] | \n", + "[[GO:0006888, GO:0048193, GO:0006891, GO:0034067, snare complex assembly.\\n\\nmechanism and]] | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[[GO:0098869, GO:0006750, GO:0042744, oxidation-reduction process, GO:0006979]] | \n", + "[[cellular redox homeostasis, GO:0006979, protein disulfide reduction, GO:0006749, GO:0003954, GO:0004601, GO:0006826, GO:0016209, MESH:D015227]] | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[[GO:0045454, GO:0006979, GO:0016209, GO:0004602, GO:0004784, GO:0004601, GO:0003954, GO:0032981]] | \n", + "[[GO:0045454, GO:0006979]] | \n", + "||
| HALLMARK_SPERMATOGENESIS-0 | \n", + "[[GO:0005515, GO:0005524, GO:0042802, GO:0016301, GO:0000166]] | \n", + "[[GO:0005515, GO:0016301, GO:0051726, GO:0010467]] | \n", + "||
| HALLMARK_SPERMATOGENESIS-1 | \n", + "[[identical protein binding activity, protein folding chaperone binding activity, GO:0004672, rna binding activity, chromatin binding activity, atp binding activity, nucleotide binding activity, GO:0004722, GO:0061630, calcium ion binding activity, rna polymerase iii binding activity, cytokine binding activity, GO:0004930, integrin binding activity, many others]] | \n", + "[[GO:0005515, GO:0008047, atp binding activity]] | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[[GO:0007178, GO:0010862, GO:0010991, GO:0045668, GO:0030512, GO:0010604, GO:0009967]] | \n", + "[[GO:0060395, GO:0006357, GO:0010604, GO:0090101, GO:0045668, establishment of sert, positive regulation of vascular associated smooth muscle cell proliferat, several others]] | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[[signal transduction; regulation of gene expression; transcription regulation; protein phosphorylation; smad protein signal transduction.\\n\\nmechanism: these genes are involved in various aspects of signal transduction, including regulation of gene expression, transcription regulation, MESH:D016212, where they regulate transcription of target genes. genes in this list may activate or inhibit smad signaling and affect downstream transcriptional regulation. additionally, many of these genes play roles in other signaling pathways and regulatory processes, such as the wnt signaling pathway and negative regulation of protein degradation]] | \n", + "[[GO:0005024, GO:0046332, GO:0009967, GO:0006357, GO:0000122, GO:0007166, GO:0010604, nucleic acid binding activity]] | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[[GO:0005125, GO:0003700, enzyme binding activity, GO:0006955]] | \n", + "[[GO:0003700, rna polymerase ii-specific; cytokine activity; protein binding activity.\\n\\nmechanism: these genes are involved in the regulation of transcription and cytokine activity, likely playing a role in immune responses and cellular differentiation. they are involved in binding to dna and rna polymerases to regulate the expression of genes, as well as in the production and regulation of cytokines and growth factors that play a role in cell signaling and differentiation]] | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[[cytokine activity; dna-binding transcription factor activity; enzyme binding activity; phosphatidylinositol-3,4-bisphosphate binding activity; g protein-coupled receptor activity.\\n\\nmechanism: the enriched terms suggest that the genes on the list are involved in signaling pathways that regulate gene expression and cellular responses through cytokine receptors, GO:0035556, and various enzymatic activities. these pathways play essential roles in several biological processes, including immune responses, cell differentiation and development, cell survival death]] | \n", + "[[GO:0005125, GO:0008009, GO:0001216, GO:0006955, interleukin-12 alpha subunit binding activity, GO:0004707, protein kinase binding activity, GO:0001817, GO:0002682, smad binding activity, transcription factor binding activity]] | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[[protein folding and processing, GO:0015031, GO:0003723, GO:0043022, GO:0003743]] | \n", + "[[protein folding and chaperone activity, rna binding and transcriptional regulation, rna processing and degradation]] | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[[rna binding activity, protein folding chaperone binding activity, ribosome binding activity, histone binding activity, dna-binding transcription factor binding activity, ubiquitin protein ligase binding activity]] | \n", + "[[GO:0003723, GO:0051087, GO:0090304, endoplasmic reticulum stress response pathway]] | \n", + "||
| HALLMARK_UV_RESPONSE_DN-0 | \n", + "[[extracellular matrix organization; growth factor signaling; regulation of transcription, dna-templated; positive regulation of protein kinase activity; organic acid metabolic process.\\n\\nmechanism: these genes are involved in extracellular matrix structural constituent, growth factor signaling, GO:0000988, GO:0005515, and nucleotide binding. this suggests that they may be involved in the regulation of gene transcription, cellular growth and differentiation, and the organization of extracellular matrices. a hypothesis for the underlying biological mechanism or pathway is that these genes may be involved in the regulation of extracellular matrix formation and growth factor signaling pathways, which then contribute to cellular differentiation and growth. additionally, the binding of proteins with transcription factor activity and nucleotide binding activity suggests that these genes are involved in the regulation of gene transcription, which may have downstream effects on cellular function and behavior]] | \n", + "[[GO:0005201, identical protein binding activity, enzyme binding activity, smad binding activity]] | \n", + "||
| HALLMARK_UV_RESPONSE_DN-1 | \n", + "[[GO:0005201, GO:0005178, identical protein binding activity, protease binding activity, calcium binding, platelet-derived growth factor binding activity]] | \n", + "[[GO:0005201, GO:0005515, GO:0016563, GO:0005102]] | \n", + "||
| HALLMARK_UV_RESPONSE_UP-0 | \n", + "[[enzyme binding activity, protein kinase binding activity, GO:0042803, rna binding activity, atp binding activity, identical protein binding activity, ubiquitin protein ligase binding activity, GO:0001228, ion binding activity, g protein-coupled receptor binding activity, dna polymerase binding activity, peptide hormone receptor binding activity. \\n\\nmechanism: these genes are involved in a variety of molecular activities, including enzyme activity, protein binding, and transcription factor activity. one potential underlying biological mechanism is the regulation and interaction of proteins in various cellular processes]] | \n", + "[[enzyme binding activity, GO:0003700, protein kinase binding activity, identical protein binding activity, rna binding activity, atp binding activity, ubiquitin protein ligase binding activity]] | \n", + "||
| HALLMARK_UV_RESPONSE_UP-1 | \n", + "[[atp binding activity, GO:0001216, identical protein binding activity, rna binding activity, protein kinase binding activity, cysteine-type endopeptidase activity involvement in apoptotic signaling, GO:0004602, histone binding activity, GO:0030594, glucagon receptor binding activity, GO:0004499, peptide hormone receptor binding activity, gtp binding activity, more]] | \n", + "[[enzyme binding activity, GO:0006508, protein phosphatase binding activity, GO:0004725]] | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[[GO:0090090, regulation of transcription, GO:0000981, histone deacetylase binding activity, ubiquitin protein ligase binding activity, notch binding activity, protein kinase binding activity, GO:0003713, identical protein binding activity]] | \n", + "[[GO:0060070, transcription regulation, MESH:D012319, transcription activator, beta-catenin complex, GO:0007219]] | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[[GO:0060070, GO:0031398, GO:0090090, GO:0031397, GO:0030162]] | \n", + "[[GO:0060070, GO:0010468]] | \n", + "||
| T cell proliferation-0 | \n", + "[[GO:0050776, intracellular signaling, GO:0008037, GO:0009617, GO:0008284, GO:0005125, protein kinase binding activity, identical protein binding activity]] | \n", + "[[GO:0050852, GO:0005125, interleukin-2 receptor binding activity, negative regulation of peptid, intracellular signal transduction\\n\\nmechanism: the genes analyzed in this study are primarily involved in signaling and receptor binding activities. this suggests that these genes may play an important role in the communication between cells and regulation of immune response. \\n\\n t cell receptor signaling pathway, cytokine activity, interleukin-2 receptor binding activity, negative regulation of peptid..., and intracellular signal transduction]] | \n", + "||
| T cell proliferation-1 | \n", + "[[GO:0042110, GO:0001816, GO:0010468, GO:0050671, GO:0001819, GO:0001933, GO:0045840, protein kinase binding activity, GO:0004697, GO:0004911, GO:0004896, GO:0097190, GO:0007005, GO:0043065, GO:0042100, GO:0004931]] | \n", + "[[GO:0050863, GO:0001819, GO:0006468, GO:0043066, GO:0002687, GO:0030890, GO:0006879, GO:0010468]] | \n", + "||
| Yamanaka-TFs-0 | \n", + "[[transcription regulation, GO:0010468, GO:0045944, GO:0003700, cellular differentiation]] | \n", + "[[transcriptional regulation, GO:0010467, GO:0003700, GO:0009889, GO:0019219]] | \n", + "||
| Yamanaka-TFs-1 | \n", + "[[GO:0010468, transcriptional regulation, GO:0003700, GO:0001714, GO:0045944]] | \n", + "[[GO:0010467, transcription regulation, dna binding activity, rna polymerase ii-specific, GO:0010468, transcription cis-regulatory region binding activity]] | \n", + "||
| amigo-example-0 | \n", + "[[GO:0030198, GO:0007165, GO:0007596]] | \n", + "[[GO:0007160, GO:0030198, GO:0030199, GO:0008034]] | \n", + "||
| amigo-example-1 | \n", + "[[GO:0005178, GO:0005201, GO:0008083, platelet-derived growth factor binding activity, GO:0030199]] | \n", + "[[GO:0007160, GO:0030199, GO:0030198, GO:1902533, GO:0010604, GO:0030334]] | \n", + "||
| bicluster_RNAseqDB_0-0 | \n", + "[[GO:0005515, GO:0005216, transcriptional regulation, ubiquitin-protein ligase activity]] | \n", + "[[GO:0003700, identical protein binding activity, protein kinase binding activity, actin binding activity, sequence-specific double-stranded dna binding activity, metal ion binding activity, calcium ion binding activity, chromatin binding activity, rna binding activity]] | \n", + "||
| bicluster_RNAseqDB_0-1 | \n", + "[[metal ion binding activity, calcium ion binding activity, GO:0000981, g protein-coupled receptor binding activity, enzyme binding activity, sequence-specific double-stranded dna binding activity, cytoskeletal protein binding activity, GO:0061630]] | \n", + "[[binding activity, GO:0003700, GO:0046872, GO:0019904, GO:0061630]] | \n", + "||
| bicluster_RNAseqDB_1002-0 | \n", + "[[GO:0006936, GO:0030239, GO:0043502, GO:0051015, GO:0005523]] | \n", + "[[GO:0006936, GO:0043502, GO:0016567]] | \n", + "||
| bicluster_RNAseqDB_1002-1 | \n", + "[[GO:0003009, GO:0060048, GO:0010628, actin filament binding activity, GO:0008307]] | \n", + "[[GO:0006936, GO:0003009, GO:0016567, ion channel activity.\\n\\nmechanism: these genes likely play a role in muscle contraction and structure, possibly through the regulation of ion channels and protein ubiquitination]] | \n", + "||
| endocytosis-0 | \n", + "[[GO:0006897, GO:0015031, GO:0006898]] | \n", + "[[GO:0006897, GO:0007165, cellular adhesion, GO:0006869, GO:0030163, GO:0007009]] | \n", + "||
| endocytosis-1 | \n", + "[[GO:0006897, lysosomal function, GO:0038023, GO:0006955, GO:0008152]] | \n", + "[[GO:0006897, membrane traffic, GO:0015031]] | \n", + "||
| glycolysis-gocam-0 | \n", + "[[GO:0006006, GO:0005975, GO:0019725, GO:0008104, GO:0070062, GO:0005634]] | \n", + "[[GO:0006096, GO:0005975, GO:0006000, metabolic homeostasis]] | \n", + "||
| glycolysis-gocam-1 | \n", + "[[GO:0006096, GO:0005975, GO:0006000, cell development.\\n\\nhypotheses: the enriched terms suggest that these genes are involved in the glycolysis pathway, contributing to carbohydrate metabolic processes and the production of energy for cellular development. specifically, fructose metabolic processes are enriched, indicating that the genes may play a role in the conversion of fructose to glucose during glycolysis]] | \n", + "[[GO:0006096, GO:0005975, GO:0006002, GO:0005945]] | \n", + "||
| go-postsynapse-calcium-transmembrane-0 | \n", + "[[GO:0006816, GO:0007268, GO:0005245, GO:0098978, GO:0004972]] | \n", + "[[GO:0006816, GO:0005245, GO:0008066, GO:0005892]] | \n", + "||
| go-postsynapse-calcium-transmembrane-1 | \n", + "[[GO:0005509, GO:0006836, GO:0001505, GO:0016079, GO:0035235, GO:0007186, GO:0071318]] | \n", + "[[GO:0019722, voltage-gated calcium channel, GO:0051480, GO:0008066, GO:0017146, GO:0007268, GO:0051899, g-protein coupled receptor signaling pathway]] | \n", + "||
| go-reg-autophagy-pkra-0 | \n", + "[[GO:0006468, GO:0010604, GO:0038202, GO:0032006, GO:0016241, positive regulation of cyclin-dependent protein serine/threonine kinase activity.\\n\\nmechanism and]] | \n", + "[[GO:0006468, GO:0035556, GO:0031929, GO:0097190, kinase activity regulation, GO:0010604]] | \n", + "||
| go-reg-autophagy-pkra-1 | \n", + "[[intracellular signaling, pathway regulation, GO:0006915, GO:0004672, GO:0006468, GO:0010604, GO:0045859]] | \n", + "[[GO:0035556, protein kinase activity regulation, GO:0010604, GO:0038202, GO:0032008, GO:0045859, apoptosis signaling pathway, chromatin binding activity]] | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[[GO:0046479, GO:0006516, GO:0006032, GO:0030214]] | \n", + "[[GO:0016052, GO:0006516, GO:0006032, GO:0030214]] | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[[GO:0005975, MESH:D054794, glycan catabolism, GO:0006516, GO:0019377, GO:0006032, GO:0006004]] | \n", + "[[GO:0016052, GO:0030214, GO:0006516, GO:0019377, GO:0006032, GO:0006491, GO:0006517, mannose trimming involved in glycoprotein erad pathway.\\n\\nmechanism: one potential underlying biological mechanism is the regulation of cell surface and extracellular matrix composition, as well as the breakdown and recycling of molecules within these structures. glycosidases play a key role in breaking down complex carbohydrates into smaller subunits, which can then be reassembled into new molecules. the ability to break down specific types of carbohydrates, such as hyaluronic acid and chitin, may also be important for cellular processes such as cell migration and host defense]] | \n", + "||
| ig-receptor-binding-2022-0 | \n", + "[[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253]] | \n", + "[[immunoglobulin receptor binding activity, antigen binding activity]] | \n", + "||
| ig-receptor-binding-2022-1 | \n", + "[[GO:0002253, GO:0098542, GO:0019731, GO:0006959, GO:0002377, GO:0051130, GO:0045657]] | \n", + "[[GO:0006955, GO:0006952, antigen binding activity]] | \n", + "||
| meiosis I-0 | \n", + "[[GO:0061982, GO:0007131, GO:0007129, GO:0000712, GO:0000724]] | \n", + "[[homologous chromosome pairing, GO:0042138, GO:0000706, GO:0007131, GO:0000724, GO:0000712, GO:0000795]] | \n", + "||
| meiosis I-1 | \n", + "[[meiotic recombination, GO:0035825, GO:0006302]] | \n", + "[[meiotic recombination, GO:0006302, GO:0035825, chromosomal segregation, GO:0007130]] | \n", + "||
| molecular sequestering-0 | \n", + "[[molecular sequestering, protein binding activity, transport of metal ions, GO:0048523, response to infection and stress, GO:0010468, GO:0019722, regulation of transcription]] | \n", + "[[GO:0140313, GO:0140311, identical protein binding activity, GO:0060090, ubiquitin protein ligase binding activity, GO:0016567]] | \n", + "||
| molecular sequestering-1 | \n", + "[[GO:0140311, GO:0010468, GO:0031398, GO:0051238]] | \n", + "[[GO:0010468, GO:0042742, GO:0045185, GO:0002376, GO:0009267, GO:0032387, GO:0035556]] | \n", + "||
| mtorc1-0 | \n", + "[[binding activity, enzymatic activity, GO:0006412, GO:0023052, GO:0008152]] | \n", + "[[GO:0005515, GO:0003723, enzymatic activity, structural constituent of cytoskeleton. \\n\\nmechanism: these genes likely play a role in cellular processes such as transcription, translation, protein folding, and cytoskeletal organization]] | \n", + "||
| mtorc1-1 | \n", + "[[GO:0005515, GO:0042802, GO:0019899, GO:0043167, GO:0005524, GO:0031625, GO:0003723, GO:0003677, GO:0097159, GO:0017076, GO:0051015, GO:0042802, GO:0016491, phosphoprotein binding activity, GO:0005215, GO:0006793, GO:0044237, GO:0006457, GO:0003677, GO:0008380]] | \n", + "[[GO:0005515, GO:0003824, GO:0005215]] | \n", + "||
| peroxisome-0 | \n", + "[[GO:0017038, peroxisomal biogenesis, GO:0140036, atp binding and hydrolysis activity, lipid binding activity]] | \n", + "[[peroxisome biogenesis, peroxisome matrix targeting, GO:0017038]] | \n", + "||
| peroxisome-1 | \n", + "[[GO:0007031, GO:0016558, GO:0005778, peroxisomal biogenesis disorder, GO:0008611, lipid binding activity, atp binding activity, GO:0016887, ubiquitin-dependent protein binding activity, enzyme binding activity]] | \n", + "[[peroxisome biogenesis, GO:0017038, GO:0005778, ubiquitin-dependent protein binding activity, atp binding activity, GO:0016887]] | \n", + "||
| progeria-0 | \n", + "[[GO:0006259, GO:0006325, GO:0033554, GO:0006281, GO:0007568]] | \n", + "[[GO:0006259, GO:0006325, GO:0033554]] | \n", + "||
| progeria-1 | \n", + "[[GO:0006281, GO:0006950, GO:0090398, GO:0000723, chromatin condensation]] | \n", + "[[GO:0006281, GO:0000723, GO:0007568]] | \n", + "||
| regulation of presynaptic membrane potential-0 | \n", + "[[GO:0015276, GO:0099505, GO:0060078, GO:0071805, GO:0035725, GO:0035235]] | \n", + "[[GO:0007214, GO:0022849, GO:0005242, GO:0035235, GO:0015276, GO:0071805, GO:0005244]] | \n", + "||
| regulation of presynaptic membrane potential-1 | \n", + "[[GO:0007214, GO:0007215, GO:0006811, GO:0006836, GO:0007268]] | \n", + "[[GO:0006811, GO:0007268, membrane potential regulation, GO:0008066, GO:0007214]] | \n", + "||
| sensory ataxia-0 | \n", + "[[GO:0042552, GO:0007422, MONDO:0005071, GO:0022011, MONDO:0005244]] | \n", + "[[MONDO:0015626, GO:0042552, GO:0007422, GO:0006457, GO:0007600, nucleic acid metabolism, mitochondrial function]] | \n", + "||
| sensory ataxia-1 | \n", + "[[GO:0007399, GO:0042552, mitochondrial metabolism, GO:0030163, protein regulation, GO:0071260]] | \n", + "[[GO:0007399, MONDO:0015626, GO:0042552, UBERON:0000010, mitochondrial dysfunction, protein ubiquitination.\\n\\nmechanism]] | \n", + "||
| term-GO:0007212-0 | \n", + "[[GO:0007186, GO:0007212]] | \n", + "[[GO:0007212, GO:0007190, calcium ion regulation, g protein-coupled receptor pathway]] | \n", + "||
| term-GO:0007212-1 | \n", + "[[GO:0007212, GO:0007186, GO:0051480, GO:0004016, GO:0006469, GO:0050821, GO:0060828, GO:0007220, GO:0034205, GO:0006508, GO:0046325, GO:1904227, GO:0051247, GO:0015171, GO:0015108]] | \n", + "[[GO:0007186, GO:0004952, GO:0004016, GO:0051480, negative regulation of glycogen synthase activity, GO:0004672, GO:0019538, GO:0006468]] | \n", + "||
| tf-downreg-colorectal-0 | \n", + "[[dna-binding transcription factor, rna polymerase ii-specific transcription regulation, GO:0000122, GO:0045944, GO:0006355]] | \n", + "[[GO:0001216, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, GO:0045944, GO:0000122, GO:0006355, transcription factor binding activity, nucleic acid binding activity, chromatin binding activity, GO:0003713]] | \n", + "||
| tf-downreg-colorectal-1 | \n", + "[[GO:0000988, GO:0006355, GO:0045893, GO:0045892, dna-binding, GO:0003702]] | \n", + "[[GO:0003700, GO:0006355, GO:0010468, GO:0006337]] | \n", + "||
| text-davinci-003 | \n", + "narrative_synopsis | \n", + "EDS-0 | \n", + "[[connective tissue formation and repair, protein binding and folding, GO:0006955, GO:0042060, GO:0006024]] | \n", + "[[GO:0032964, collagen fiber formation, extracellular matrix maturation, transcriptional regulation, procollagen protein, MESH:D006025, metalloproteinase, proteolytic processing, peptidyl prolyl cis-trans isomerase, MESH:M0465019, tumor-rejection antigen, sulfotransferase, transmembrane protein, beta-1,3 galactosyltransferase]] | \n", + "
| EDS-1 | \n", + "[[collagen maturation, GO:0006024, transcriptional regulation, GO:0006829]] | \n", + "[[GO:0006486, extracellular matrix remodeling, collagen production, GO:0061448, immunity response, GO:0006508, tumor rejection, MESH:M0465019, MESH:D008565, transcriptional repressor, peptidyl-prolyl isomerase, complement system, GO:0004226, peptidase s1]] | \n", + "||
| FA-0 | \n", + "[[GO:0006281, GO:0035825, GO:0016310, nucleoprotein complex assembly, formation of nuclear foci, double-strand dna repair, holliday junction resolution, function in tumor suppression, reca/rad51-related protein family, dna lesions, structural specific endonucleases, rad51 family, cellular responses to replication fork failure, brc motif]] | \n", + "[[GO:0006281, genome maintenance, MESH:D004249, nucleoprotein complex, GO:0035825, double-strand dna repair, holliday junction resolution, monoubiquinated, MESH:D051135, nuclear foci, structure-specific endonucleases, MESH:D051135, recq deah helicase, tumor suppression, ssdna-binding proteins]] | \n", + "||
| FA-1 | \n", + "[[GO:0006281, GO:0035825, monoubiquitination, holliday junction resolution, rad51 binding]] | \n", + "[[GO:0006281, nucleoprotein complex, GO:0035825, dna lesion, MESH:M0443450, fanconi anemia complementation group (fanc), GO:0006302]] | \n", + "||
| HALLMARK_ADIPOGENESIS-0 | \n", + "[[GO:0006629, GO:0006633, GO:0022900, GO:0005739, MESH:D000975, GO:0045333, MESH:D010084, acyltransferase, carboxylase, acyl-coenzyme a synthetase, ubiquitin protease, MESH:C021451, MESH:D010743, oxidoreductase, plasma lipase, hydratase]] | \n", + "[[GO:0010467, GO:0140657, GO:0006468, ubiquitin-mediated degradation, GO:0051726, GO:0005525, GO:0006839, GO:0006118, GO:0006119, MESH:D004789, enzyme inhibition, GO:0016491, GO:0016482, GO:0005515, GO:0006629, GO:0036211, ubiquitinylation]] | \n", + "||
| HALLMARK_ADIPOGENESIS-1 | \n", + "[[GO:0005515, transcription regulation, atpase, MESH:D020558, transcript processing, protein transduction, MESH:D014451, GO:0044237, energy production, GO:0006508]] | \n", + "[[atp production, GO:0005746, GO:0006118, GO:0030497, rna/dna binding, GO:0015031, MESH:D054875, GO:0016310, GO:0008017, GO:0006869]] | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[[immune/cytokine responses, GO:0006412, GO:0006351, cell surface signaling, receptor activation, MESH:D054875, MONDO:0002123, GO:0005524]] | \n", + "[[cell signalling, cytokine production/regulation, chemokine production/regulation, antimicrobial defence, plasma protein regulation, immune regulation, inflammatory regulation, transcriptional regulation, GO:0004672, GO:0008233, glycoprotein activity, receptor protein activity]] | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[[GO:0006412, cellular regulation, GO:0008152, cell signaling, GO:0006351, immunoregulation, stability, GO:0005515, GO:0016310, GO:0010467, g-protein coupled receptor, transmembrane protein, t-cell development]] | \n", + "[[integrin, cytokine, g-protein coupled receptor, MESH:D007372, MESH:D018124, MESH:D008562, MESH:D011494, chemokine, transmembrane receptor, GO:0007165, transcriptional regulation, GO:0006412, GO:0006955]] | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[[MESH:D011494, GO:0000981, GO:0005530, adhesion molecule, GO:0016538, MESH:D016601, protein tyrosine phosphatase, g protein, serine/threonine protein kinase, MESH:D008565, MESH:D006657, ubiquitin ligase, MESH:C052123, microtubule-associated protein, atp-binding cassette, alpha/beta-hydrolase, integrin alpha-chain, signal transducion, protein inhibitor of activated stat]] | \n", + "[[GO:0005524, GO:0006351, GO:0016310, MESH:D011494, protein tyrosine phosphatase, GO:0065007, GO:0005515, hydrolase, ribosomal s6 kinase, GO:0016192, regulatory subunit, acetyltransferase, modulation, GO:0005509, GO:0005783, GO:0000981, GO:0003723, n-myc downregulated, polypeptide, GO:0016125, MESH:D006657, protein inhibitor, MESH:D051116, structural fibre, disulfide oxidoreductase, adenine dinucleotide, non-sterol metabolism, calcium-induced, GO:0042593]] | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[[GO:0008283, GO:0006351, GO:0007165, structural components, metabolism of proteins, GO:0006629, GO:0005975, GO:0007155, binding activity, GO:0010467, GO:0003677, MESH:D011494, oxidoreductase, anchoring kinase to microtubules, GO:0005102, molecule transport, MESH:D010455]] | \n", + "[[transcriptional regulation, GO:0004672, GO:0005515, GO:0003723, GO:0007165, proteolytic enzyme activity, GO:0003677]] | \n", + "||
| HALLMARK_ANGIOGENESIS-0 | \n", + "[[this is a list of genes involved in a variety of pathways and processes related to cell adhesion, GO:0040007, GO:0008152, and other physiologic functions. the terms “cell adhesion”, “cell signaling”, “extracellular matrix”, “transcriptional regulation”, and “cell cycle progression and differentiation” are all enriched among this group of genes. a hypothesis of the underlying biological mechanism at work is that these genes work together to promote cell growth and regulation, that many of these genes interact to achieve greater cellular complexity]] | \n", + "[[GO:0042157, GO:0050817, GO:0007599, MESH:D016207, MESH:D018925, receptors, transporters, secreted extracellular matrix proteins, GO:0004868, MESH:D011509, GO:0007155, GO:0016477, GO:0023052, GO:0008283, GO:0006915, transcriptional regulation, tissue development and regeneration, GO:0006955]] | \n", + "||
| HALLMARK_ANGIOGENESIS-1 | \n", + "[[GO:0007155, extracellular matrix remodeling, GO:0007165, protease inhibition, transcriptional regulation]] | \n", + "[[cell-cell interactions, cell-matrix interactions, extracellular matrix production, processing of proteoglycans and glycoproteins]] | \n", + "||
| HALLMARK_APICAL_JUNCTION-0 | \n", + "[[GO:0005207, GO:0007155, calcium-dependent proteins, MESH:D008565, intronless proteins, intracellular scaffolding proteins, fibrillin proteins, signaling receptors, MESH:D051193, MESH:D003598, tubulin proteins, type ii membrane proteins, MESH:D006023]] | \n", + "[[integrin, GO:0008014, GO:0005530, MESH:C119025, map kinase, protein tyrosine kinase, guanine nucleotide binding protein, MESH:D020558, act]] | \n", + "||
| HALLMARK_APICAL_JUNCTION-1 | \n", + "[[GO:0007155, GO:0007165, actin binding and assembly, membrane localization, ecm protein binding and assembly]] | \n", + "[[GO:0007155, GO:0023052, scaffolding, cytoskeleton maintenance, GO:0031012, MESH:D016023, MESH:D057167, MESH:C119025, MESH:D011494, GO:0008014]] | \n", + "||
| HALLMARK_APICAL_SURFACE-0 | \n", + "[[GO:0007160, GO:0007165, MESH:D008565, transcriptional coactivation, signal recognition, GO:0055085, GO:0006898]] | \n", + "[[GO:0007155, GO:0006457, GO:0007154, GO:0006898, gpi-anchored cell surface proteins, cation transport atpase, transcriptional coactivation, interleukin signaling, hormone-dependence, MESH:D019812, heparin-binding, GO:0007160]] | \n", + "||
| HALLMARK_APICAL_SURFACE-1 | \n", + "[[GO:0007160, cell-matrix interactions, carbohydrate binding activity, GO:0007155, GO:0038023, GO:0007165, GO:0008284, GO:0048681, GO:0030506, protein tyrosine kinase, sh2 domain binding activity, sh3 domain binding activity]] | \n", + "[[cell signal transduction, GO:0007160, GO:0006457, GO:0030308, ligand binding, cell-surface glycoprotein, cation transmembrane transporter, growth arrest, MESH:D051246, transmembrane protein, regulatory subunit, membrane-bound glycoprotein, ammonium transmembrane transporter, cell surface receptor, insulin-regulated facilitative glucose transporter, cell surface adhesion molecule, GO:0140326, glycosylphosphatidylinositol-anchored protein]] | \n", + "||
| HALLMARK_APOPTOSIS-0 | \n", + "[[GO:0006915, cytoplasmic signaling, transcriptional regulation, GO:0005515, cellular organization]] | \n", + "[[GO:0006915, transcriptional regulation, GO:0003677, tnf receptor superfamily, bcl-2 protein family]] | \n", + "||
| HALLMARK_APOPTOSIS-1 | \n", + "[[cell death processes, GO:0023052, cytoplasmic proteins, MESH:M0015044, MESH:D015533, MESH:D004798, toxin removal, GO:0005102]] | \n", + "[[the genes summarized are involved in a wide range of processes, including apoptosis, tumor suppression, inflammation, thioredoxin binding, cytoplasmic protein and membrane glycoprotein regulation, dna topoisomerase and transcriptional activation. the commonalities that emerge from the enrichment test point to a specific biological pathway known as cell death regulation and signal transduction. this involves the interconnected network of genes that regulate apoptosis and maintain genetic stability, as well as others involved in the modulation of immune response pathways. enriched terms include apoptosis, cytoplasmic protein regulation, transcriptional regulation, tumor suppression, GO:0006954, MESH:D004264, thioredoxin binding, membrane glycoprotein regulation, transcriptional coactivation, death agonist, GO:0048018, serine/threonine phosphatase, voltage-dependent anion channel, MESH:D006136, class-1 polypeptide chain release factor, proapoptotic, nf-kappa-b.\\n\\nsummary: genes related to cell death regulation signal transduction pathways.\\nmechanism: interconnected network of genes that regulate apoptosis maintain genetic stability, as well as those involved in the modulation]] | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[[atp-binding, GO:0006810, GO:0004768, MESH:D010084, enzyme catalysis, GO:0000981]] | \n", + "[[GO:0006629, atp binding cassette, MESH:M0011631, GO:0005490, peroxin, gamma-glutamylcysteine synthetase, GO:0050632, MESH:D002785, flavoenzymes, GO:0042446, GO:0016209]] | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[[GO:0015031, GO:0006412, GO:0006629, MESH:D010084, hormone regulation, transcription regulation, GO:0006805, calcium binding, GO:0005524, MESH:D005982, GO:0008203, MESH:M0011631, sulfate conjugation, 2-hydroxyacid oxidase, MESH:D000214, MESH:D000215, coenzyme a ligase, natriuretic peptide, peroxisome biogenesis, tgf-beta ligand, adrenal steroid synthesis, nuclear receptor, copper zinc binding, GO:0050632, MESH:D012319, gamma-glut]] | \n", + "[[GO:0006629, GO:0006810, oxidation, bile acids synthesis, GO:0006790, GO:0005777, oxidative stress response]] | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[[MESH:D008565, MONDO:0018815, acetoacetyl-coa thiolase, cytosolic enzyme, actin isoforms, activation transcription factor (creb), annexin family, fructose-biphosphate aldolase, immunoglobulin superfamily, g-protein coupled receptor (gpcr), homotetramer, hydratase/isomerase superfamily, MESH:C022503, mal proteolipid, MESH:M0476528, sre-binding proteins (srebp), peroxisomal enzyme, transmembrane 4 superfamily, transmembrane protein, multispan transmembrane protein, tetr]] | \n", + "[[GO:0048870, energy generation, GO:0008652, GO:0009063, GO:0009101, GO:0016126, GO:0016127, GO:0006629, GO:0006869, transcriptional regulation]] | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[[GO:0006629, GO:0005543, GO:0004768, atp-binding cassette, GO:0016126, cytochrome p450 family proteins]] | \n", + "[[GO:0006695, GO:0006629, GO:0006636, cell growth/regulation, GO:0051726, GO:0005515, mhc class ii presentation, cellular antioxidant activity, GO:0000988]] | \n", + "||
| HALLMARK_COAGULATION-0 | \n", + "[[complement system, GO:0007596, peptide hydrolysis, GO:0016485, inflammation regulation]] | \n", + "[[analysis of this set of human genes revealed high enrichment for terms related to proteases and protease inhibitors, GO:0005209, MESH:D006023, and serine proteinases. of particular note is the abundance of genes related to the regulation of the complement system and to the coagulation cascade, GO:0004235, there appears to be a strong emphasis on proteins that are involved in the maintenance of cellular integrity and in the regulation of inflammatory and immune responses. in particular, it appears that the presence of proteases, MESH:D011480, GO:0005209, MESH:D006023, and serine proteinases is significantly enriched. this suggests that these proteins are involved in the regulation of a variety of processes, including the complement system and the coagulation cascade. furthermore, the presence of various mmps suggests a regulatory role in the breakdown of proteins in the extracellular matrix, which is important for tissue remodeling and wound healing]] | \n", + "||
| HALLMARK_COAGULATION-1 | \n", + "[[matrix metalloproteinase, cysteine-rich protein, serine protease inhibitor, transforming growth factor-beta, MESH:D054834, guanine nucleotide-binding proteins, peptidase s1 family, integrin beta chain, MESH:D001779, dipeptidyl peptidase, vitamin k-dependent glycoprotein, vitamin k-dependent coagulation factor, regulator of complement activation, protein tyrosine kinase, MESH:D006904, iron-sulfur cluster scaffold, disulfide bridge, kunitz-type serine protease, MESH:D042962, MESH:D037601, g-protein coupled receptor, cytosolic peptidase, GO:0030165, basic leucine zipper, a disintegrin and metalloprote]] | \n", + "[[cysteine-aspartic acid protease, MESH:D020782, peptidase, guanine nucleotide-binding proteins, GO:0030165, metalloproteinase, MESH:D042962, regulator of complement activation, regulator of g protein signal transduction, rnase a superfamily, MESH:D011505, subtilisin-like proprotein convertase, MESH:D011973, vitamin k-dependent plasma glycoprotein, vitamin k-dependent coagulation factor, GO:0005161, lysosomal cysteine proteinase, MESH:D015842, transforming growth factor-beta, MESH:D006904, kunitz-type serine protease, integ]] | \n", + "||
| HALLMARK_COMPLEMENT-0 | \n", + "[[cell signaling, cell structure/stability, GO:0008152, vitamin k/clotting, GO:0005856, GO:0005886, GO:0006954]] | \n", + "[[MESH:D010770, GO:0000502, GO:0004868, cysteine-aspartic acid protease (caspase), GO:0006915, inflammation signalling, MESH:D005165, factor]] | \n", + "||
| HALLMARK_COMPLEMENT-1 | \n", + "[[protein production, cell surface glycoprotein regulation, GO:0006956, GO:0007165, heat shock protein, MESH:D003564, metalloproteinase, guanine nucleotide-binding protein, lysosomal cysteine protease, zinc finger protein, cysteine-aspartic acid protease, MESH:D001053, metallothionein.\\nmechanism: the genes may be involved in various signalling pathways to facilitate the regulation of cell surface glycoprotein as well as the production of proteins. cytidine deaminase, metalloproteinase, guanine nucleotide-binding protein and cysteine-aspartic acid protease are likely enzymes that the list of genes may be involved in. heat shock proteins and zinc finger proteins, in addition to apolipoproteins and metallothionein, may be involved in the regulation and transportation of cell proteins]] | \n", + "[[cell signaling, GO:0007155, GO:0008233, transcriptional regulation, GO:0008152, cytoskeletal functions]] | \n", + "||
| HALLMARK_DNA_REPAIR-0 | \n", + "[[summary: this enrichment test provides evidence of a common biological mechanism underlying many genes in human genetics: dna repair, replication, and transcription.\\n\\nmechanism: the mechanism underlying this term enrichment is the need for accurate dna repair, replication, and transcription, which all require the co-ordinated efforts of many protein families, such as those encoded by the wd-repeat, MESH:D000262, argonaute, MESH:D000263, purine/pyrimidine phosphoribosyltransferase, b-cell receptor associated proteins, MESH:C056608, clp1, GO:0016538, MESH:C010098, dna helicase, MESH:M0251357, general transcription factor (gtf) ii, MESH:D005979, histone-fold proteins, mhc, MESH:C110617, GO:0005662, saccharomyces cerevisiae rad52, schizosaccharomyces pombe rae1, splicing factor (sf3a), GO:0003734, MESH:D011988, transcription factor b (tfb4), trans]] | \n", + "[[GO:0003677, transcription control, post-splicing, MESH:D012319, GO:0006281, GO:0071897]] | \n", + "||
| HALLMARK_DNA_REPAIR-1 | \n", + "[[GO:0003677, transcription regulation, GO:0006281, GO:0000394, GO:0006397, GO:0003723, GO:0003682, GO:0019899, GO:0003684, general transcription factor, transcription/repair factors, MESH:M0006668, hypothalamic hormone receptor binding, GO:0004016, nuclear cap-binding protein, GO:0016567, transcription initiation, dna polymerase, GO:0006605]] | \n", + "[[GO:0019899, GO:0003723, GO:0003677, GO:0005515, chromosomal binding, dna polymerase, MESH:D012321, phosphorolysis, GO:0010629, GO:0016567]] | \n", + "||
| HALLMARK_E2F_TARGETS-0 | \n", + "[[GO:0006260, GO:0006281, GO:0006351, GO:0003682, GO:0016569, GO:0051726, ran binding, GO:0000808, atpase, GO:0016538, cyclin-dependent kinase, polycomb, dead box protein, gtpase activating protein, GO:0042393, GO:0003723, nucleolar protein, ubiquitously expressed protein, smc subfamily protein, pp2c family, elongation of primed dna template synthesis, dna interstrand cross-linking, import of proteins into nucleus, MESH:D004264, tumor suppressor protein, MESH:D051981, ubr box protein, p80 autoantigen]] | \n", + "[[dna replication/repair, chromatin regulation, GO:0006396, ser/thr protein kinase, MESH:D063146, nuclear transport and export, GO:0016567, gtpase activation, GO:0006413, GO:0003723, GO:0003677, GO:0042393, ubiquitin protein ligase, cyclin-dependent kinase, MESH:D000251, MESH:D003842]] | \n", + "||
| HALLMARK_E2F_TARGETS-1 | \n", + "[[GO:0003676, GO:0006260, GO:0036211, GO:0006259, GO:0000785, GO:0051726, GO:0016570, protein assembly and disassembly]] | \n", + "[[GO:0006260, nuclear import/export, GO:0003723, chromatin regulation/modification, GO:0030163, GO:1901987, GO:0006281]] | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[[cell signaling, extracellular matrix formation, GO:0007155, connective tissue formation, GO:0001525, metabolic regulation, MESH:D016207, tissue repair]] | \n", + "[[GO:0003779, actin regulation, GO:0007155, cell signaling, GO:0005518, cytokine regulation and signaling, GO:0005207, growth factor family members, peptidase genes]] | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[[MESH:D016326, GO:0005202, MESH:D007797, MESH:D005353, MESH:D014841, integrin, MESH:D016189, fibulin proteins]] | \n", + "[[GO:0007155, GO:0005518, GO:0003779, MESH:D024022, MESH:D016326, cytoskeletal components, cell signalling]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[[GO:0042277, membrane structure modification, GO:0003677, GO:0006631, GO:0051427, signalling transcription, gtpase activation, adenylate cyclase modulation, GO:0016301, GO:0006897, glycoprotein production, GO:0019838, GO:0016570, GO:0006644, zinc-binding]] | \n", + "[[GO:0007165, GO:0010467, GO:0006810, MESH:D008565, GO:0043687, GO:0005515, ligand binding, acyltransferase]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[[dna-binding, GO:0005515, GO:0043687, GO:0007165, metabolic activity]] | \n", + "[[cytoskeletal organization, dna-binding transcription regulation, GO:0055085, membrane-associated signaling, receptor activation and signaling, cytokine and growth factor signaling]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[[MESH:D011494, GO:0000981, GO:0005509, MESH:D054794, hormone receptors, GO:0007155, GO:0006457, GO:0010467]] | \n", + "[[g-protein signaling, ion channel transport, membrane receptor signalling, cytoskeletal protein scaffolding, enzyme regulation, glycoprotein modulation.\\nmechanism: the genes identified as being related to these topics are involved in the regulation of cell signalling pathways and the transport of ions across cellular membranes. in addition, the genes are involved in biochemical processes such as enzyme regulation and glycoprotein modulation, which may be important in modulating the amount or type of molecules entering the cell and in organizing the cytoskeleton]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[[membrane processes, transmembrane processes, GO:0006811, GO:0007155, GO:0016049, GO:0008152, MESH:D011506, GO:0023052, processing, MESH:D048788, reparative pathways, immune pathways, disease pathways]] | \n", + "[[GO:0007165, gene transcription, ion transport and binding, protein-protein interaction, GO:0043687, GO:0007155, MESH:M0518050, GO:0016310, MESH:D011494, membrane recognition, GO:0003676, MESH:D018118, enzymatic reactions, lipid transport, glucose transport, cytokine receptor, molybdenum cofactor biosynthesis]] | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[[GO:0006732, GO:0006754, GO:0006096, oxidative decarboxylation, GO:0006631, nad/nadh-dependent oxidation, pyridine nucleotide oxidation, amino acid oxidation, glycerol-3-phosphate dehydrogenase activity, GO:0022900, MESH:D042942, nadp-dependent oxidation, l-amino acid oxidation, endogenous and xenobiotic n-methylation, conversion of pyruvate to acetyl coa, 2-oxoglutarate catabolism, galectin family activity]] | \n", + "[[GO:0008152, GO:0009117, GO:0006631, GO:0006096, oxidation-reduction processes, GO:0006595, GO:0003824, amino acid metabolism, protein homodimerization, protein biotransformation, protein-macromolecule adaptor, protein-tat binding]] | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[[GO:0008152, fatty acid transport and processing, oxidoreductase, GO:0009653, GO:0030154, GO:0030674]] | \n", + "[[GO:0006099, GO:0006118, GO:0005504, MESH:D042964, pyruvate dehydrogenase, nad-dependent glycerol-3-phosphate dehydrogenase, nad-dependent dehydrogenase, MESH:D013385, MESH:D000154, lyase, flavin adenine dinucleotide-dependent oxidoreductase, gtp-specific beta subunit, MESH:D006631, nad-retinol dehydrogenase, hydratase/isomerase, MESH:D006631, carnitine o]] | \n", + "||
| HALLMARK_G2M_CHECKPOINT-0 | \n", + "[[GO:0006325, GO:0051726, GO:0016570, MESH:D011494, atp-binding, rna-binding]] | \n", + "[[transcriptional regulation, epigenetic regulation, GO:0051169, GO:0043687, dna replication and repair, chromatin structure, GO:0140014, GO:0036211, GO:0006397]] | \n", + "||
| HALLMARK_G2M_CHECKPOINT-1 | \n", + "[[GO:0051301, GO:0003677, GO:0003723, transcriptional regulation, chromatin restructuring, GO:0004672, GO:0051169, cytoplasmic transport, nucleic acid metabolism, GO:0016570, GO:0016310, GO:0032259, MESH:D000107, MESH:D054875]] | \n", + "[[GO:0006913, GO:0016573, chromatin-associated processes, GO:0051726, transcriptional regulation, signal- and energy- dependent processes, nuclear phosphoproteins, GO:0006334, dna unwinding enzymes, protein heterodimers, GO:0000910, GO:0000398, MESH:D004264, GO:0035064, rna binding proteins, microtubule polymersization, nuclear localization, ubiquitin modification, mitosis regulation, centromere-interacting proteins.\\nmechanism: the genes in this list participate in a wide variety of mechanisms in the context of cellular development, including nucleocytoplasmic transport, histone acetylation, chromatin-associated processes, cell cycle regulation, and transcriptional regulation. these mechanisms are often interdependent and]] | \n", + "||
| HALLMARK_GLYCOLYSIS-0 | \n", + "[[GO:0016310, GO:0009100, GO:0007155, transcription regulation, GO:0009117, energy production]] | \n", + "[[MESH:D006023, transmembrane protein, cell-surface protein, enzymes plus coenzymes, GO:0000981, hormones, cytokines, and growth factors, ligand-receptor interaction, regulatory proteins, cargo-binding proteins, cell adhesion and morphogenesis, MESH:D000604, metabolism and transport within the cell, metabolism of macromolecules, cellular energy metabolism, cellular homeostasis and signaling, cell signaling and transcription, protein modification and degradation, GO:0007049, dna replication and repair, GO:0008219, enzyme-substrate interaction\\n\\nmechanism:\\nthis list of genes is primarily involved in cellular metabolism, ligand-receptor interactions, and cell signaling and transcription. there are a variety of molecules that are acted upon, such as glycoproteins, transmembrane proteins, hormones, enzymes, and transcription factors. in terms of metabolic functions, the gene list includes proteins for metabolic control, cargo-binding proteins, and enzymes involved in macromolecule metabolism and transport within the cell. additionally, many of these genes are involved in the regulation of cell cycle and homeostasis, as]] | \n", + "||
| HALLMARK_GLYCOLYSIS-1 | \n", + "[[GO:0008152, GO:0005975, GO:0048468, GO:0009100, GO:0006629, GO:0015031, nucleic acid metabolism, GO:0009117, GO:0070085, ferric ion binding, GO:0016491, GO:0003677, GO:0000988, GO:0031545, GO:0004736]] | \n", + "[[enzyme function, GO:0005488, GO:0006810, GO:0008152, MESH:D007477, sugars, GO:0006351, cytoskeleton structure, GO:0007155]] | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[[GO:0007155, GO:0007165, GO:0000981, MESH:D018121, MESH:D039921, rho-gtpase-activating protein, transmembrane protein, GO:1902911, transduction pathway, growth factor, g protein-coupled receptor, cadherin superfamily, basic helix-loop-helix, phosphoprotein, zinc finger protein, cytoplasmic domain, dna-binding, GO:0005886, neurotransmitter, MESH:D057057, coiled-coil, pdz binding motif, cholesterol moiety, fibronectin-like repeat, MESH:D000070557, GO:0016604, MESH:D006655, collapsin response mediator, tripartite motif, hedgehog signaling.\\nmechanism: the genes seem to be primarily involved in regulating signal transduction pathways that control cell migration, proliferation and differentiation, by modulating transcription, cell adhesion and receptor activities. the proteins encoded by these genes interact]] | \n", + "[[GO:0006897, GO:0019838, receptor-mediated pathways;neuron survival;neuron differentiation;neuronal development;cell adhesion, transcription factor regulation, GO:0007165, extracellular protein interaction]] | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[[GO:0007155, GO:0007165, neuron signalling, regulatory activity, GO:0009987, GO:0040007, differentiation, motility, GO:0032502]] | \n", + "[[structure-specific proteins, GO:0006898, g-protein coupled receptors, GO:0007155, gene transcription, post-translational regulation]] | \n", + "||
| HALLMARK_HEME_METABOLISM-0 | \n", + "[[GO:0005515, GO:0000910, transcription regulation, metabolic & enzymatic function, cell cortex formation, GO:0006810, GO:0016310, MESH:D000107, protein formation & modification]] | \n", + "[[GO:0005515, GO:0006351, catalyzing reactions, gtpase activating protein activation, GO:0016575, carbohydrate & lipid metabolism, receptor binding & signaling, GO:0005574]] | \n", + "||
| HALLMARK_HEME_METABOLISM-1 | \n", + "[[GO:0006351, GO:0003723, post-transcriptional regulation, GO:0006096, GO:0006090, GO:0006749, GO:0006508, transcriptional regulation, MESH:D054875, GO:0003677, MESH:D006655, GO:0006915, cytoskeletal protein, atp-binding, GO:0048870, ubiquitin specific protease, MESH:D015220, voltage-gated chloride channel, GO:0004384, GO:0023052, GO:0051726, cation transporters]] | \n", + "[[GO:0003677, GO:0016573, GO:0005515, transcription regulation, leucine residue modification, GO:0003729, zinc metalloenzymes, atp-binding, protein serine/threonin, endoribonuclease, GO:0031545, 6-phosphogluconate dehydrase, GO:0003723, dynein heavy chain, MESH:C052997, chloride intracellular channel, GO:0003779, MESH:D051528, hexameric atpase, GO:0006814, rho gtpase, inositol polyphosphate, MESH:D011766, selenium-binding protein, clathrin assembly, c-myc, dual specificity protein kinase, MESH:D006021, gtpase-activating-protein, GO:0006914, ring between two helices]] | \n", + "||
| HALLMARK_HYPOXIA-0 | \n", + "[[GO:0006096, GO:0016310, GO:0004672, GO:0006508, GO:0085029, transcription regulation, GO:0051726, GO:0097009, GO:0006954, cell-cell communication, oxidative stress response]] | \n", + "[[cell signaling, metabolic regulation, GO:0043687]] | \n", + "||
| HALLMARK_HYPOXIA-1 | \n", + "[[GO:0006915, GO:0016310, MESH:D011494, GO:0005515, GO:0006351, GO:0031005, glycolytic enzyme, carboyhydrate binding, cell binding, GO:0042157, GO:0007165, UBERON:2000098, GO:0040007]] | \n", + "[[cellular transport, GO:0008152, scaffolding, transcriptional regulation, GO:1901987, transcription activity, GO:0016310, cysteine-aspartic acid, GO:0016020, cell surface heparan sulfate, glycosyl hydrolase family, MESH:D000263, MESH:D000262, glyceraldehyde-3-phosphate, cytokine, glycosyltransferase, MESH:D000070778, sulfatase, sulfotransferase, serine/threonine kinase, MESH:D016232, MESH:D008668, MESH:D011973, basic helix-loop-helix]] | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[[GO:0051726, receptor signaling, MESH:D008565, GO:0000981]] | \n", + "[[GO:0005515, GO:0005102, transcription regulation, enzyme regulation, GO:0001816, GO:0007155, structure, membrane-associated]] | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[[GO:0007165, protein homodimerization, GO:0005525, GO:0003676, GO:0055085, GO:0004672, GO:0007049, GO:0006955, GO:0006915]] | \n", + "[[an underlying biological mechanism of intracellular signaling and cell adhesion proteins working together to regulate gene expression and control cell functions was identified. enriched terms related to this mechanism include gtpases, MESH:D008565, intracellular signaling, calcium-dependent proteins, rna and dna binding, GO:0007155, GO:0000981, enzyme regulation, GO:0005515]] | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[[MESH:D016207, GO:0016049, GO:0048468, transmembrane proteins, MESH:D011494, GO:0000981, cell cycle progression]] | \n", + "[[MESH:D018121, MESH:D018925, tgf-beta superfamily, transcriptional regulation, MESH:D017027, MESH:D011494]] | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[[the list of gene summaries reveals a group of genes involved in cell trafficking, GO:0007165, GO:0007155, ligand binding, and regulation of the immune response. enriched terms include cytokine, chemokine, MESH:D007378, receptor, GO:0007155, ligand binding, GO:0007165, and regulation of the immune response.\\n\\nmechanism: the mechanism involving these genes involve ligand binding to cytokine, chemokine, or other receptors, resulting in the activation of intracellular pathways leading to signal transduction, GO:0007155, regulation of the immune response]] | \n", + "[[the genes identified are part of the cytokine signaling system and its related pathways involved in immune response and regulation. more specifically, they belong to the type i cytokine receptor family, the phospholipase a2 family, the tumor necrosis factor receptor superfamily, the gp130 family of cytokine receptors, the toll-like receptor family, the interferon regulatory factor family, the bcl2 protein family, the reg gene family, the type ii membrane protein of the tnf family, the ring finger e3 ubiquitin ligase family, the protein tyrosine phosphatase family, the tgf-beta superfamily proteins, the hemopoietin receptor superfamily, the chemokine family, the integrin alpha chain family of proteins and the adapter protein family. there is a common function of these genes in the signaling of cell growth, UBERON:2000098, GO:0006915, migration, and differentiation, as well as the regulation of gene transcription, apoptosis and immune response. \\n\\nmechanism:\\nthe genes identified are part of a gene network that functions together to allow for cell signaling, GO:0040007, and differentiation, as well as inflammatory and immune responses. the various cytokine receptors, protein ty]] | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[[GO:0005102, cytokine signalling, GO:0016049, cellular function regulation, immune signalling, inflammation regulation, GO:0051726, apoptosis coordination]] | \n", + "[[MESH:D008565, g protein-coupled receptors, MESH:D018121, interferon-induced proteins, MESH:M0013343, MESH:D051116, MESH:D018925, MESH:D016023, MESH:D020782, MESH:D061566, tol-like receptors]] | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[[interactions, GO:0023052, MESH:D008055, GO:0000981, MESH:D016207, MESH:D006728, MESH:D021381, receptors, GO:0007165]] | \n", + "[[GO:0005102, GO:0023052, GO:0055085, calcium binding, GO:0055085]] | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[[protein-binding, subunit-binding, rna-binding, transcriptional regulation, GO:0007165, GO:0006955, ligand binding, GO:0032991, GO:0036211]] | \n", + "[[ligand binding, GO:0005102, GO:0003824, GO:0003677, GO:0003723, protein activation, GO:0030163, MESH:D054875]] | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[[transcriptional regulation, GO:0008181, MESH:D010447, cytoplasmic proteins, antiviral, MESH:M0369740, GO:0009165, chemokine receptor, dna-binding, rna-binding, lipid-binding, protein adp-ribosylation, GO:0016567, GO:0048255, GO:0016556, GO:0006479, gtp-metabolizing, GO:0008283, GO:0006955, GO:0006952]] | \n", + "[[these genes are connected by their participation in immune regulation and defense, either directly regulating the innate and acquired immune response, or acting as downstream inhibitors and activators of such responses. specific enriched terms include interferon regulation, transcriptional regulation, tumor suppression, MESH:D054875, chemokine receptor signaling, GO:0003723, GO:0009165, GO:0051607, GO:0048255, GO:0005525, GO:0008289, viral invasion, GO:0045087, GO:0030701, GO:0008134, and antigen presentation.\\n\\nmechanism: the commonalities between these genes suggest that they act at various levels of a complex innate and acquired immune response, controlling transcriptional regulation, protein modification and silencing, viral response, and antigen presentation. there are multiple pathways overlapping or influencing each gene's particular role in the overall immune defense, merging into a greater shared mechanism of host immunity]] | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[[immune regulation, GO:0003677, GO:0003723, GO:0016567, anti-viral response, cytokine signaling, GO:0006954]] | \n", + "[[the genes in the list encode proteins involved in a variety of processes including immunity, GO:0006954, GO:0006351, GO:0007165, and protein folding and assembly. these processes are typically carried out by two main classes of molecules; ubiquitin ligases and cytokines. the genes in this list are enriched for terms including \"signal transduction\", \"ubiquitin ligases\", \"immune modulation\", \"cytokine activity\", \"transcription regulation\", \"proteasome activity\", \"rna binding\", and \"metallothionein\".\\n\\nmechanism:\\nthe genes in this list encode proteins involved in a variety of processes, with an emphasis on immunity and inflammation. these processes are typically mediated by ubiquitin ligases, MESH:D016207, and other signal transduction proteins. ubiquitin ligases mark target proteins for ubiquitination and other modifications, while cytokines affect the activity of multiple cells. signal transduction proteins transmit signals across cell membranes, affecting the activity of cells. metallothioneins play a role in detoxification and protein folding and assembly, while proteasomes carry out protein degradation within the cell. transcripts are regulated by transcription factors, many genes contain rna binding domains]] | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[[GO:0006954, immune cell signaling and development, immune regulation, GO:0044237, regulation of innate and adaptive immunity, metabolic and transcriptional regulation, GO:0003677, GO:0003723]] | \n", + "[[transcriptional regulation, GO:0003824, binding ability, protein structure, cell signalling, MESH:D016207, growth factor signalling, MESH:D007109, GO:0000981, MESH:D054875, MESH:D006136, tripartite motif, GO:0070085, atpase, intracellular sensor, MESH:D015088, GO:0003723, calcium-binding, GO:0004930, MESH:M0476528, cysteine-aspartic acid protease, regulator of complement activation, protein tyrosine phosphatase, ubiquitin-specific protease, antiviral activity, inter]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[[protein-binding, transcriptional regulation, GO:0007155, cell membrane channel activity, protein metabolism/modification, receptor signalling]] | \n", + "[[ion channels & transporters, receptor proteins, MESH:D002135, MESH:D004798, cell signaling, hormone regulation, GO:0008152]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[[MESH:D011506, GO:0016049, cellular development, MESH:D009068, GO:0001508, calcium binding, GO:0005496, GO:0008152, GO:0006351, GO:0005488, MESH:C062738, GO:0005562, g proteins, dna-binding]] | \n", + "[[catalyzing reactions, GO:0055085, GO:0023052, dna-binding, GO:0006351, extracellular signaling, calcium-ion binding, immune system signaling, cell growth/maintenance, GO:0007154, hormone regulation, GO:0032502, GO:0008152]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[[GO:0007155, regulation of growth factors, cytokine regulation, calcium activation, transcriptional regulation]] | \n", + "[[MESH:D008565, MESH:D010447, receptor proteins, MESH:D004268, MESH:D010770, GO:0000981, GO:0008217, MESH:M0022898, GO:0007165, transcriptional regulation, GO:0006811, GO:0006936, immunologic regulation, GO:0001816, GO:1901987, GO:0006915, GO:0007155, MESH:D063646]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[[GO:0003677, MESH:D015533, cytokine regulation, GO:0008083, GO:0005515, GO:0007165, transmembrane protein activity, GO:0004930, GO:0003723, GO:0003924, GO:0005509, GO:0016571, glutamine-fructose-6-phosphate transaminase activity, cell growth control, GO:0019725, GO:0016491]] | \n", + "[[receptor functions]] | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[[cytoskeletal organization, GO:0003677, microtubule organization, gtpase regulation, centrosome interaction, chromatin structure, protein homodimerization]] | \n", + "[[cytoskeleton regulation, cellular communication, gtpase regulation, actin-binding, dna-dependent protein binding, microtubule-associated protein, filamentous cytoskeletal protein, 14-3-3 family protein, MESH:D020662]] | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[[MESH:D020558, nucleotide exchange regulation, cellular signaling, GO:0006338, cytoskeleton structure, GO:0006260, GO:0007155, GO:0003779, actin regulation]] | \n", + "[[gtpase activation, GO:0005525, structural maintenance, GO:0003677, GO:0005856, GO:0006915, GO:0007049]] | \n", + "||
| HALLMARK_MTORC1_SIGNALING-0 | \n", + "[[GO:0006412, GO:0015031, protein signaling, GO:0008152, GO:0010467]] | \n", + "[[GO:0006412, GO:0008152, GO:0006457, MESH:D054875, GO:0006351, GO:0003677, damage control, GO:0032502, cellular pathway regulation, GO:0006915, GO:0007049, GO:0030163]] | \n", + "||
| HALLMARK_MTORC1_SIGNALING-1 | \n", + "[[GO:0005515, MESH:D054875, GO:0006351, GO:0003824, GO:0006457, chaperoning, GO:0051726, GO:0006629, GO:0046323, cytoskeleton formation]] | \n", + "[[atp production, amino acid homeostasis and metabolism, stress response, transcription and mrna regulation, chaperones and proteasome degradation pathways, GO:0006629]] | \n", + "||
| HALLMARK_MYC_TARGETS_V1-0 | \n", + "[[GO:0006351, GO:0006412, GO:0003729, MESH:D054657, MESH:D000072260, GO:0043687, cytoplasmic proteins, MESH:M0015044, GO:0003677, GO:0032508, GO:0005652, GO:0005681]] | \n", + "[[GO:0006351, GO:0006412, GO:0006413, GO:0003723, MESH:D054875, GO:0005840, GO:0006412, GO:0032508, MESH:D039102, GO:0003734, GO:0045292, heat shock proteins, MESH:D006655, MESH:D011073, MESH:D000604, GO:0043687]] | \n", + "||
| HALLMARK_MYC_TARGETS_V1-1 | \n", + "[[GO:0009299, GO:0042254, GO:0006412, MESH:D049148, GO:0003723, GO:0043687, GO:0045292, polymerase, GO:0006913, MESH:D054875, GO:0006457, 14-3-3 family proteins]] | \n", + "[[poly(a)-binding, GO:0003723, GO:0032508, GO:0006913, GO:0032183, GO:0000394, GO:0003676, GO:0006473, GO:0006413, GO:0036211, GO:0006457, MESH:D014176, GO:0006412, MESH:D018832, peptidyl-prolyl cis-trans isomerization, antioxidant function, heat shock protein, ubiquitin protein ligase, 14-3-3 family, dna-unwinding enzymes, dna polymerase, voltage-dependent anion]] | \n", + "||
| HALLMARK_MYC_TARGETS_V2-0 | \n", + "[[GO:0003723, ribosomal biogenesis, GO:0008283, GO:0006335, GO:0007165, cell cycle progression, GO:0003682]] | \n", + "[[GO:0005515, transcriptional regulation, cell cycle progression, protein chaperoning, GO:0008283, nuclear localization, rna binding activity, pre-rrna processing, GO:0042254]] | \n", + "||
| HALLMARK_MYC_TARGETS_V2-1 | \n", + "[[GO:0006351, rna binding activity, GO:0006457, cell cycle progression, GO:0006281, protein homodimerization, GO:0006468, GO:0065003, protein kinase/phosphatase activity, mitochondrial mrna processing. mechanism: this list of genes encodes proteins which work together to regulate key cellular activities such as dna replication, transcription, cell cycle progression, and rna processing. these proteins can either complex together or work in tandem to form kinase/phosphatase complexes, which control phosphorylation of key substrates and regulate protein folding to ensure proper protein function. these proteins also interact with dna to regulate genomic activities such as dna replication, transcription, and repair processes]] | \n", + "[[rna binding activity, GO:0006364, protein homodimerization, GO:0008283, GO:0007165, GO:0042254, GO:0006457, GO:0034246]] | \n", + "||
| HALLMARK_MYOGENESIS-0 | \n", + "[[motor protein activity, GO:0019722, GO:0006936, transcriptional regulation, intracellular fatty acid-binding, ligand binding, MESH:D007473, GO:0005884, MESH:D008565, regulation of transcription, phosphorylation of proteins]] | \n", + "[[GO:0006936, calcium channel regulation, ion channel regulation, protein ubiquitination/degradation, actin-based motor proteins, GO:0007165, MESH:D004734]] | \n", + "||
| HALLMARK_MYOGENESIS-1 | \n", + "[[MESH:M0496924, protein regulation, ion channeling, cellular transport, GO:0006629, GO:0010468, neurotransmitter signaling, small molecules, large molecules]] | \n", + "[[summary: the list of genes provided contains components of muscle formation, GO:0023052, and growth.\\nmechanism: the genes encode the components of signaling pathways and physical structures involved in the formation of muscle, including proteins that serve as receptors, binders, MESH:D004798, and structural components like spectrins, GO:0005202, laminin.\\nenriche terms: muscular development; musculosketetal function; signal transduction; protein phosphorylation degradation; cytoplasmic proteins; structural proteins; cytochrome oxidase]] | \n", + "||
| HALLMARK_NOTCH_SIGNALING-0 | \n", + "[[cell fate decisions, GO:0007219, GO:0007165, wnt signalling pathway, cell-cell interaction, GO:0016567, GO:0006355, protein ligase activity, GO:0006468]] | \n", + "[[GO:0007219, GO:0016055, GO:0016567, transcriptional repressor, MESH:D015533, cell fate decisions, MESH:D044767, MESH:D011494]] | \n", + "||
| HALLMARK_NOTCH_SIGNALING-1 | \n", + "[[notch signaling, GO:0016567, cell-cycle regulation, protein breakdown and turnover, intracellular signalling pathways, cell fate]] | \n", + "[[GO:0007219, GO:0016567, GO:0001709, transcriptional regulation, GO:0031146, gamma secretase complex, MESH:D011493, wnt family, basic helix-loop-helix family of transcription factors]] | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[[GO:0005739, MESH:D004798, MESH:D010088, MESH:D010088, GO:0006754]] | \n", + "[[GO:0006006, GO:0006631, amino acid metabolism, GO:0005746, MESH:D007506, nadh-ubiquinone oxidoreductase, MESH:D009245, pyruvate dehydrogenase, GO:0022900, oxidative decarboxylation, nad+/nadh oxidoreductase, GO:0016467, MESH:D003576, MESH:D063988, matrix processing, shuttling mechanism.\\n\\nmechanism: the gene products involved in this metabolic pathways work to convert small molecules such as glucose and fatty acids into energy-containing molecules, such as atp and nadh, through a combination of redox reactions, electron transfer processes, and other catalytic systems. these processes involve the participation of numerous proteins, including membrane-associated proteins, enzymes, and enzyme complexes. these proteins form a complex network of interactions that enable the conversion of energy from one form to another, ultimately leading to atp production]] | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[[oxidative decarboxylation, MESH:D010088, MESH:D010084, GO:0006754, mitochondrial respiration, GO:0008152, MESH:D003580, MESH:D000214, pyruvate dehydrogenase, MESH:D005420, hydratase/isomerase, leucine-rich protein, 3-hydroxyacyl-coa]] | \n", + "[[terminal enzyme, GO:0006754, GO:0005746, nad/nadh-dependent, cytochrome c oxidase (cox), GO:0006118]] | \n", + "||
| HALLMARK_P53_PATHWAY-0 | \n", + "[[GO:0007049, GO:0006351, GO:0023052, GO:0006412, GO:0065007, GO:0042592]] | \n", + "[[GO:0005515, GO:0003677, transcriptional regulation, GO:0051726, cell signaling]] | \n", + "||
| HALLMARK_P53_PATHWAY-1 | \n", + "[[GO:0051726, GO:0016049, GO:0006915, GO:0007165, GO:0006281, transcriptional regulation, chromatin structure, tumor suppression, enzymatic activity, GO:0000988, GO:0004725, GO:0003925]] | \n", + "[[MESH:D011494, GO:0000981, GO:0007049, GO:0006281, GO:0003677, GO:0006412, tnf receptor superfamily, zinc finger, calcium-activated, cyclin dependent, iron-sulfur, GO:0015629, GO:0007165]] | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[[analysis of the human genes abcc8, akt3, chga, dcx, dpp4, elp4, foxa2, foxo1, g6pc2, gcg, gck, hnf1a, iapp, UBERON:0002876, insm1, isl1, lmo2, mafb, neurod1, neurog3, nkx2-2, nkx6-1, pak3, pax4, pax6, pcsk1, pcsk2, pdx1, pklr, scgn, sec11a, slc2a2, spcs1, srp14, srp9, srprb, UBERON:0035931, stxbp1, syt13, vdr was performed to determine commonalities in gene function. term enrichment indicated a commonalty in genes that are involved in the regulation of glucose and insulin metabolism, GO:0008283, differentiation and apoptosis, as well as glycogen synthesis and glucose uptake. additionally, many of the genes are involved in the development of neural tissues and the regulation of gene transcription. the underlying biological mechanism could involve alterations in the phosphorylation of proteins and signaling pathways,]] | \n", + "[[GO:0000981, homeobox domain, signal peptide cleavage, MESH:D011494, atp-binding, chromogranin/secretogranin, GO:0005180, protease, MESH:D011770, MESH:D005952, MESH:D000243, MESH:D006593, nuclear receptor, dna-binding, g-protein linked receptor, cysteine-rich protein, gtp-bound proteins, GO:0048500, bhlh transcription factor, doublecortin, calcium-binding protein\\n\\nsummary: genes identified in this list facilitate a variety of essential biological processes, particularly in terms of cell signaling and transcription regulation. among these processes are signal peptide cleavage, atp-binding, peptide hormone secretion and regulation, protease activity, glucose metabolism, adenosine deaminase, gtp-bound protein binding, and transcription factor actions. \\n\\nmechanism: these genes are involved in transcriptional regulation and signaling processes through binding of dna and g-protein linked receptors, homeobox domains, cysteine-rich proteins]] | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[[this analysis identifies the common functions of 18 human genes: dpp4, scgn, pklr, pax4, neurod1, srprb, srp14, isl1, insm1, pak3, pax6, elp4, dcx, iapp, lmo2, neurog3, gck, stxbp1, nkx2-2, pdx1, UBERON:0035931, pcsk1, nkx6-1, UBERON:0002876, pcsk2, spcs1, g6pc2, foxo1, sec11a, vdr, foxa2, slc2a2, mafb. they are related to metabolic regulation (glucose, GO:0016088, MESH:D004837, citrate), developmental regulation (neural tissues, UBERON:0001264, UBERON:0002107, lymph nodes), signal transduction (g proteins, ace, atp binding proteins) and hormone regulation related (somatostatin, GO:0016088, vitamin d3). these factors likely work in concert to control and maintain metabolic parameters throughout the body. mechanism: these genes act through various methods including transcriptional regulation, protein interactions, protein cleavage, signaling casc]] | \n", + "[[transcriptional regulation, MESH:M0496924, endocrine system regulation, GO:0006006, cell signalling, MESH:D020558, GO:0000981, GO:0005180, MONDO:0018815, MESH:D043484]] | \n", + "||
| HALLMARK_PEROXISOME-0 | \n", + "[[MONDO:0018815, an antioxidant enzyme, a hormone binding protein, a nuclear receptor transcription factor, a fatty acid desaturase, a carnitine acyltransferase, an isocalate dehydrogenase, a peroxisomal membrane protein, MESH:D005182, antioxidant enzyme, hormone binding protein, nuclear receptor transcription factor, GO:0004768, carnitine acyltransferase, isocalate dehydrogenase, peroxisomal membrane protein, and fad-dependent oxidoreductase.\\n\\nmechanism: many of the genes are involved in regulating the production and movement of lipids and fatty acids, as well as the synthesis of hormones, MESH:D000305, and signalling receptors. the underlying biological mechanism is that these genes act as regulators of metabolic pathways, ensuring that their respective pathways are functioning correctly and that metabolites are transported correctly]] | \n", + "[[GO:0140359, oxidoreductase, dehydrogenase/reductase, hydratase/isomerase, enzymes responsible for fatty acid beta-oxidation, enzymes catalyzing the]] | \n", + "||
| HALLMARK_PEROXISOME-1 | \n", + "[[GO:0006629, GO:0006635, GO:0006281, transcription and replication, MESH:D018384, GO:0006536, GO:0005502, GO:0008202]] | \n", + "[[MESH:D018384, MONDO:0018815, atpases associated with diverse cellular activities, vitamin a family, GO:0004879, nad-dependent oxidoreductases, GO:0005783, MESH:D015238, cyclin-dependent protein kinase, hydratase/isomerase superfamily, GO:0005515, GO:0003677, GO:0050632, carnitine acyltransferase, MESH:D011960]] | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[[GO:0016310, GO:0006412, mrna expression, GO:0005515, cell signalling, MESH:D054875, protein phosphatase]] | \n", + "[[MESH:D011494, GO:0016791, GO:0005525, protein-protein interaction, GO:0030552, GO:0000981, peptidyl-prolyl cis/trans isomerase, cytoskeletal function, protein tyrosine phosphatase, protein phosphatase, GO:0140597, MESH:D020662, receptor interacting protein, transmembrane glycoprotein, MESH:D018123, MESH:D054387, inositol trisphosphate receptor, plexin domain, phosphoinositide 3-kinase, ubiquitin activation/conjugation, GO:0003925]] | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[[GO:0007165, MESH:D011494, GO:0004707, MONDO:0008383, gpcr, GO:0016791, MESH:D020662, endoplasmic reticulum chaperone protein]] | \n", + "[[MESH:D011494, guanine nucleotide-binding protein, receptor-interacting protein, chaperone protein, protein tyrosine kinase, MESH:D020558, MESH:D000262, protein phosphatase, cytoplasmic face, GO:0006468, GO:0007165, GO:0036211]] | \n", + "||
| HALLMARK_PROTEIN_SECRETION-0 | \n", + "[[GO:0005480, GO:0006897, GO:0006887, intracellular trafficking, MESH:D001678, MESH:D008565, GO:0005906, MESH:D020558, GO:0005794, GO:0005484]] | \n", + "[[MESH:D008565, MESH:D020558, coatomer complex, GO:0016192, MESH:D001678, GO:0035091, GO:0065007, MESH:D002966, GO:0005906, GO:0005794, GO:0030136, MONDO:0018815, GO:0042393, GO:0005802, MESH:M0013340, GO:0006811, GO:0005159, GO:0005783, MESH:D057056, GO:0005483, GO:0005764, GO:0005794, multifunctional proteins]] | \n", + "||
| HALLMARK_PROTEIN_SECRETION-1 | \n", + "[[GO:0003924, snare binding activity, GO:0005484, phosphoinositide-binding, coatomer protein complex, MESH:D052067, protein kinase binding activity, adaptor complexes, atpases associated with diverse cellular activities, snare recognition molecules, gold domain, GO:0030136, transmembrane 4 superfamily, GO:0070273, sec7 domain, membrane mannose-specific lectin, signal-transducing adaptor molecule, identical protein binding activity]] | \n", + "[[this list of genes codes for proteins of various functions, primarily related to organelle trafficking, membrane associations, and receptor binding activities. these proteins are involved in the regulation of intracellular vesicles, endoplasmic reticulum and golgi organization, protein sorting and secretion, cell surface receptor binding, cell-signaling and immunity, protein phosphorylation and kinase binding, and lipid protein modifications. the enriched terms found in the functions of these genes include vesicular transport, MESH:M0354322, organelle trafficking, GO:0007030, GO:0005102, GO:0006457, GO:0006468, snare recognition molecules, clathrin coated vesicles, endoplasmic reticulum-golgi transport, MESH:D025262, GO:0005906, and dystrophin-glycoprotein complex. \\n\\nmechanism: the enriched terms in the gene functions indicate that these proteins are involved in various pathways and process of intracellular cargo trafficking, where proteins, membranes and signaling molecules are sorted, distributed and regulated. the processes are involved with vesicular transport, protein co-translocation, GO:0030258, and protein phosphorylation, which coordinate the mobilization and distribution of proteins, MESH:D008055]] | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[[MONDO:0018815, copper chaperone, MESH:D002374, GO:0004861, hypoxia inducible factor (hif), nucleotide excision repair pathway, GO:0004672, GO:0009487, MESH:D005979, MESH:D009195, MESH:D010758, phosphofructokinase, MESH:D054464, GO:0050115, arginine/serine-rich splicing factor, iron/manganese superoxide dismutase, GO:0016491, germinal centre kinase iii (gck iii) subfamily, thioredoxin (trx) system]] | \n", + "[[this list of genes were found to be involved in oxidoreductase activity, intracellular binding and catalytic activity, cellular response regulation, dna and transcription regulation, membrane function, mitochondrial function and antioxidant activity. the enriched terms include oxidoreductase activity, intracellular binding, GO:0003824, cell growth regulation, transcription regulation, membrane function, mitochondrial function, GO:0016209, GO:0020037, GO:0005507, GO:0003677, GO:0043565, tyrosine-specific protein kinase activity, f-actin binding. the underlying biological mechanism is probable related to redox homeostasis, the oxygen metabolism pathway, the cell cycle dna repair pathways, the regulation of transcription membrane function]] | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[[GO:0016049, GO:0007049, GO:0006351, redox regulation, MESH:D018384, MESH:D005721, hydroxylase, protease, free-radical scavenging, protein phosphatase]] | \n", + "[[redox processes, MESH:D018384, GO:0006281, GO:0008152, cell growth regulation, inflammation control, cellular defense, MESH:D006419, MESH:D005980, superoxide dism]] | \n", + "||
| HALLMARK_SPERMATOGENESIS-0 | \n", + "[[protein binding activity, GO:0003714, dna binding activity, rna binding activity, zinc ion binding activity, GO:0004596, serine/threonine-protein kinase activity, GO:0004016, snare binding activity, clathrin binding activity, myosin light chain binding activity, double-stranded dna binding activity, phosphatidic acid phosphohydrolase activity, ubiquitin-protein ligase activity, rna polymerase binding activity, GO:1990817, GO:1990817, GO:0060090, phosphatase binding activity, atp-ases associated activity, GO:0044183, GO:0016165, adp-ribosylation factor-like activity]] | \n", + "[[cell cycle regulatory proteins and kinases, dna binding proteins and chaperones, nucleotide and polypeptide binding proteins, GO:0016791, proteins involved in transcription, gene transcription, GO:0051276, apoptosis regulation, GO:0006281, protein folding and transport, cell signaling and growth regulation, MESH:D004734, cytoskeletal organization, vesicular trafficking\\n\\nmechanism: the underlying biological mechanism is likely involved in multiple steps in cell division and the regulation of gene expression, and in the maintenance of cell homeostasis]] | \n", + "||
| HALLMARK_SPERMATOGENESIS-1 | \n", + "[[GO:0006457, transcriptional regulation, GO:0007165, GO:0051726, chromatin structure and nuclear envelop function, cell adhesion and motility, GO:0008152, GO:0016567, detection and binding, enzymatic activity, GO:0042311]] | \n", + "[[this list of genes is associated with a range of diverse functions, including intracellular and intercellular trafficking, adhesion, enzyme regulation, transcriptional regulation, ion channel and receptor regulation, and processes related to stress, GO:0007568, and metabolism. common enriched terms include protein kinase and phosphatase, GO:0140359, g-protein coupled receptors, receptors, transcriptional regulation, GO:0016569, GO:0051726, heat shock, GO:0005515, ubiquitin-protein ligase and ubiquitin protease, zinc metalloproteases, and peptide n-acetyltransferase. the underlying biological mechanism or pathway associated with these genes may involve signal transduction as mediated by enzyme activity, MESH:D007473, receptors, and other proteins, as well as cell-to-cell adhesion and trafficking processes involved in membrane dynamics.\\n\\nsummary: list of genes associated with diverse functions including intracellular and intercellluar trafficking, adhesion, regulation of enzymes, GO:0006351, ion channels and receptors, and processes related to stress, GO:0007568, and metabolism.\\nmechanism: signal transduction as mediated by enzyme activity, MESH:D007473, receptors, and other proteins, as well as cell-to]] | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[[transmembrane proteins, receptor signaling pathways, transcription regulation, cell signaling, GO:0007155, GO:0016049, tgf-beta superfamily, MESH:D010749, ubiquitin ligases, tight junction adaptors]] | \n", + "[[the human gene summaries represent a variety of cell signaling, cell growth and differentiation, transcription regulation, adhesion and migration, and apoptosis-related functions. several genes in the list (acvr1, GO:0005680, arid4b, bmpr1a, bmpr2, cdh1, ifngr2, junb, lefty2, map3k7, ncor2, ppm1a, pp1ca, rahb, smad1, smad3, smad6, smurf1, smurf2, tgfb1, tgfbr1, MESH:D016212, cdk9, cdkn1c, ctnnb1, eng, fnta, MESH:D045683, hipk2, id1-3, klf10, ltbp2, pmepa1, ppp1r15a, serpine1, ski, skil, slc20a]] | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[[transmembrane serine/threonine kinases, transcriptional repressors, transforming growth factor (tgf)-beta superfamily, rho family of small gtpases, smad family, c2h2-type zinc finger domains, MESH:M0460357, caax geranylgeranyltransferase, smad interacting motif (sim), homeodomain-interacting protein kinase, MESH:D004122, transforming growth factor-beta (tgfb) signal transduction, MESH:D018398, MESH:D054645, protein folding and trafficking]] | \n", + "[[GO:0007165, transcription regulation, cell-to-cell communication, MESH:D018398, serine/threonine protein kinase, disulfide-linked homotrimeric proteins, protein phosphatase, transmembrane proteins, smurf protein, cystein-rich motif, GO:0006457]] | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[[GO:0006351, cytokine, inflammatory, UBERON:2000098, GO:0006915, cell signalling, receptor regulation, GO:0003924, GO:0003723]] | \n", + "[[transcriptional regulation, GO:0005125, GO:0008283, GO:0006629]] | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[[MESH:D016207, MESH:D018925, MESH:D010770, GO:0000981, MESH:D016212, nf-kappa-b, myc/max/mad, jagged 1, stat-regulated pathways, MESH:D008074, MESH:M0496065]] | \n", + "[[GO:0006954, GO:0007165, transcriptional regulation, GO:1901987, cytokine, MESH:D011506, receptor, GO:0000981, enzyme, growth factor, MESH:D019204, chemokine, MESH:D008074, pentraxin protein, GO:0016791, MESH:D010770, stress response]] | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[[rna-binding, protein-binding, GO:0019538, GO:0009058, GO:0044183, GO:0000981, GO:0006457]] | \n", + "[[GO:0003723, transcription regulation, GO:0006457, protein targeting and covalent modifications, endoplasmic reticulum function, GO:0006413]] | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[[GO:0003723, GO:0005783, transcriptional regulation, GO:0006457, GO:0140597, mrna decapping, MESH:M0465019, GO:0030163, MESH:D021381]] | \n", + "[[GO:0006412, endoplasmic reticulum stress response, GO:0003723, protein expression, conformation folding]] | \n", + "||
| HALLMARK_UV_RESPONSE_DN-0 | \n", + "[[cellular response regulation, GO:0007165, transcriptional regulations, MESH:D011956, GO:0016310, calcium binding, MESH:D011494, transmembrane proteins, protein tyrosine kinases, MESH:D017027, MESH:M0015044, protein inhibitor of activated stats, integrin beta, annexin family, adp-binding cassette family, MESH:D020690, arfaptin family, wd repeat proteins, maguk family, camp-dependent pathways, MESH:D000071377, MESH:D008869, pak family, MESH:D015220, mitogen-responsive phosphoproteins, nuclear histone/protein, celf/brunol family, four-and-a-half-lim-only proteins]] | \n", + "[[GO:0007155, GO:0005207, nuclear phosphoprotein, phosphoprotein, cytoplasmic receptor, MESH:D020558, GO:0016791, receptor tyrosine kinase, GO:0006351, camp, ion transport atpase, transmembrane protein]] | \n", + "||
| HALLMARK_UV_RESPONSE_DN-1 | \n", + "[[GO:0007165, MESH:D016326, cellular adhesion, GO:0000981, MESH:D011494, MESH:D020558, camp, calcium-dependent phospholipid binding protein, MESH:D011505, MESH:D017868, scaffolding protein, MESH:D020690, MESH:D010711, protein tyrosine phosphatase, rho-like gtpase, calcium-activated bk channel, cyclin-dependent kinase, n6-methyladenosine-containig protein, helix-loop-helix proteins, MESH:D016601, atpase, guanine nucleotide-binding protein, cytoplasmic surface protein, serine protease inhibitor, protein inhibitor of activated stat, GO:0004384, mitogen-responsive]] | \n", + "[[GO:0000981, receptor, GO:0005488, growth factor, phosphoprotein, MESH:D010770, cytoplasmic surface, nuclear histone/protein methyltransferase, MESH:D020558, wd repeat protein, protein tyrosine phosphatase, serine/threonine kinase, caveolae plasma membrane, g-protein coupled receptor, MESH:D000071377, ab hydrolase superfamily, microtubule-associated protein, protein-tyros]] | \n", + "||
| HALLMARK_UV_RESPONSE_UP-0 | \n", + "[[cell regulation, GO:0055085, metabolic catabolism, transcription support, GO:0006468, non-classical heavy chain, GO:0020037, GO:0007165, cytoskeleton formation, GO:0030163, cell signaling, GO:0006412, GO:0010467]] | \n", + "[[GO:0005515, MESH:D002384, transcriptional regulation, cell signaling, metabolic reactions]] | \n", + "||
| HALLMARK_UV_RESPONSE_UP-1 | \n", + "[[GO:0005515, GO:0005525, GO:0005215, reactive catalysis, cell signaling, membrane-associated functions]] | \n", + "[[regulatory proteins, GO:0000981, membrane and transport proteins, structural proteins, MESH:D004798, biosynthesis of heme, cellular signaling, transcription control, GO:0008152, GO:0006955]] | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[[wnt signalling pathway, transmembrane glycoprotein, MESH:D006655, GO:0000981, GO:0007219, GO:0005515, GO:0007165, GO:0006511, transcriptional regulation, dna replication and repair]] | \n", + "[[cell-cell interactions, MESH:D047108, transcriptional regulation, GO:0006281, wnt signaling, notch signaling, hedgehog signaling, MESH:D044783]] | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[[wnt signaling, notch signaling, hedgehog signaling, transcriptional regulation, cell cycle progression, developmental events, dna replication and repair, transcriptional silencing, GO:0043161]] | \n", + "[[transcriptional regulation, GO:0001709, signaling pathway activation, MESH:D060449, notch pathway, hedgehog pathway, protein interactions, cell growth regulation, GO:0004672, GO:0030163, cell-cell interaction, cell-matrix interaction, protein ligase binding activity, GO:0004842, membrane-bound protease activity, transcriptional repressor, GO:0006338, notch receptor cleavage, intracellular domain formation, ectodomain shedding, MESH:D015533, nuclear receptor co-repressor]] | \n", + "||
| T cell proliferation-0 | \n", + "[[GO:0004888, calmodulin binding activity, GO:0061630, GO:0033192, GO:0004721, GO:0004725, GO:0004672, MESH:D015533, guanine nucleotide exchange activity, ligand binding activity]] | \n", + "[[the provided list of genes and associated descriptions demonstrates variation in generic cellular processes like protein degradation, protein and nucleic acid binding and kinase activity, as well as specific pathways involving cytokine and chemokine signaling, transcriptional regulation and regulation of immune cell activity. across these processes, the significant terms enriched across the genes include: protein tyrosine kinase activity; protein/nucleic acid/oligomeric binding activities; protein ubiquitination; transcriptional and immune cell activation and proliferation; intracellular receptor signaling and nf-kappab pathways; and cell cycle regulation.\\n\\nmechanism:\\nthe identified genes likely affect several common pathways, including signaling pathways that mediate cell division, motility, adhesion, chemokine- and cytokine-mediated responses, and immune cell function. in particular, the proteins encoded by these genes likely play roles in the regulation of post-translational modifications, such as protein ubiquitination, and the regulation of gene transcription, likely in response to extracellular cues. additionally, the identified proteins may mediate the recruitment of the cbm signalosome, leading to the activation of nf-kappab pathways. finally, cell cycle-related processes]] | \n", + "||
| T cell proliferation-1 | \n", + "[[transcriptional regulation, cellular signaling pathways and processes, GO:0016049, differentiation, GO:0006950, GO:0006955, protein folding and trafficking, MESH:D051192, transmembrane proteins, receptor tyrosine kinases, ubiquitin e3 ligases, MESH:D020134, cgmp-binding phosphodiesterase]] | \n", + "[[GO:0007165, GO:0008037, GO:0004721, GO:0061630, lipid enzyme, MESH:D011505, cgmp kinases, GO:0000981, protein scaffold, cytokine, adaptor protein, GO:0051301, adhesion, differentiation, GO:0006950, negatively regulated, MESH:D021381, cell fate and patterning, MESH:D002470, ligand-gated ion channel, GO:0051092, GO:0006569, er stress-induced protection, transmembrane glycoprotein, MESH:D050503, wnt gene family, GO:0016020]] | \n", + "||
| Yamanaka-TFs-0 | \n", + "[[this set of genes is involved in embryonic development, stem cell pluripotency, stem-cell maintenance, and dna damage response. commonly enriched terms include cell cycle regulation, transcription regulation, GO:0006915, cellular transformation, and dna damage repair. mechanism:these genes control critical functions of cell cycle progression, gene transcription, and dna repair, providing the necessary foundation for the development of the organism. these pathways provide the structural and biochemical features of embryonic development, maintenance of stem cells and pluripotency, response to cellular damage]] | \n", + "[[genes in this list are transcription factors involved in the development of various organ systems, such as the skin and cns, as well as responding to dna damage, GO:0006915, and cellular transformation. the enriched terms are transcription factor activity; gene expression regulation; cell cycle regulation; dna damage response; pluripotency; and embryo development.\\n\\nmechanism: the transcription factors in this list interact with dna, regulate gene expression, and influence cell cycle progression, GO:0006915, and cellular transformation. combined, these genes are thought to play a role in creating and maintaining cellular and tissue identity, as well as responding to environmental changes. this could be part of a larger mechanism that governs organism development and homeostasis]] | \n", + "||
| Yamanaka-TFs-1 | \n", + "[[GO:0000981, MESH:D047108, stem cell maintenance, MESH:D063646, GO:0030154]] | \n", + "[[GO:0000981, zinc finger proteins, GO:0007049, MESH:D004249, MESH:D016147, MESH:D047108, stem cell maintenance, translocation, homeodomain]] | \n", + "||
| amigo-example-0 | \n", + "[[GO:0007155, MESH:D016326, MESH:M0023728, cellular communication, GO:0042592, GO:0042060, GO:0006915, motility, GO:0001525]] | \n", + "[[GO:0007155, GO:0016477, cell signalling, GO:0008152, GO:0006915, GO:0009653, GO:0007599, MESH:D007109, extracellular matrix maintenance]] | \n", + "||
| amigo-example-1 | \n", + "[[GO:0007219, osteoclast attachment/mineralized bone matrix, jagged 1/notch 1 signaling, GO:0007155, GO:0006915]] | \n", + "[[GO:0048729, matrix metalloproteinase inhibitor, regulated cell adhesion, cytoplasmic protein tyrosine kinase, GO:0005161, cytokine-induced gene expression, GO:0005583, cell signaling pathway, MESH:D015533, antimicrobial activity, GO:0031012, GO:0016477, GO:0008283]] | \n", + "||
| bicluster_RNAseqDB_0-0 | \n", + "[[GO:0055085, growth factor regulation, calcium regulation, transcription regulation, MESH:D007473, calcium-dependent processes, protein binding activity, chromatin binding activity, gtpase activating protein binding activity, histone binding activity, dna-binding activity, sequence-specific double-stranded dna binding activity, GO:0000988]] | \n", + "[[GO:0007165, transcription regulation, ion regulation, GO:0005515, cytoskeletal adaptor, MESH:D006023]] | \n", + "||
| bicluster_RNAseqDB_0-1 | \n", + "[[this list of genes is involved predominantly in processes related to binding activities, dna-binding transcription factor activities, chromatin binding activities, and protein domain-specific binding. the underlying biological mechanism involves pathways that regulate cell morphology and cytoskeletal adaptor proteins. the enriched terms include: binding activity, GO:0003700, chromatin binding activity, protein domain-specific binding activity, cell morphology, MESH:D051179]] | \n", + "[[GO:0000988, metal ion binding activity, dna binding activity, chromatin binding activity, rna binding activity, protein domain-specific binding activity, histone binding activity, methylated histone binding activity]] | \n", + "||
| bicluster_RNAseqDB_1002-0 | \n", + "[[GO:0007165, protein-protein interactions, MESH:D004734, GO:0051015, troponin binding, GO:0005523, GO:0051219, GO:0032515, GO:0043531, atp binding. mechanism: these genes are involved in pathways of signal transduction, protein-protein interactions, and energy metabolism, which lead to muscle contraction and tissue development. activation of these pathways leads to calcium release, which in turn activates contractile proteins such as troponin, tropomyosin, and actin. these proteins act together to promote muscle contraction and cytoskeletal structure]] | \n", + "[[GO:0051015, GO:0048870, GO:0004722, myosin-binding proteins, MESH:D002154, GO:0045010, GO:0005523, calcium sensitivity, MESH:D044767, GO:0003735, GO:0004930, GO:0042923, GO:0050262, GO:0061769, GO:0019674, GO:0007015, GO:0006936, GO:0055008, GO:0030838]] | \n", + "||
| bicluster_RNAseqDB_1002-1 | \n", + "[[MESH:D024510, actin and tropomyosin binding, calcium- and energy-regulation, ion channeling, negative regulation of cytokine signaling pathways, GO:0033173]] | \n", + "[[actin filament binding activity, muscle alpha-actinin binding activity, actin monomer binding activity, tropomyosin binding activity, GO:0006936, GO:0045214, GO:0071691, GO:0045010, GO:0030838, muscle excitation-contraction coupling, calcium release complex, muscle associated proteins, GO:0030036, GO:0007507]] | \n", + "||
| endocytosis-0 | \n", + "[[GO:0006897, GO:0015031, GO:0051639, endoplasmic reticulum and recycling endosome membrane organization, GO:0044351, GO:0016043, intracellular signaling, GO:0051260]] | \n", + "[[GO:0030030, MESH:D021381, MESH:D011494, GO:0048870, membrane reorganization, GO:0006897, cytoskeletal reorganization, mitogen-activated protein kinase, lysosomal degradation, GO:0051168]] | \n", + "||
| endocytosis-1 | \n", + "[[GO:0015031, GO:0006897, GO:0006898, GO:0051260, GO:0007155, GO:0048870, amino acid residues, MESH:D054875, GO:0015908, cytoskeletal reorganization, GO:0016192, signaling complex regulation, GO:0140014, GO:0006919]] | \n", + "[[GO:0006897, lysosomal degradation, GO:0015031, GO:0006898, membrane processes, gtpase regulation, MESH:D044767, death domain-fold]] | \n", + "||
| glycolysis-gocam-0 | \n", + "[[GO:0006096, GO:0016310, MESH:D006593, glucose phosphate isomerase, phosphofructokinase, MESH:D005634, fructose-1,6-bisphosphate, MESH:D014305, glyceraldehyde-3-phosphate dehydrogenase, MESH:D010736, MESH:D011770, MESH:D010751]] | \n", + "[[GO:0006006, GO:0006096, GO:0016310, GO:0006000, GO:0006094, GO:0004332, glycogen storage, GO:0016853, GO:0004743, GO:0004396]] | \n", + "||
| glycolysis-gocam-1 | \n", + "[[muscle maturation, MESH:D024510, GO:0001525, GO:0006096, MONDO:0003664, MONDO:0002412, plasmin regulation]] | \n", + "[[GO:0006096, GO:0008152, regulation of energy conversion, MESH:D024510, tumor progression, GO:0006094, GO:0001525, neurotrophic factor, MESH:M0025255]] | \n", + "||
| go-postsynapse-calcium-transmembrane-0 | \n", + "[[GO:0006816, calcium ion regulation, postsynaptic ion channel, GO:0005892, glutamate receptor channel, g protein-coupled receptor, plasma membrane protein, ligand-gated ion channel]] | \n", + "[[calcium homeostasis, calcium-channel activity, MESH:D007473, g-protein coupled receptor, ligand-gated ion channel]] | \n", + "||
| go-postsynapse-calcium-transmembrane-1 | \n", + "[[calcium ion regulation, GO:0006816, n-methyl-d-aspartate receptor family, MESH:C413185, MESH:D011954, p-type primary ion transport atpases]] | \n", + "[[calcium homeostasis, calcium influx, GO:0007268, neuronal development, MESH:D058446, purinergic receptor, GO:0004972, MESH:C413185, g-protein coupled receptor]] | \n", + "||
| go-reg-autophagy-pkra-0 | \n", + "[[GO:0043539, protein serine/threonine kinase binding activity, GO:0004860, GO:0005085, GO:0032008, GO:0010605, GO:0032956, GO:0032006, GO:0016241, regulation of nf-kappab activation, GO:0001558, regulation of cell survival, GO:0038187, GO:0006281, GO:0045087]] | \n", + "[[GO:0016049, GO:0006915, GO:0007165, serine/threonine kinase activator activity, GO:0035004, GO:0005085]] | \n", + "||
| go-reg-autophagy-pkra-1 | \n", + "[[this term enrichment test looked at a list of human genes together with their functions. it found that the genes have functions related to cell cycle regulation, GO:0007165, GO:0043170, protein kinase binding and regulating chromatin remodeling and transcription. the enriched terms include cell cycle regulation, GO:0007165, GO:0043170, GO:0019901, GO:0016310, chromatin remodeling and transcriptional regulation.\\n\\nmechanism: the genes in this list are involved in processes such as cell cycle regulation, GO:0007165, GO:0043170, GO:0019901, phosphorylation and chromatin remodeling and transcription, which are interconnected. these processes all depend on the activity of various protein kinases and their activation by various components, including snca, MESH:D053148, trib3, ccny, pik3ca, akt1, nod2, kat5, rptor, smcr8, mlst8, tab2, hspb1, irgm, GO:0033868, cdk5r1 and other proteins. they interact and cooperate with each other to form pathways and complexes responsible for cell cycle regulation and activation or inhibition of specific genes. ph]] | \n", + "[[GO:0006281, apoptosis regulation, GO:0007165, GO:0016049, nutrient and insulin levels, macromolecule metabolic process regulation, GO:1901987, GO:0006338]] | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[[GO:0016798, GO:0005980, GO:0006516, GO:0051787, GO:0036503, glycosaminoglycan hydrolysis, heparan sulfate hydrolysis, cell surface hyaluronidase.\\nhpyothesis: the genes listed serve key roles in the degradation of polysaccharides and glycoproteins, the recognition of misfolded proteins and their subsequent degradation by endoplasmic reticulum-associated degradation, the hydrolysis of glycosaminoglycans, and the hydrolysis of heparan sulfate for the maintenance of cell proteins and structure]] | \n", + "[[glycosyl hydrolase, glycosyl bond hydrolysis, oligosaccharide processing, MESH:D006023, MESH:D011134, n-linked oligosaccharide, o-linked n-acetylglucosamine, β-1,4-glucosidase, β-glucosidase, β-hexosaminidase]] | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[[glycohydrolase enzymes, glycosaminoglycans (gag]] | \n", + "[[glycosyl hydrolase, glycohydrolytic enzyme, MESH:D006821, MESH:D005644, lysosomal hydrolase, n-linked oligosaccharide processing, MESH:D001616, MESH:D001619, MESH:D001617, MESH:D009113, alpha-1,4-glucosidase, MESH:D043323, MESH:D000520, MESH:D055572, mannosidase, MESH:M0012138, alpha-l-iduronic acid, alpha]] | \n", + "||
| ig-receptor-binding-2022-0 | \n", + "[[antigen binding activity, immunoglobulin receptor binding activity, GO:0002377, GO:0002250, protein homodimerization]] | \n", + "[[antigen binding activity, immunoglobulin receptor binding activity, activated/inactivated immune response, GO:0042803, peptidoglycan binding activity]] | \n", + "||
| ig-receptor-binding-2022-1 | \n", + "[[immunoglobulin receptor binding activity, GO:0002253, antigen binding activity, GO:0042803, immunoglobulin lambda-like polypeptides, preb cell receptor, src family of protein tyrosine kinases, c-type lectin/c-type lectin-like domain]] | \n", + "[[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253, GO:0042803, peptidoglycan binding activity, phosphatidylcholine binding activity, transduction of signals, allelic exclusion, myristylation, palmitylation, protein tyrosine kinases, sh2 and sh3 domains, MESH:D008285, MESH:D010455, antigen presenting cells, preb cells, src family of protein tyrosine kinases (ptks), c-type lectin domain]] | \n", + "||
| meiosis I-0 | \n", + "[[GO:0004519, bcl-2 homology domain 3 binding, GO:0003682, GO:0003677, GO:0003678, GO:0003697, 3'-5' exode]] | \n", + "[[the gene summaries indicate that most of the genes are involved in processes related to dna binding, GO:0006281, GO:0006310, and meiotic processes. the enriched terms include \"dna binding\", \"dna repair\", \"dna recombination\", \"meiosis\", \"double-stranded dna binding\", \"single-stranded dna binding\", GO:0003682, GO:0004519, dead-like helicase activity, and bcl-2 homology domain activity.\\n\\nmechanism: the mechanism underlying the enrichment of these gene functions appears to be related to the repair and maintenance of chromosomal integrity as well as the regulation of cell division, differentiation, and development. through their combined activities, the genes appear to be involved in the maintenance of genome stability and the efficient transmission of genetic information from one generation to the next]] | \n", + "||
| meiosis I-1 | \n", + "[[meiotic recombination, GO:0006281, GO:0007059, double-strand dna break repair, homologous chromosome pairing, dna binding activity, GO:0051289]] | \n", + "[[GO:0006281, meiotic recombination, GO:0006302, GO:0035825, chromosome synapsis, GO:0007059, MESH:D023902, holliday junction resolution, dna strand-exchange, reciprocal recombination, GO:0007130, GO:2000816, positive regulation of response to dna damage, GO:0006611, GO:0031297, GO:0000712, GO:0060629, GO:0003677, GO:0003697, single-str]] | \n", + "||
| molecular sequestering-0 | \n", + "[[this list of genes encodes proteins involved in a range of cellular processes such as cell cycle progression, GO:0006897, iron storage and regulation, cellular response to stress and inflammation, GO:0006915, transcriptional regulation, GO:0046907, GO:0016567, and toxic metal and cytosolic signaling. enriched terms include protein binding, lipid and hormone transport, GO:0003779, GO:0003724, GO:0006511, cell cycle progression, and negative regulation of nitrogen compound metabolic process. mechanism: these genes are involved in a wide range of processes related to regulating cell growth, GO:0032502, and homeostasis. they play a role in pathways such as the cell cycle, GO:0006915, inflammatory metabolic processes]] | \n", + "[[GO:0005515, GO:0046907, GO:0043161, GO:0051726, regulation of cell growth and survival, cholesterol and lipids metabolism, nf-κb inhibiting proteins, GO:0009792, GO:0007283, GO:0045087, cytokines and growth factors, antioxidant enzymes, GO:0030097]] | \n", + "||
| molecular sequestering-1 | \n", + "[[GO:0005515, MESH:D015533, GO:0008152, MESH:D007109, GO:0006915, GO:0007049, GO:0016310]] | \n", + "[[GO:0006897, iron storage, GO:0008610, GO:0006915, GO:0008283, GO:0030154, defense from bacterial infection, transcription regulation, translation regulation]] | \n", + "||
| mtorc1-0 | \n", + "[[GO:0006412, GO:0015031, protein signaling, GO:0008152, GO:0010467]] | \n", + "[[GO:0006412, GO:0008152, GO:0006457, MESH:D054875, GO:0006351, GO:0003677, damage control, GO:0032502, cellular pathway regulation, GO:0006915, GO:0007049, GO:0030163]] | \n", + "||
| mtorc1-1 | \n", + "[[metabolic reactions, GO:0051726, energy production, MESH:D011494, GO:0016791, MESH:D003577, MESH:D000604, peptidase c1 family, GO:0031545, ion transporter, ubiquitin-like proteases, ubiquitin ligases, serine/threonine protein kinases, glyceraldehyde-3-phosphate dehydrogenase, nadp-dependent dehydrogenases, rna binding protein, GO:0016467, pyruvate dehydrogenase, MESH:D012321, GO:0016538, MESH:D005634, heat shock protein, hetero trimeric co-factors, MESH:D050603, MESH:D000263, MESH:D013762, MONDO:0008090]] | \n", + "[[GO:0008152, GO:0023036, GO:0007165, transcriptional regulation, epigenetic regulation, GO:0044183, proteolytic activity, GO:0051726]] | \n", + "||
| peroxisome-0 | \n", + "[[this set of genes are enriched for terms related to peroxisomal biogenesis and peroxisomal protein import. the aaa atpase family, peroxisomal membrane proteins, c-terminal pts1-type tripeptide peroxisomal targeting signals, and peroxisomal targeting signal 2 are all over-represented in the gene list.\\n\\nmechanism: the mechanism behind these genes is the import of proteins into peroxisomes, resulting in peroxisomal biogenesis. the aaa atpases, peroxisomal membrane proteins, c-terminal pts1-type tripeptide peroxisomal targeting signals, peroxisomal targeting signal 2 are all involved in either targeting or catalyzing this protein import]] | \n", + "[[peroxisome biogenesis, peroxisomal protein import, tripeptide peroxis]] | \n", + "||
| peroxisome-1 | \n", + "[[this set of genes is related to the function of peroxisome biogenesis and associated disorders. the enriched terms are peroxisome biogenesis, GO:0017038, peroxisomal matrix proteins, atpase family, and pti2 receptor/pex7.\\n\\nmechanism: peroxisomes are important organelles for a variety of metabolic functions, and the synthesis and organization of these organelles is mediated by the pex genes. pex6 and pex2 are involved in protein import, where the pex2 protein forms a membrane-restricted complex, and pex6 is predominantly cytoplasmic and plays a direct role in peroxisomal protein import and receptor activity. pex3 and pex7 are required for peroxisomal biogenesis, and pex7 is the cytosolic receptor for the set of peroxisomal matrix enzymes targeted to the organelle by the peroxisome targeting signal 2. lastly, pex1 forms a heteromeric complex and plays a role in the import of proteins into peroxisomes and peroxisome biogenesis]] | \n", + "[[aaa atpase family, MONDO:0019234, peroxisomal protein import, peroxisomal matrix protein import, heteromeric complex, peroxisome targeting signal 2]] | \n", + "||
| progeria-0 | \n", + "[[GO:0000785, nuclear membr]] | \n", + "[[the genes in this list are associated with post-translational proteolytic cleavage, intermolecular integration, dna repair and dna helicase activity, and nuclear stability and chromatin structure. the underlying mechanism is likely related to protein modification and regulation of cellular components involved in dna metabolism and gene expression. the enriched terms include protein modification, proteolytic cleavage, GO:0003678, intermolecular integration, GO:0006281, chromatin structure, nuclear stability]] | \n", + "||
| progeria-1 | \n", + "[[these genes are all related to essential functions that facilitate the proper structure and organization of the nucleus and genome, primarily through the formation and maintenance of nuclear lamin, dna helicases and chromatin structures. there is evidence that all of these genes are involved in the proper functioning of cell division, GO:0006281, and transcription, as well as the maintenance of genome stability. the most enriched terms related to the functions of these genes are nuclear lamina, dna helicase, chromatin structure, GO:0006281, GO:0006351, genome stability, GO:0051301, nuclear membrane proteins, and nuclear localization signal. \\n\\nmechanism: the genes may be involved in pathways that coordinate the formation and maintenance of nuclear lamin, dna helicase, and chromatin structures, which are necessary for cell division and transcription, as well as the maintenance of genome stability. these pathways may involve the direct interactions between the gene products, as well as the recruitment of nuclear membrane proteins and signals involved in maintaining nuclear organization]] | \n", + "[[this set of genes is involved in the maintenance of genome stability and chromosome integrity, likely in terms of forming the nuclear lamina and promoting nuclear reassembly. the enriched terms are genome stability, chromosome integrity, GO:0005652, nuclear reassembly.\\n\\nmechanism: the set of genes are likely working together to form and maintain a matrix of proteins which form the nuclear lamina next to the inner nuclear membrane, thus providing stability to the genome and the chromosomes by helping to organize the dna within the nucleus. this is achieved through binding with both dna and inner nuclear membrane proteins and recruiting chromatin to the nuclear periphery to achieve nuclear reassembly]] | \n", + "||
| regulation of presynaptic membrane potential-0 | \n", + "[[neuronal signaling, neuron communication, MESH:D007473, excitatory dependent channels, inhibitory neurotransmitter, ligand-gated ion channel, g protein-coupled membrane receptor]] | \n", + "[[MESH:D007473, voltage-gated ion channel, MESH:D015221, ligand-gated ion channel, MESH:D018079, MESH:D017470, MESH:D015222]] | \n", + "||
| regulation of presynaptic membrane potential-1 | \n", + "[[MESH:D017981, MESH:D058446, GO:0009451, voltage-gated ion channels, channel subunits, channel polymorphisms, g-protein-coupled transmembrane receptors, MESH:D017470, MESH:D018079, MESH:D015221]] | \n", + "[[GO:0007268, MESH:D009482, inhibitory, excitatory, MESH:D017981, MESH:D015221, MESH:D018079, MESH:D017470, MESH:D007649, GO:0009451, voltage-gated, MESH:D007473, MESH:D058446, MESH:D019204]] | \n", + "||
| sensory ataxia-0 | \n", + "[[transcriptional regulation, mitochondrial rna synthesis, neurodevelopment, GO:0030218, GO:0036211, nucleolar function, neuronal network formation, sensory receptor function]] | \n", + "[[GO:0000981, GO:0009056, moonlighting proteins, GO:0002377, adapter molecules, heme transporter, myelin upkeep, GO:0005643, mitochondrial dna polymerase, ubiquitin ligase, aminoacyl-trna synthetase.\\n\\nmechanism: these genes work together in a joint mechanism to regulate biological processes like cell replication, neuronal development, protein folding, and enzymatic activity. in particular, their collective involvement in the coordination of transcriptional activity, ion transport, and dna-binding suggests a complex integrated process by which these genes serve to facilitate normal cell functions]] | \n", + "||
| sensory ataxia-1 | \n", + "[[GO:0000981, dna helicase, hexameric dna helicase, neurotrophic factor, pdz domain, ma cation channels, MESH:D005956, protein synthetase, mitochondrial dna polymerase, heme transporter, GO:0005643, MESH:D044767, transmembrane glycoprotein]] | \n", + "[[GO:0000981, dna helicase, nerve myelin maintenance, mechanically-activated cations channels, nerve motor neuron survival, MESH:D054875]] | \n", + "||
| term-GO:0007212-0 | \n", + "[[g-protein coupled receptor signaling, g-protein subunit signaling, GO:0004016, phospholipase c-beta activity, GO:0005102, GO:0007165, second messenger synthesis, transmembrane signaling]] | \n", + "[[the summaries of the provided gene functions describe proteins linked to the activity and regulation of g-protein coupled receptor signaling pathways, including dopamine, MESH:D016232, and serotonin receptors, as well as proteins involved in calcium ion regulation, GO:0003677, and apoptosis. statistically over-represented terms include: g-protein coupled signaling; calcium ion regulation; transmembrane signaling; dna binding; and apoptotic process. \\n\\nmechanism:\\nthe common function of these genes is likely to be linked to the regulation of g-protein coupled signaling pathways, which regulate a variety of cellular processes, including cellular signaling and growth, neuronal development, apoptosis. calcium ion regulation transmembrane signaling are also likely to be important for the functioning of these genes. dna binding proteins proteins that enable clathrin light chain binding activity may be involved in the transcriptional regulation of these signals]] | \n", + "||
| term-GO:0007212-1 | \n", + "[[the list of human genes supplied involves several different cell signaling pathways, including the dopamine receptor (drd1, drd2, drd3 and drd5) pathway, g-protein coupled receptor (gpcr) signalling pathway (gnas, gnai3, gnaq, gna11, gna14, gna15, gnb1, gnb5, gnao1, gng2, sl]] | \n", + "[[this gene set was comprised of dopamine and g-protein coupled receptors that participate in cellular signaling pathways and influence cellular functions such as metabolism and behavior. the genes are involved in a wide range of pathways such as signal transduction, transcriptional regulation, memory and behavior, GO:0007612, neural development and synaptic plasticity. the enriched terms in this list include: signal transduction, g protein-coupled receptor, camp, MESH:D000262, MESH:D054799, MESH:D017868, calcium ions, transcriptional regulation, GO:0000981, MESH:D011954, wnt and pi3k signaling pathways, neuronal growth and development, GO:0010467, and synaptic receptors.\\n\\nmechanism: this gene set is involved in many pathways such as signal transduction, transcriptional regulation, and synaptic organization. signal transduction occurs through g-protein coupled receptors and camp, which in turn regulate downstream effectors including adenylyl cyclase, MESH:D017868, and calcium ions. furthermore, transcriptional regulation occurs through various receptor signaling pathways, such as those related to the wnt and pi3k pathways, while dopamine receptors regulate neuronal growth and development, GO:0010467, and behavior. finally, synaptic receptors enable]] | \n", + "||
| tf-downreg-colorectal-0 | \n", + "[[transcriptional regulation, GO:0006338, GO:0003677, GO:0000981, coactivator, heterodimer, response element]] | \n", + "[[dna-binding, chromatin-binding, transcriptional regulation, e-box dna consensus sequence binding, dna damage response regulation, dna damage response maintenance, phosphoprotein shutting, MESH:D016335, interaction with cellular retinol-binding protein, hormone-dependent transcription, receptor-dependent transcription, nuclear hormone receptor-dependent transcription, transcriptional coactivator complex recruitment, GO:0000785]] | \n", + "||
| tf-downreg-colorectal-1 | \n", + "[[transcription factor regulation, GO:0016569, dna-binding activity, zinc-finger binding, GO:0032183, retinoid x receptor responsive element binding]] | \n", + "[[transcriptional regulation, dna-binding, chromatin binding activity, histone binding activity, GO:0000988]] | \n", + "||
| no_synopsis | \n", + "EDS-0 | \n", + "[[GO:0031012, ecm components, matrix components, ecm regulators]] | \n", + "[[GO:0001501, GO:0032964, cell-matrix interactions, extracellular matrix remodeling, cell signaling]] | \n", + "|
| EDS-1 | \n", + "[[extracellular matrix protein network, collagen fibril formation, GO:0030199, ecm protein network assembly, UBERON:2007004]] | \n", + "[[collagen production, GO:0061448, matrix remodeling, zinc finger protein regulation]] | \n", + "||
| FA-0 | \n", + "[[MONDO:0100339, \"double strand break repair\", \"fanconi anemia protein complex\", \"ubiquitin ligase complex formation\"]] | \n", + "[[GO:0006281, homologous recomination, MESH:M0006667, GO:0004518]] | \n", + "||
| FA-1 | \n", + "[[GO:0006974, dna damage recognition, GO:0006281, GO:0035825, double-stranded break repair, double-stranded break recognition]] | \n", + "[[MONDO:0100339, dna/rna damage response, dna/rna metabolism, GO:0051726, genome stability, MONDO:0019391]] | \n", + "||
| HALLMARK_ADIPOGENESIS-0 | \n", + "[[MESH:D004734, GO:0006631, GO:0045444, GO:0006695, GO:0006699]] | \n", + "[[metabolic regulation, GO:0050658, GO:0006412, cell membrane transport, transcription regulation, GO:0006915, GO:0006457, GO:0019432, GO:0003676, GO:0006633, GO:0006096, GO:0045454]] | \n", + "||
| HALLMARK_ADIPOGENESIS-1 | \n", + "[[MESH:D004734, cell death regulation, cell proliferation signaling, dna replication/remodeling, GO:0006396, GO:0006629]] | \n", + "[[GO:0008152, MESH:D004734, GO:0007165, GO:0006119, transcriptional regulation, GO:0006468, GO:0051726, GO:0006629, GO:0006457, protein assembly, mitochondrial function, GO:0006915, GO:0006839, GO:0055085, GO:0007010, GO:0006094, GO:0006096, GO:0042632]] | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[[cell surface molecules, MESH:D016207, MESH:M0000731, receptor signalling, transcriptional regulation, GO:0006915]] | \n", + "[[immune signalling, GO:0051726, cellular differentiation, transcriptional regulation]] | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[[GO:0019882, GO:0007165, b and t cell metabolism, GO:0001816, GO:0006935]] | \n", + "[[genes in this list are representative of various pathways involved in cell movement, GO:0019882, GO:0006954, immune regulation, and cell signaling events including jak-stat and mapk- pi3k pathways. enriched terms include “immune system processes”; “immune recognition pathways”; “cytokine-mediated signaling pathways”; “inflammatory response”; “cellular immune activation”; “intestinal immune network for iga production”; “cytokine secretion”; “tcr signaling pathway”; “cd4 t cell activation”; “t lymphocyte differentiation”; “innate immune response”; and “cytokine-cytokine receptor interaction”.\\n\\nmechanism: the genes are involved in pathways that affect cell movement, GO:0019882, GO:0006954, immune regulation, and cell signaling. these pathways control the activation, response, differentiation, and survival of t cells by regulating cytokine expression, activation of specific receptors, production of antibodies, regulation of transcription factors and their binding to promoters, other immune system processes]] | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[[genes in this list are involved in developmental processes, metabolism, and the inflammatory response. the terms enriched in these genes include: cell cycle regulation, GO:0008152, GO:0006260, GO:0015031, receptor signaling, GO:0006954, GO:0006915, GO:0006351, GO:0006457, GO:0016477, developmental processes.\\n\\nmechanism: these genes appear to work together to regulate a variety of cellular processes, such as cellular metabolism, transcription, growth, and differentiation, as well as communication between cells and the environment. these genes likely act in concert to coordinate the intricate interplay between these processes and respond to changes in the environment. furthermore, they likely play a role in the body’s inflammatory response when faced with a variety of external stimuli]] | \n", + "[[genes in this list are mainly involved in regulation of skeletal tissue formation and development, signal cascade activation, protein folding, cellular metabolism and movement, cell cycle regulation, and transcriptional regulation. the underlying biological mechanism may be related to the complex network of interactions among these genes in controlling the basic functions of a cell. the enriched terms are: bone morphogenesis, GO:0001501, signal cascade activation, GO:0006457, GO:0044237, cellular movement, GO:0051726, transcriptional regulation, chromatin and dna modification]] | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[[GO:0065007, GO:0023052, GO:0019538, GO:0051726, transcription regulation, MESH:D021381, GO:0007165, membrane trafficking, protein kinase regulation, GO:0044237, GO:0006259, GO:0006468, GO:0030163, mitochondrial function, GO:0006629, cytoskeleton regulation, GO:0007155, GO:0009117]] | \n", + "[[gene transcription and regulation, protein translation and metabolism, cytoskeletal organization, GO:0006629]] | \n", + "||
| HALLMARK_ANGIOGENESIS-0 | \n", + "[[extracellular matrix formation and maintenance, fibrous tissue development, vascular development, cell-cell communication and migration, extracellular secreted signaling, collagen and laminin-fibrillin proteins]] | \n", + "[[GO:0030198, vascularization, endothelial cell aggregation, GO:0007155, cell surface interactions]] | \n", + "||
| HALLMARK_ANGIOGENESIS-1 | \n", + "[[GO:0032502, GO:0009653, GO:0009888, GO:0030198, GO:0006954, MESH:D066253, cell-cell communication]] | \n", + "[[cytokine receptor signaling, growth factor signal transduction, transmembrane and extracellular matrix proteins, development of muscle, bone, and neuronal networks]] | \n", + "||
| HALLMARK_APICAL_JUNCTION-0 | \n", + "[[this term enrichment test suggests that the genes provided are involved in cell adhesion, GO:0006955, and tissue morphogenesis. specifically, the adhesion-associated genes enriched in this dataset include icam1, icam2, icam4, icam5, nectin1, nectin2, nectin3, nectin4, nrxn2, ptprc, sdc3, thy1, vcam1, and vwf. the immune response-associated genes enriched in this dataset include cd34, cd86, cd209, ctnna1, icam2, icam4, icam5, map4k2, msn, pard6g, and tnfrsf11b. lastly, the tissue morphogenesis-associated genes enriched in this dataset include acta1, actb, actc1, actg1, actn1, actn2, actn4, adam15, adra1b, akt2, alox15b, amigo2, baiap2, cadm2, cadm3, MESH:M0359286, col9a1, MONDO:0011642, ctnnd1, MESH:C040896]] | \n", + "[[GO:0060348, joint development, MESH:D024510, GO:0061448, GO:0007155, adhesion receptor complex formation, GO:0007165, receptor-mediated signaling cascades]] | \n", + "||
| HALLMARK_APICAL_JUNCTION-1 | \n", + "[[GO:0009653, GO:0016049, MESH:D047108, cellular signaling, GO:0031012, cytoskeletal organization, basal membrane assembly, GO:0098609, GO:0006915, GO:0016477, GO:0001816, growth factor production, tyrosine kinase activity, g-protein coupled receptor signaling pathway, nuclear receptor signaling pathway, GO:0016055, phosphatidylinositol 3-kinase signaling pathway, protein kinase b signaling pathway, map kinase signaling pathway, cell adhesion molecule signaling pathway, focal adhesion signaling pathway]] | \n", + "[[GO:0007155, GO:0016477, migration and interaction, cytoskeletal organization, actin cytoskeletal regulation, GO:0007165, regulation of actin cytoskeletal organization]] | \n", + "||
| HALLMARK_APICAL_SURFACE-0 | \n", + "[[GO:0016477, membrane receptor signaling, GO:0009100, protein tyrosine kinases, GO:0007155, cytoskeletal dynamics, receptor-mediated lectin binding, GO:0006629, GO:0007015]] | \n", + "[[cell regulation, GO:0007165, GO:0007155, GO:0006457, GO:0030198]] | \n", + "||
| HALLMARK_APICAL_SURFACE-1 | \n", + "[[cell signaling, GO:0032502, transcription regulation, GO:0008152, MESH:D049109, MESH:D005786]] | \n", + "[[cell adhesion and migration, cell signaling, GO:0030154, protein kinase and phosphatase activities, transcription and dna metabolism, MESH:D056747, glycosylation and carbohydrate metabolism, cell growth and proliferation]] | \n", + "||
| HALLMARK_APOPTOSIS-0 | \n", + "[[transcriptional regulation/control, cell cycle/apoptosis, GO:0006955]] | \n", + "[[GO:0006915, transcription regulation, cell cycle progression, GO:0006954, GO:0006260, GO:0006281, oxidative stress response, immune system activation]] | \n", + "||
| HALLMARK_APOPTOSIS-1 | \n", + "[[the genes listed are mainly involved in the regulation and expression of genes, inflammation pathways and cell cycle regulation. specifically, enriched terms include gene expression and transcriptional regulation, dna damage and repair, GO:0007165, GO:1901987, metabolism and apoptosis.\\n\\nmechanism: the commonality in the function of these genes is likely related to the roles they play in the regulation of gene expression by affecting signal transduction, GO:0008152, cell cycle control and apoptosis. these gene functions may lead to a variety of processes, including inflammation pathways related to immunity, UBERON:2000098, MESH:D002470]] | \n", + "[[cell death regulation, GO:0006954, immune reaction, growth and morphogenesis, UBERON:2000098, GO:0006915, GO:0006281, GO:0030217, GO:0001816, GO:0051726, fast axonal transport, extracellular proteolysis, GO:0007155, GO:0042060, MESH:D009362, MESH:D063646, GO:0016477, regulation of nf-kb pathway]] | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[[MESH:M0496924, GO:0006869, development of connective tissues, GO:0006633, GO:0006699, GO:0006805, GO:0006694, cellular transport, MESH:M0023727, connective tissue formation, digit development, GO:0060173]] | \n", + "[[GO:0006629, GO:0006869, organ development, cell signaling, GO:0006412, transport processes]] | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[[this set of genes is related to lipid metabolism and lipid transport, protein homeostasis, retinol metabolism, developmental processes, and transportation of lysosomal hydrolases and oxygen-carrying molecules. the set includes genes involved in lipid metabolism (aqp9, atxn1, GO:0033781, abcg4, acsl1, fdxr, aldh8a1, hsd17b11, aldh9a1, aldh1a1, cyp7a1, cp25h, gstk1, MONDO:0100102, acsl5), lipid transport (abca1, abca2, abca3, abca4, abca5, abca8, abca9, abcg8), protein homeostasis (pex12, pex16, pex19, pex11a, pex11g, GO:0005053, pex6, pex26), retinol metabolism (abcd1, abcd2, abcd3), developmental processes (lck, nr3c2, retsat, klf1, ephx2, phyh, bbox1, MONDO:0004277]] | \n", + "[[GO:0006629, GO:0006536, serine metabolism, transcription factor regulation, oxidative stress response]] | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[[transcriptional regulation, MESH:D006026, GO:0006629, GO:0005509, GO:0001525, MESH:D016326, receptor signaling; transcription regulators; calcium signaling; glycoside hydrolases; lipid metabolism; cell adhesion; extracellular matrix proteins; signaling receptor molecules.\\n\\nmechanism: this set of genes is likely involved in regulating transcriptional responses, MESH:D006026, GO:0006629, GO:0005509, GO:0001525, MESH:D016326, and receptor signaling. many of these genes interact with each other, forming complex cellular networks and pathways. the particular genes identified in this list are likely related to stimulating or inhibiting the expression of specific genes or pathways, as well as modulating or mediating responses to various environmental signals or stimuli. these gene functions likely interact to maintain homeostasis, contribute to cellular development and processes, promote angiogenesis, and provide a structural and functional framework for the extracellular matrix. furthermore, these genes may be involved in signaling pathways that involve receptor molecules by modulating intracellular calcium levels]] | \n", + "[[GO:0006629, GO:0008203, cell signaling and regulation, GO:0032502, GO:0007155, GO:0006915, GO:0006351]] | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[[GO:0006629, transcriptional regulation, cellular adhesion, GO:0032502, GO:0042592]] | \n", + "[[GO:0006629, cholesterol control, GO:0009062, GO:0006699, hmgcr regulation, pmvk regulation, fads2 regulation, srebf2 regulation, s100a11 regulation, mvk regulation]] | \n", + "||
| HALLMARK_COAGULATION-0 | \n", + "[[inflammatory response regulation, extracellular matrix formation regulation, proteolytic activities]] | \n", + "[[extracellular matrix remodeling; angiogenesis and vascular development; immune response and platelet activation; collagen and fibronectin metabolism and regulation; endocytosis and signal transduction; \\nmechanism: the genes in this list work together to control and regulate multiple relevant processes, such as extracellular matrix remodeling, which is the process of breaking down and reorganizing the components of the extracellular matrix in order to facilitate tissue development and repair, angiogenesis and vascular development, which regulate the formation of new blood vessels and ensure proper blood flow throughout the body, immune response and platelet activation, which are necessary to protect the body from foreign agents and to form healthy blood clots, collagen and fibronectin metabolism and regulation, which are important for tissue integrity and structure, and endocytosis and signal transduction, which are necessary for cellular communication and regulation]] | \n", + "||
| HALLMARK_COAGULATION-1 | \n", + "[[GO:0007165, GO:0030198, matrix molecular regulation, GO:0006508, GO:0050817, matrix remodeling, GO:0009653]] | \n", + "[[GO:0007155, proteolysis regulation, extracellular protein-cell interaction, migration, GO:0050817, GO:0006956]] | \n", + "||
| HALLMARK_COMPLEMENT-0 | \n", + "[[GO:0030198, immune system/inflammation/interferon response, GO:0000988]] | \n", + "[[development of tissue and organs, GO:0007165, cell surface receptor binding, GO:0050896, UBERON:0002405, GO:0006955, GO:0005125]] | \n", + "||
| HALLMARK_COMPLEMENT-1 | \n", + "[[immunoglobulin like domains, GO:0042113, GO:0050852, integrin mediated cell adhesion, GO:0006915, regulation of transcription, GO:0007165, receptor mediated endocytosis and exocytosis, GO:0030198, calcium mediated signaling]] | \n", + "[[cellular signalling, GO:0006954, cell stress response, cell-cell interaction, GO:0007165, GO:0045087, cytoskeletal remodelling, GO:0006457, GO:0050900, GO:0004672, GO:0007155, MESH:D005786, GO:0006260, protein activation, GO:0019763, GO:0002377, GO:0016791]] | \n", + "||
| HALLMARK_DNA_REPAIR-0 | \n", + "[[GO:0006259, GO:0016070, GO:0006412, dna damage repair, GO:0006351, GO:0006325]] | \n", + "[[GO:0032502, GO:0006260, MESH:D047108, GO:0030154, transcription regulation, GO:0006335, nuclear mrna surveillance pathway, GO:0016070, GO:0006281, GO:0140014, rna-dependent dna replication]] | \n", + "||
| HALLMARK_DNA_REPAIR-1 | \n", + "[[GO:0006260, transcription regulation, GO:0006412, GO:0043687, nucleic acid metabolism, GO:0010467, GO:0006397, GO:0006412]] | \n", + "[[nucleic acid metabolism, GO:0006351, post-transcriptional modifications, GO:0006338, GO:0000398, GO:0006281, rna polymerization, GO:0006397, GO:0051028, GO:0006413]] | \n", + "||
| HALLMARK_E2F_TARGETS-0 | \n", + "[[GO:0006260, GO:0006281, gene transcription, GO:0006412, GO:0016569, GO:0007049, GO:0010468]] | \n", + "[[transcriptional regulation, GO:0016569, mitotic division, GO:0051726, MESH:D004268, MESH:D006657, GO:0000981, MESH:D004259, MESH:D012321, chromatin remodeling proteins, ubiquitin ligases, nucleosome assembly proteins, helicases, motor proteins, GO:0000075]] | \n", + "||
| HALLMARK_E2F_TARGETS-1 | \n", + "[[GO:0006260, GO:0006351, GO:0030261, transcriptional regulation, GO:0006338, GO:0006974, chromatin structure modifications, GO:0006281, GO:0006306, GO:0030163, GO:0007094, GO:1901987, GO:0006468]] | \n", + "[[GO:0006260, GO:0006281, GO:0016569, transcription regulation, translation regulation, protein-protein networks, GO:0051225, kinesin motor proteins, dynein motor proteins]] | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[[genes in this list are enriched for functions related to modulating extracellular matrix, cell adhesion and morphogenesis, as well as playing roles in development, growth and signal transduction pathways. enriched terms include:extracellular matrix modulation; cell adhesion; morphogenesis; development; growth; signal transduction.\\n\\nmechanism: many of the genes listed are involved in the signaling, development and maintenance of the extracellular matrix, cell adhesion and morphogenesis, which can be regulated through diverse pathways involving the growth factors (bdnf, MESH:D016222, igfbp2, igfbp3, igfbp4, wnt5a), proteoglycans (comp, cspg4, MONDO:0021055, lamc1, lamc2, dcn, has3, sdc1) and adhesion molecules and receptors (acta2, abi3bp, cadm1, cap2, capg, cd44, cdh11, cdh2, cdh6, fn1, grem1, itga2, itga5, itgav, itgb1, itgb3, itgb5, lrp1, tagl]] | \n", + "[[GO:0031012, GO:0007155, GO:0048870, cell-matrix interaction, growth factor signaling, cytokine signaling, matrix remodeling]] | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[[GO:0030198, GO:0009653, collagen production, matrix metalloproteinase activity, GO:0009100, cytoskeletal component organization, regulation of growth and reproduction, regulation of skin morphogenesis]] | \n", + "[[GO:0048705, cell-cell adhesion and motility, extracellular matrix production and remodeling, connective tissue development and differentiation, collagen production and turnover, cytokine and chemokine signaling]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[[cell morphology; homeostasis & regulation; innervation; cellular metabolism.\\nmechanism: the genes are likely to be involved in various pathways, such as the regulation of gene expression, protein synthesis and structure, cell motility and differentiation, tissue repair regeneration]] | \n", + "[[GO:0006260, GO:0006351, GO:0010467, GO:0016049, differentiation, GO:0016485, trafficking, GO:0060349, cancer-related pathways, GO:0098609, matrix remodeling, intracellular signaling, external signals, internal signals]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[[immunological response, GO:0007155, transcription regulation, GO:0016477, GO:0008544, GO:0060348, MESH:D024510, GO:0015031, GO:0006915]] | \n", + "[[transcriptional regulation, GO:0007165, protein-protein interactions, GO:0055085, GO:0008610]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[[MESH:D023281, cytoskeletal processes, GO:0006955, extracellular modification]] | \n", + "[[GO:0030198, GO:0007155, GO:0016477, GO:0048870, growth factor signaling, cytoskeletal organization]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[[the commonalities in the functions of these genes are involved in transcription, post-transcriptional regulation, GO:0009966, and cell-cycle related processes. the enriched terms are: transcription; post-transcriptional regulation; signal transduction; cell cycle; dna binding; regulation of transcription; regulation of protein abundance; chromatin remodeling; ubiquitination; and protein-protein interaction.\\n\\nmechanism: the underlying mechanism may be related to the regulation of intricate pathways leading to the expression of specific genes in conversion of genetic information into protein-based processes. these genes may be involved in a variety of biological processes, such as transcriptional and post-transcriptional regulation of gene expression, GO:0007165, cell-cycle related processes, GO:0003677, regulation of transcription, regulation of protein abundance, GO:0006338, MESH:D054875, protein-protein interaction]] | \n", + "[[GO:0030198, GO:0000988, receptor signaling pathway, GO:0007269, GO:0019725, GO:0006508, immunological responses, GO:0016049, GO:0003677, GO:0006629]] | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[[GO:0006631, oxidation of lipids, GO:0006695, GO:0005977, GO:0009117, GO:0006862, GO:0009165, electron transport activity, enzyme regulation, regulation of metabolic pathways, GO:0006915]] | \n", + "[[metabolic pathways; cellular functions; energy metabolism; lipid metabolism; amino acid metabolism; dna damage repair; cell signaling.\\nmechanism: the genes listed here are likely involved in the various metabolic pathways and cellular functions, perhaps through the production of enzymes, MESH:D011506, or other molecules that contribute to energy metabolism, GO:0006629, amino acid metabolism, dna damage repair, cell signaling]] | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[[GO:0008152, energy production and storage, lipid metabolism and transport, acetyl-coa biosynthesis and catalysis, oxidation, GO:0006631]] | \n", + "[[GO:0006629, cell cytoskeleton, GO:0008610, GO:0016042, lipid transportation, GO:0034440, cell membrane biogenesis, GO:0048870, cell traffic, cell signaling]] | \n", + "||
| HALLMARK_G2M_CHECKPOINT-0 | \n", + "[[GO:0051726, GO:0006260, GO:0006338, cyclin b-cdk1 activation, cks1b, cdc25a, wee1, cdc20, apc/]] | \n", + "[[GO:0006260, GO:0006351, GO:0051726, protein binding/interaction, chromatin modifiers/modification, GO:0006281, GO:0000988, GO:0006397, GO:0006915, ubiquitination and proteasomal degradation]] | \n", + "||
| HALLMARK_G2M_CHECKPOINT-1 | \n", + "[[nuclear processes, GO:0006260, gene transcription, GO:0006338, GO:1901987, GO:0006281, GO:0010467, GO:0010468]] | \n", + "[[genes involved in the list are mainly associated with dna replication, cell division and related functions. enriched terms include \"cell cycle\", \"dna replication\", \"chromatin modification\", \"transcription regulation\", \"cell division\", \"dna repair\", \"transcriptional regulation\", \"chromosome segregation\".\\n\\nmechanism: these genes likely play a role in the coordination of the many steps and activities involved in dna replication, GO:0051301, and related cellular processes. the cell cycle is an area of particular interest due to its critical role in the growth and division of cells. dna replication, modification, repair occur during cell division in order to produce maintain copies of genetic information. chromatin modifications occur during cell division in order to package regulate genomic information. transcriptional regulation involves the control of gene expression the production of proteins other materials essential for the maintenance of cellular functions. chromosome segregation cell division serve to divide replicated genetic material into daughter cells]] | \n", + "||
| HALLMARK_GLYCOLYSIS-0 | \n", + "[[developmental process: digit development, GO:0001525, GO:0030154, GO:0005488, transporting, GO:0008152, GO:0008152, cell signalling]] | \n", + "[[the genes in this list are involved in a variety of cellular processes including protein translation, GO:0070085, regulation of ion channels, gene transcription and dna replication. the enriched terms identified are: translation; glycosylation; ion channels; gene transcription; and dna replication.\\n\\nmechanism: the common underlying mechanisms of the genes in this list likely involve cellular processes such as protein translation, GO:0070085, regulation of ion channels, gene transcription and dna replication. these processes are essential for the regulation of cell functions and the maintenance of a stable organism]] | \n", + "||
| HALLMARK_GLYCOLYSIS-1 | \n", + "[[GO:0005975, MESH:D004734, GO:0046785, dna binding and replication, actin cytoskeleton dynamics, ion channel regulation, transcriptional regulation, GO:0007155]] | \n", + "[[structural proteins, GO:0006096, GO:0006098, GO:0006099, GO:0007155, GO:0030166, extracellular matrix formation, cytoskeletal assembly]] | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[[GO:0009653, GO:0022008, GO:0016049, GO:0030154, GO:0001764, thalamocortical pathway development, GO:0001764, GO:0007399, neural crest migration]] | \n", + "[[the provided genes are involved in a variety of different processes ranging from morphogenesis, development and growth of the digits/limbs, neuronal migration and regulation of cell proliferation. the underlying biological mechanism might be related to the modulation of cell migration, development of neural connections, formation of complex structures, maintenance of body plan and tissue development. enriched terms are: morphogenesis, digit/limb development, GO:0001764, GO:0042127, modulation of cell migration, development of neural connections, formation of complex structures, maintenance of body plan, GO:0009888]] | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[[GO:0009653, GO:0007155, GO:0032502, GO:0007268, GO:0008283, GO:0016477, GO:0030154, MESH:D009473]] | \n", + "[[neuron formation, GO:0007155, migration, GO:0007165, GO:0048729, GO:0007399]] | \n", + "||
| HALLMARK_HEME_METABOLISM-0 | \n", + "[[GO:0055085, MESH:D004734, GO:0003735, GO:0003676, GO:0015031, negative regulation of transcription, regulation of transcription, positive regulation of transcription, GO:0071840, iron metabolism, GO:0007165, GO:0045087, GO:0042803, GO:0051276, GO:0050794, GO:0016569, GO:0008380, GO:0005515, GO:0000075, GO:0006006, GO:0000088, GO:0009116]] | \n", + "[[GO:0044237, energy production and transport, cytoskeleton modification, cytoskeleton remodelling, GO:0007155, MESH:D004735, MESH:M0496924, cellular transport, cellular reorganization]] | \n", + "||
| HALLMARK_HEME_METABOLISM-1 | \n", + "[[GO:0048468, GO:0010467, GO:0048513, nucleic acid metabolism, transcriptional regulation, GO:0006259, GO:0016070, cytoskeletal dynamics, GO:0007165, GO:0006412]] | \n", + "[[MESH:D047108, GO:0001501, GO:0048513, GO:0009653, GO:0040007, GO:0002376, GO:0048870, GO:0003707, receptor signaling pathway, GO:0006810, GO:0006897, GO:0019725]] | \n", + "||
| HALLMARK_HYPOXIA-0 | \n", + "[[gene enrichment analysis of the gene list showed that the majority of genes are involved in cellular proliferation, GO:0006915, GO:0006811, GO:0005102, and development. the enriched terms associated with this list include cell proliferation, GO:0006915, GO:0006811, GO:0005102, cell signaling, transcriptional regulation, and development.\\n\\nmechanism: the genes are likely involved in an intricate, interconnected biological network that involves numerous signaling pathways and transcription factors necessary for cellular proliferation, GO:0006915, ion transport and receptor binding. these gene functions result in the regulation of numerous cellular processes and ultimately the development of various diseases. in addition, the genes may be regulating a number of other processes such as metabolism, cell-cell communication, energy production]] | \n", + "[[GO:0007049, remodeling proteins, stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, GO:0000981, chromatin-associated proteins, MESH:D010770]] | \n", + "||
| HALLMARK_HYPOXIA-1 | \n", + "[[GO:0048468, cell metabolism, transcription regulation, GO:0010468, GO:0006974, GO:0007155, GO:0030154, GO:0042440, MESH:M0352612, GO:0006412, GO:0051726, MESH:D004734]] | \n", + "[[GO:0032502, cell structure and movement, cell cycle and division, GO:0007165, GO:0006810, energy production]] | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[[GO:0016049, cell regulation, GO:0009988, MESH:D007109, signal transduction and regulation, GO:0032502, transcriptional regulation, GO:0030198, cytokine-receptor-mediated signaling pathway]] | \n", + "[[immunological function, GO:0030036, MESH:D011956, pro-inflammatory regulation]] | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[[this list of genes are involved in developmental processes, GO:0006955, GO:0006954, GO:0007165, and cell adhesion functions. the enriched terms are \"development\"; \"signal transduction\"; \"cell adhesion\"; \"immune response\"; \"inflammation\"; \"transmembrane transport\"; \"protein metabolism\"; \"cardiovascular function\".\\n\\nmechanism: the underlying biological mechanisms involves the coordination of different pathways, genes and proteins. these genes are involved in cellular processes and regulation, including cell proliferation, differentiation, adhesion and migration, GO:0007165, and immunity. the genes also influence signaling pathways, protein metabolism and other functions that have roles in cardiovascular and carcinogenesis. the mechanisms through which these genes affect development, GO:0006954, other immunological responses are complex dependent on the coordination between multiple pathways]] | \n", + "[[MESH:D007109, GO:0006954, GO:0016049, differentiation, GO:0032502, GO:0007165]] | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[[pain sensing and signal transduction, GO:0006935, GO:0019221, leukocyte transendothelial migration, GO:0006955, GO:0030168]] | \n", + "[[cell signaling, GO:0001816, cytokine regulation, MESH:D005786, transcription regulation, GO:0007155]] | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[[GO:0007165, MESH:D056747, immune signaling, transcription regulation, cytokine regulation, GO:0030155, MESH:D005786, cell growth regulation, metabolism regulation, MESH:D002470, cell death regulation, antifungal immunity]] | \n", + "[[cytokine regulation, chemokine regulation, interleukin regulation, cellular differentiation, cell motility and adhesion, GO:0007165, GO:0006954]] | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[[MESH:M0000731, GO:0006954, GO:0007165, transcription regulation, intercellular signaling, GO:0045087, MESH:D056704]] | \n", + "[[this list of genes is significantly enriched for the functions of cell signalling, cytokine mediated immunity, receptor signalling, and tissue morphogenesis. furthermore, the list contains several genes associated with the immune response, including tlrs and ifns, as well as cytokines and chemokines such as ccl17, ccl20, cxcl10, cxcl9, ifnar1, tnfrsf1b, and tnfsf10. in addition, several receptors were found to be enriched on the list, including gpr132, axl, c3ar1, MONDO:0043317, and ccr7. finally, key genes involved in tissue morphogenesis were also found on the list, such as adgre1, edn1, btg2, ccl2, tacr1, and cxcr6.\\n\\nmechanism: \\nthe underlying mechanism for this enrichment of genes is likely related to the common activities of cell signalling, cytokine mediated immunity and tissue morphogenesis. the list of genes is likely regulating common processes such as cell-cell communication and inflammation. additionally, the list of genes may be involved in the development and maintenance of tissue structures, such as muscle tissue]] | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[[immune cell signaling, GO:0006928, cell surface receptor activity, GO:0006954, GO:0016477, cell–cell interactions, immune cell receptor-mediated signaling]] | \n", + "[[GO:0006955, cellular activation, receptor-coupled pathways, transcriptional regulation, cytokine and cytokine receptor binding, GO:0006629, GO:0007155]] | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[[GO:0006954, neutroph]] | \n", + "[[analysis of this list of genes reveals that they are all involved in the functioning of the immune system in some way, either through regulation of inflammatory response pathways, recognition of foreign agents, or production of molecules defending against potentially harmful intruders. the enriched terms include \"immune system regulation\"; \"inflammatory response\"; \"foreign agent recognition\"; \"antimicrobial defense\"; \"interferon signaling\"; \"antiviral defense\". \\n\\nmechanism: the genes in this list combined likely regulate a wide variety of immune system functions, including modulating inflammation, recognizing and responding to foreign antigens, producing effector molecules against potentially harmful microorganisms, promoting interferon signaling cascades to defend from viral invasion]] | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[[interferon signalling pathway, interferon gamma activity, interferon regulatory factor activity, status response to interferon, GO:0006915, GO:0008289, GO:0005509, GO:0002446]] | \n", + "[[GO:0006955, GO:0006954, cytokine signaling, interferon response, GO:0006355, interferon-stimulated genes]] | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[[GO:0006955, cell signaling, cytokine response, interferon response, nuclear factor kappab-dependent transcriptional regulation]] | \n", + "[[MESH:M0000731, GO:0019882, GO:0006954, chemokine signaling, GO:0007155, cytokine interactions]] | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[[MESH:D007109, interleukin regulation, transcription regulation, GO:0006954, cell signaling, GO:0006915]] | \n", + "[[interferon signaling, antigen processing, presentation, and recognition, cytokine signaling, cell cycle and dna damage response, GO:0006915]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[[GO:0060348, GO:0009653, growth maintenance, GO:0007267, cell-cell communication, GO:0036211, GO:0006810]] | \n", + "[[digit development, neural development, GO:0002520, transcriptional regulation, g-protein coupled receptors, MESH:D011494, MESH:D020662]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[[GO:0009653, cell-cell communication, GO:0032502, hormone regulation, cellular differentiation, cell-cycle, cell-signalling]] | \n", + "[[our analysis revealed the enrichment of the gene functions related to development, GO:0007165, transcription and metabolism. specifically, some of the enriched terms include cellular development, GO:0016049, GO:0001501, GO:0048598, cell junction organization and assembly, GO:0007165, GO:0007049, GO:0006351, and cellular metabolism.\\n\\nmechanism: these gene functions may be related to the biological mechanism of growth, differentiation, and development of cells. the signals and transcription are likely involved in regulating and controlling these processes, as well as providing energy through metabolic pathways. additionally, the cell junction processes are likely involved in the coordination and communication between cells, which is essential to development]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[[GO:0007165, GO:0000902, GO:0050896, GO:0001525, GO:0065009, GO:0030198]] | \n", + "[[GO:0007165, GO:1901987, cell-to-cell adhesion]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[[GO:0009653, GO:0009888, cell signaling, immune regulation, transcription modulation, GO:0007165, GO:0007155, GO:0016477]] | \n", + "[[integrin, chemokine receptor, MESH:D011494, g-protein-coupled receptor, cytoskeleton proteins, cell-extracellular matrix interaction, type i ifn-mediated innate immunity, wnt signaling, MESH:D020558, MESH:D010740, MESH:D008565, MESH:D016326, receptor tyrosine kinase, toll-like receptor signaling, tlr adaptor proteins]] | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[[the human genes abi1, abl1, abr, actn4, akap13, alms1, MONDO:0008780, anln, GO:0005680, arap3, arf6, arfgef1, arfip2, arhgap10, arhgap27, arhgap29, arhgap4, arhgap5, arhgdia, arhgef11, arhgef12, arhgef2, arhgef3, arhgef7, arl8a, atg4b, MESH:D064096, bcar1, bcl2l11, bcr, bin1, birc5, brca2, bub1, capzb, ccdc88a, ccnb2, cd2ap, cdc27, cdc42, cdc42bpa, cdc42ep1, cdc42ep2, cdc42ep4, cdk1, cdk5rap2, cenpe, cenpf, cenpj, cep131, cep192, cep250, cep57, GO:0047849]] | \n", + "[[GO:0007049, GO:0007155, cytoskeletal organization, GO:0004672, GO:0003924]] | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[[cytoskeletal organization, GO:0016477, GO:0051301, GO:0006260, GO:0006281, GO:0006605, GO:0065007]] | \n", + "[[GO:0051301, GO:0006468, GO:0006338, GO:0008017, microtubule organization, GO:0051225, GO:0007059, GO:0051305, cell-cycle control, GO:0140014]] | \n", + "||
| HALLMARK_MTORC1_SIGNALING-0 | \n", + "[[the human genes abcf2, acaca, acly, acsl3, actr2, actr3, add3, adipor2, ak4, aldoa, arpc5l, asns, atp2a2, atp5mc1, atp6v1d, MESH:D064096, bcat1, bhlhe40, btg2, bub1, cacybp, calr, canx, ccnf, ccng1, cct6a, cd9, cdc25a, cdkn1a, cfp, cops5, coro1a, cth, ctsc, GO:0038147, cyb5b, cyp51a1, dapp1, ddit3, ddit4, ddx39a, dhcr24, dhcr7, GO:0004146, ebp, edem1, eef1e1, egln3, eif2s2, elovl5, elovl6, eno1, eprs1, ero1a, etf1, MONDO:0100101, MONDO:0100102, fdxr, fgl2, MESH:D010649]] | \n", + "[[genes in this list are involved in various aspects of cellular metabolism, GO:0065007, and development.a number of the genes have roles in energy production and metabolism such as, atp2a2, aldoa, MONDO:0009214, fao1, fgl2, gapdh, gbe1, MONDO:0015408, glrx, MONDO:0005775, me1, phgdh, and pgm1. there is a strong presence of genes involved in protein synthesis and transport, including the ribosomal proteins, the eukaryotic translation factors and initiation factors (eif2s2, eif1e1, elovl5, and elovl6). this gene set is also enriched for a number of ubiquitin and ubiquitin-like proteins (ube2d3, ufm1, uso1, tomm40, hspd1, hspe1, sytl2, nherf1, and hk2). many of these genes are involved in regulation through multiple pathways including regulation of transcription (add3, actr2, actr3, cct6a, gga2, gdh2, mef2b, ykt]] | \n", + "||
| HALLMARK_MTORC1_SIGNALING-1 | \n", + "[[GO:0006412, MESH:D004734, cellular transport, GO:0006955, GO:0035194, mitochondrial oxidative phosphorylation, GO:0006915, GO:0016310, GO:0006096, GO:0006914]] | \n", + "[[GO:0006412, transcription regulation, GO:0009653, GO:0016049, GO:0007165, GO:0008152, GO:0006629, cellular translation]] | \n", + "||
| HALLMARK_MYC_TARGETS_V1-0 | \n", + "[[rna biogenesis, protein synthesis biosynthesis, atp-binding, cytoskeleton organization and assembly, GO:0006351, GO:0006338, GO:0007165, GO:0010467, GO:0006413, MESH:M0439896, GO:0006260]] | \n", + "[[GO:0006412, GO:0036211, GO:0006260, GO:0051726, transcription regulation, GO:0016049, GO:0048468, gene expression.\\nmechanism: the genes may constitute a pathway in which they coordinate together to regulate cell growth, development, and gene expression]] | \n", + "||
| HALLMARK_MYC_TARGETS_V1-1 | \n", + "[[GO:0000394, GO:0051028, MESH:M0439896, GO:0006412, GO:0042254, GO:0035194, GO:0006338]] | \n", + "[[developmental regulation, energy production, GO:0006412, structural maintenance of cell components, GO:0006260, transcription regulation, protein assembly]] | \n", + "||
| HALLMARK_MYC_TARGETS_V2-0 | \n", + "[[genes in this list are primarily involved in cell development, including the processes of rna metabolism, dna replication and cell cycle control. enriched terms include: rna metabolism; dna replication; cell cycle control; chromatin regulation; transcription regulation; cell differentiation; gene expression; and protein synthesis.\\n\\nmechanism: the genes in this list are part of a complex network of molecular pathways involved in regulating the expression, replication and maintenance of genetic material. this includes the transcription, splicing and translation of rnas as well as the replication and repair of dna. the multiple genes in this list suggest coordination and control of various steps in these processes, such as chromatin regulation, which is directly responsible for how genetic material is packaged and regulated. additionally, the genes may be involved in regulating cell cycle progression, transcription regulation and cell differentiation]] | \n", + "[[protein post translational modification, GO:0016310, GO:0006351, GO:0006412, GO:0042254]] | \n", + "||
| HALLMARK_MYC_TARGETS_V2-1 | \n", + "[[GO:0001775, GO:0008283, GO:0006260, dna transcription, rna translation.\\nmechanism: the genes may indicate an underlying biological pathway involving the coordinated expression of these gene sets to regulate the cell cycle, dna replication, transcription, and translation in order to enable cell proliferation]] | \n", + "[[transcription regulation, GO:0006338, nucleosome remodeling, GO:0006260, nuclear localization, GO:0007165, GO:0016567, GO:0006468]] | \n", + "||
| HALLMARK_MYOGENESIS-0 | \n", + "[[gene expression and structure, cytoskeletal structure and dynamics, calcium regulation and signaling, cell adhesion and migration, cell death biochemistry, metabolic regulation]] | \n", + "[[genes in this list are associated with various cellular functions, including cell cycle regulation, developmental pathways, contractile force generation, protein synthesis and degradation, GO:0006915, GO:0000988, and metabolic processes. enriched terms include: cell cycle; cell differentiation; transcriptional regulation; intracellular signaling; muscle contraction; metabolism; apoptosis; protein synthesis; protein degradation.\\n\\nmechanism:\\n\\nthe genes in this list code for proteins involved in a range of cellular processes, including transcription factors that regulate gene expression, receptors that initiate intracellular signaling cascades, enzymes involved in metabolic pathways or apoptosis, and ion channels involved in muscle contraction and cell cycle regulation. these proteins interact to regulate the expression and activity of other proteins, impacting the activity of many important pathways that together coordinate cell growth, differentiation, MESH:D009068, GO:0008152]] | \n", + "||
| HALLMARK_MYOGENESIS-1 | \n", + "[[GO:0031012, GO:0005856, UBERON:0005090, GO:0032502, neuromuscular structure, MESH:D007473, GO:0006811]] | \n", + "[[the genes that were analyzed were related to development, cell signalling, GO:0008152, GO:0065007, GO:0006936, MESH:D055550, and transport. the enriched terms were cellular development, actin cytoskeleton regulation, cell migration and adhesion, GO:0051726, calcium homeostasis and signaling, GO:0006936, GO:0006119, receptor tyrosine kinase signaling, apoptosis and programmed cell death, GO:0030198, GO:0016567, GO:0042632, metabolism and energy production, cell death and apoptosis, cytoskeletal protein binding and regulation of transcription and translation.\\n\\nmechanism: the underlying biological mechanism or pathways involved in these genes include regulation of muscle contraction, cell adhesion and migration, calcium homeostasis, protein ubiquitination and stability, receptor signaling, GO:0051726, GO:0006119, GO:0008219, and regulation of transcription and translation. these mechanisms are essential for cellular development and function, and thus, are enriched in these gene list]] | \n", + "||
| HALLMARK_NOTCH_SIGNALING-0 | \n", + "[[MESH:D047108, GO:0051726, GO:0019722, notch signaling down-regulation, wnt signaling, hedgehog signaling, GO:0000902]] | \n", + "[[GO:0009653, GO:0048513, GO:0009888, GO:0001709, MESH:D002450, notch receptor signaling, wnt signaling, transcription factor signaling]] | \n", + "||
| HALLMARK_NOTCH_SIGNALING-1 | \n", + "[[these genes are involved in a wide range of functions related to signaling, development, and transcriptional regulation, indicating an involvement in a variety of cellular pathways. enriched terms include: cell signaling, GO:0007399, GO:0030154, wnt signaling, notch signaling, hedgehog signaling, transcription factor regulation, GO:0006338, e3 ubiquitin ligase.\\n\\nmechanism: the likely underlying biological mechanism is a complex network of interactions between these genes and their pathways, forming a web of signaling molecules that regulate cell growth, differentiation, apoptosis and other cellular processes. the genes and pathways involved in the network are likely to interact in a dynamic manner]] | \n", + "[[GO:0008283, GO:0009653, GO:0032502, nerve system differentiation, transcription regulation, wnt signalling pathway, GO:0007219]] | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[[mitochondrial activity, GO:0022900, GO:0006119, metabolic regulation, MESH:D065767]] | \n", + "[[the list of genes provided are primarily involved in energy metabolism, GO:0007585, and the electron transport chain. specifically, terms such as \"oxidative phosphorylation\", \"mitochondrial electron transport chain\", and \"tricarboxylic acid cycle\" are found to be significantly over-represented.\\n\\nmechanism: the genes provided are involved in the production of atp through metabolic pathways such as oxidative phosphorylation, GO:0005746, and the tricarboxylic acid cycle. these molecules, along with other regulatory proteins, facilitate the flow of electrons to generate energy in the form of atp. this energy is used by cells to carry out metabolic reactions and various cellular processes]] | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[[GO:0005746, electron transfer proteins, proton ion transportation proteins, oxidative phosphorylation proteins, metabolite-binding proteins, atp synthesis proteins]] | \n", + "[[mitochondrial electron transport chain complex activity, GO:0006120, GO:0005747]] | \n", + "||
| HALLMARK_P53_PATHWAY-0 | \n", + "[[cytoskeletal reorganization, calcium homeostasis, ubiquitin-proteasome pathway, GO:1901987, transcriptional regulation, GO:0006397, GO:0006974]] | \n", + "[[analysis of this list of genes suggests a function related to cell cycle regulation, GO:0006915, and protein translation. the enriched terms include 'cell cycle regulation', 'apoptosis', 'protein translation', 'transcription regulation', 'intracellular protein transport', 'protein synthesis', and 'dna repair'.\\n\\nmechanism: the list of genes may be associated with a mechanism related to the regulation of cell cycle transitions and the integration of external signals to regulate gene transcription, protein translation and stability, and cellular apoptosis. this could involve some combination of signal transduction, GO:0006355, GO:0043687, GO:0006281]] | \n", + "||
| HALLMARK_P53_PATHWAY-1 | \n", + "[[GO:0006351, chromatin dynamics, GO:0007155, MESH:D016207, GO:0007049, dna damage repair, cell signaling, GO:0016049, GO:0006915, immune modulation]] | \n", + "[[gene expression and protein metabolism are likely to be enriched. specifically, the genes are likely involved in protein folding and transport, GO:0016567, transcriptional regulation, GO:0051726, protein-protein interactions, and signal transduction. \\nmechanism: these genes likely play a role in common metabolic, GO:0023052, and regulatory pathways.\\nubiqutination terms: rchy1, hexim1, upp1, pom121, procr, tap1, phlda3, wwp11; \\ntranscription factors:cd81, sat1, ercc5, ralgdh, irak1, aen, tob1, stom, MONDO:0100339, rap2b, tm7sf3, lif, MESH:C058179, ccp110, baiap2, tnfsf9, dcxr, eps8l2, ifi30, fdxr, elp1, itgb4, hbegf, irag2, ccnd2, sertad3, mknk2, retsat, ip6k2, hmox1, zfp36l1, epha2, tpd]] | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[[GO:0031016, GO:0006006, GO:0048870, neural development]] | \n", + "[[GO:0031016, GO:0007399, development of neural structures, GO:0048513, transcription regulation, GO:0009653, cell-to-cell adhesion, GO:0006412, hormonal metabolism, hormonal signaling]] | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[[GO:0009653, neuronal development, GO:0007165, GO:0030073, transcription regulation, GO:0000988]] | \n", + "[[GO:0022008, GO:0008152, GO:0006355, GO:0006412, GO:0009653, body patterning and organization, neurological system development, GO:0030154]] | \n", + "||
| HALLMARK_PEROXISOME-0 | \n", + "[[enrichment test suggested genes are skewed towards genes involved in development, metabolic control, transport, cell cycle and homeostasis, as well as transcriptional regulation.\\n\\nmechanism: these genes appear to be involved in a diverse range of processes, suggesting multiple pathways contributing to the physiological functions of these genes. for instance, abcb1, abcb4 and abcb9 are involved in medication transport, abcc5 and abcc8 are involved in atp coupling, acaa1 is involved in fatty acid metabolism, alb is involved in heme metabolism, aldh1a1, aldh9a1, atxn1 and bcl10 are involved in transcriptional regulation, ctbp1 and ctps1 are involved in ubiquitination, dhcr24 and dhrs3 are involved in cholesterol biosynthesis, fabp6 is involved in bile acid transport, fads1 is involved in fatty acid desaturase, fis1 and gnpat are involved in lipoic acid synthesis and mitochondrial fatty acid metabolism, gstk1 is involved in gst-mediated detoxification, hmgcl is involved in steroidogenesis, hras, hsd11b2, hsd17b11]] | \n", + "[[GO:0006629, stress response, GO:0009299, GO:0006281, skeletal and cartilage development, GO:0016477, metabolic enzymes, MESH:D002352]] | \n", + "||
| HALLMARK_PEROXISOME-1 | \n", + "[[GO:0006629, GO:0008202, transcription regulation, GO:0051726]] | \n", + "[[GO:0008152, GO:0006351, GO:0065007, GO:0006810, GO:0007165, GO:0006412, GO:0030154, GO:0006260, GO:0036211, membrane trafficking]] | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[[GO:0010467, dna repair & maintenance, MESH:M0496065, cellular signaling pathways, GO:0006629]] | \n", + "[[MESH:M0023730, GO:0009653, GO:0030154, tyrosine kinase activity, GO:0038023]] | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[[GO:0051726, gene transcription, transcription factor activation, MESH:M0023730, MESH:D011494, receptor proteins, GO:0006412, GO:0016049, GO:0008283, GO:0030154]] | \n", + "[[cell signaling, GO:0019538, GO:0006629, transcription regulation, GO:1901987, GO:0007165, receptor signaling, GO:0070085, GO:0016301, GO:0006915, g-protein interactions, transcriptional regulation]] | \n", + "||
| HALLMARK_PROTEIN_SECRETION-0 | \n", + "[[gene expression regulation; co-translational protein targeting; clathrin-mediated endocytosis; endosomal protein trafficking; vesicle transport; exocytosis; receptor and ligand-mediated signaling; development and organ morphogenesis.\\nmechanism: the identified genes are likely involved in a variety of biological processes related to endocytosis, vesicle trafficking and transport, receptor and ligand-mediated signaling, MESH:D005786, co-translational protein targeting, and organ morphogenesis. these processes can be clustered into several pathways, including the calcineurin-mediated endocytosis pathway, the mapk signaling pathway, the wnt/beta-catenin signaling pathway, the clathrin-mediated endocytosis pathway, the endosomal protein trafficking pathway, the vesicle transport pathway, the exocytosis pathway, the receptor ligand-mediated signaling pathways]] | \n", + "[[cell membrane fusion, GO:0016192, intracellular trafficking, predominant cargo proteins, GO:0006900, membrane remodeling]] | \n", + "||
| HALLMARK_PROTEIN_SECRETION-1 | \n", + "[[genes belonging to this list are mainly involved in endocytosis, GO:0016192, MESH:D021381, and membrane fusion. the enriched terms include: endocytosis; vesicle trafficking; protein trafficking; membrane fusion; membrane transport; cytoskeleton organization; signal transduction; receptor internalization; and protein trafficking pathways.\\n\\nmechanism: the common characteristics shared by the genes suggest that they are all involved in some aspect of the endocytosis pathway. this biological mechanism involves signal transduction by which a signal (chemical or physical) can pass through a cell membrane and allow the cell to take up extracellular substances. through receptor internalization, molecules, like hormones, can be shuttled into intracellular vesicles and undergo further signaling events. the sequential vesicle trafficking steps then enable the cargo to be transported to their final destination. the proteins play various roles in facilitating membrane fusion, GO:0036211, GO:0007010, and vesicle transport. all of these activities act in concert to usher signals, MESH:D011506, other substances into the cell]] | \n", + "[[GO:0043687, GO:0006457, GO:0006412, GO:0006897, GO:0009311, lysosomal trafficking]] | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[[redox regulation, antioxidant defense, detoxification of reactive oxygen species, peroxisomal biogenesis, MESH:M0572479, cell metabolism]] | \n", + "[[GO:0008152, oxidative damage resistance, GO:0006281, cellular metabolic regulation, GO:0006915, regulatory pathway, GO:0006457, GO:0006749]] | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[[redox balance regulation, GO:0008152, GO:0051726, transcriptional regulation]] | \n", + "[[this list of genes is enriched for terms related to oxidative stress, GO:0008152, and immune system function. specifically, the genes represent proteins involved in oxygen-sensing, anti-oxidation, redox regulation, GO:0006281, the stress response, and cytokine signaling.\\n\\nmechanism:\\nthe underlying biological mechanism of the gene list is likely the cellular response to oxidative stress. oxidative stress is a term used to describe a disruption in the balance of antioxidant molecules and reactive oxygen species. these reactive molecules can cause damage to the cell, and thus the relevant genes likely help the cell to counteract this damage by regulating redox status, mediating oxidant stress, and participating in dna repair and other defense mechanisms. additionally, some of these genes are involved in cytokine signaling, which helps to aid the immune system in defending against potential oxidative insults]] | \n", + "||
| HALLMARK_SPERMATOGENESIS-0 | \n", + "[[cell signaling, protein regulation, GO:1901987, GO:0009653, GO:0048513, cytoskeletal regulation]] | \n", + "[[GO:1901987, GO:0006338, GO:0016567, GO:0006260, GO:0051225, GO:0006997]] | \n", + "||
| HALLMARK_SPERMATOGENESIS-1 | \n", + "[[cell cycle checkpoint regulation, GO:0009653, cell signaling, MESH:D003598, organ development]] | \n", + "[[the list of genes provided are involved in diverse processes, such as cell structure and organization, GO:0007165, transcriptional regulation and other metabolic activities. the enriched terms from performing a term enrichment test are cell cycle, GO:0051301, GO:0016569, development and differentiation, cell signaling and signal transduction, GO:0006397, transcriptional regulation, and metabolic processes.\\n\\nmechanism:\\nthe genes provided are believed to be involved in a general mechanism of cell organization and function. the enriched terms are suggestive of the genes being related to fundamental processes such as cell cycle regulation, GO:0051301, transcriptional regulation, GO:0016569, and signal transduction. through the regulation of the genes, they are thought to be capable of controlling the organization and structure of cells, as well as metabolism and other cellular activities. furthermore, these pathways likely interact with each other in a complex manner, thereby allowing for intricate coordination between the genes in order to precisely tune process]] | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[[mapk pathway, tgf-β signaling pathway, wnt/β-catenin pathway, GO:0035329, transcriptional regulation, muscle morphogenesis, GO:0048729, regulation of g-protein signaling, GO:0006954]] | \n", + "[[genes in this set are related to morphogenesis, GO:0007155, immune signaling, and transcriptional regulation. enriched terms include: morphogenesis, GO:0007155, immune signaling, transcriptional regulation, digit development, GO:0007049, protein-protein interaction, GO:0008083, and regulation of transcriptional activity.\\n\\nmechanism: morphogenesis can be regulated by the activity of kinases, cell adhesion can be mediated by the expression of cell adhesion molecules, and immune signaling can be regulated by the activity of cytokines, MESH:D018121, and transcription factors. the transcriptional regulation of these genes can be mediated by transcription factors and the regulation of transcriptional activity can be mediated by modulators of tfs, such as kinases and ubiquitin ligases. protein-protein interactions can occur between the different genes, signaling from growth factors can affect the expression of genes in this set]] | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[[these genes are involved in processes related to cell development, GO:0009653, calcium and calcium-dependent signaling, MESH:D017978, smad pathway and extracellular matrix proteins.\\n\\nmechanism: the mechanism underlying this gene list is likely related to signal transduction pathways. these may involve cell surface receptors which bind growth factors, such as tgfb1 and bmpr2, and transduce the signal through the smad pathway via the fkbp1a, bmpr1a, smurf1, smad1, ltbp2, thbs1, arid4b, ppm1a, and ctnnb1 proteins to influence the regulation of gene expression and cell fate. moreover, other molecules such as xiap, ube2d3, nog, slc20a1, serpine1, bcar3, rhoa, MESH:D045683, hipk2, ppp1ca, smad7, junb, smad6, ppp1r15a, tjp1, and ifngr2 may be involved in the signal transduction pathway. in addition, the calcium and calcium-dependent signaling by the tg]] | \n", + "[[transcriptional regulation, GO:0007165, GO:0051726, protein kinase pathways, GO:0006412, GO:0048468, GO:0008283, GO:0030054, cytoskeletal organization]] | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[[GO:0032502, GO:0006954, MESH:D056747, cell signaling, MESH:M0496924, GO:0009653, GO:0009888, GO:0008283, GO:0006915, immune system response, MESH:M0496924]] | \n", + "[[GO:0002224, GO:0032502, GO:0006954, immune-response regulation, nfkb, GO:0004707, GO:0010467, pro-inflammatory molecules]] | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[[gene transcription, actin maturation, cytoskeleton formation, signaling complex assembly, interleukin receptor signaling, GO:0051170, cytokine receptor signaling, nf-kappab signaling pathway, cytokine-mediated signal transduction, GO:0006367, MESH:D005786, cytokine receptor signaling pathway, GO:0010737, GO:0035556]] | \n", + "[[cytokine-mediated signaling, antigen-receptor mediated signaling, GO:0042100, cytokine expression and release, immunoregulatory interactions, GO:0051092, interferon (ifn) signaling]] | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[[GO:0009299, GO:0042254, GO:0006457, nucleolar activity, spliceosomal activity, protein production, GO:0015031, GO:0006396, GO:1901987]] | \n", + "[[GO:0006412, GO:0042254, GO:0006413, GO:0006457, GO:0006414, GO:0015833, peptide assembly, chaperone mediated protein folding]] | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[[GO:0008152, GO:0006412, GO:0043687, GO:0016310, pepetide binding and metabolism, protein structure and folding, rna synthesis and processing, GO:0000394, GO:0010467, GO:0051726, GO:0006915, GO:0007165, GO:0006281]] | \n", + "[[analysis of this gene list has revealed that the functions enriched in the gene set include translation and translation initiation (exosc2, eif4a3, MESH:D039561, eif4g1, eif4a2); ubiquitination (ern1, skp1, herpud1, ube2g2, ube2l3); and protein folding and stability (atf3, fkbp14, dnajb9, calr, preb, hspa5, hsp90b1).\\n\\nmechanism: the enriched functions imply a complex network of processes that is likely to involve translation initiation of mrna, GO:0016567, and chaperone activity that facilitates protein folding, stability and degradation. it is possible that this gene set is associated with a variety of cellular pathways, including those related to gene expression, GO:0007165, GO:0008152]] | \n", + "||
| HALLMARK_UV_RESPONSE_DN-0 | \n", + "[[MESH:D011494, cellular signaling pathways, GO:0001501, GO:0031012, transcriptional regulation, post-translational phosphorylation, growth regulation, development regulation, remodeling]] | \n", + "[[cell signaling, structural proteins, MESH:D004798, GO:0009653]] | \n", + "||
| HALLMARK_UV_RESPONSE_DN-1 | \n", + "[[mitotic regulation, GO:0060349, morphogenesis of specific organs and tissues, GO:0009966, regulation of transcription, GO:0042127, cellular responses to external stimuli, GO:0006468, GO:0003677]] | \n", + "[[the above list of genes is significantly enriched for terms related to the development of the connective tissue, including morphogenesis, GO:0007049, regulation of transcription, and extracellular matrix organization; as well as the regulation of cell migration, matricellular protein signaling, GO:0007165, and calcium ion binding.\\n\\nmechanism: the enriched terms suggest that these genes work together in a common and interconnected pathway to control the formation, MESH:D009068, and functioning of the connective tissue. this pathway likely involves interactions among signal transduction pathways mediated by protein-protein interactions, transcriptional regulation, and calcium ion binding. these interactions would likely affect the structure and organization of the extracellular matrix, the migration of cells, the cell cycle, signalling through matricellular proteins]] | \n", + "||
| HALLMARK_UV_RESPONSE_UP-0 | \n", + "[[GO:0032502, GO:0016049, gene transcription, GO:0008152, MESH:D011506, GO:0006412, GO:0007049, cell signaling, transcriptional regulation, MESH:D021381, GO:0010468]] | \n", + "[[MESH:D021381, organelle trafficking, GO:0006306, transcription regulation, GO:0003677, GO:0006338, GO:0051726, GO:0008152]] | \n", + "||
| HALLMARK_UV_RESPONSE_UP-1 | \n", + "[[GO:0008283, GO:0051726, dna replication and repair, GO:0007165, GO:0019722, GO:0006915, GO:0006629, oxygen pathway]] | \n", + "[[genes in this list are generally involved in the regulation of cell growth and development, in particular related to apoptosis, signaling and transcriptional pathways. enriched terms include: transcriptional regulation; cell cycle regulation; apoptosis regulation; signal transduction; dna damage response; and cellular metabolism.\\n\\nmechanism: the molecular and cellular mechanisms underlying cell growth and development are complex and interconnected. genes in this list are believed to be involved in several pathways, such as transcriptional regulation, GO:0051726, apoptosis regulation, GO:0007165, GO:0006974, and cellular metabolism. these pathways interact and regulate each other in order to ensure the healthy functioning of cells. transcriptional regulation is key in regulating gene expression, while the cell cycle is tightly regulated by the activation of cell cycle control proteins and anti-apoptotic pathways. signal transduction pathways are essential for the proper coordination of cellular responses to external stimuli, and dna damage response allows for the repair of any irregularities. cellular metabolism is necessary for providing energy for growth and repair, for controlling the production of proteins]] | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[[this examination of human genes reveals a number of gene functions that are significantly enriched and related to developmental processes, including cell proliferation and differentiation, GO:0048729, and wnt signalling pathways. \\nmechanism: cell proliferation and differentiation, GO:0048729, wnt signalling pathways are all important in the normal healthy development of cells organs. these genes provide important functions that act in cooperative downstream pathways to enable promote these developmental processes.\\nthe enriched terms are: cellular differentiation; cellular proliferation; digit development; tissue morphogenesis; wnt signalling pathway]] | \n", + "[[the genes in this list are associated with the wnt signaling pathway, modulating cell growth and mophogenesis. the enrichment terms corresponding to this list are wnt signaling, GO:0016049, GO:0009653, transcriptional regulation, and epigenetics.\\n\\nmechanism: the wnt signaling pathway activates nuclear proteins such as lef1 and tcf7, which then activate transcription of genes involved in cell growth and morphogenesis. the genes on the listed are associated with modulating the wnt pathway, including epigenetic regulation and cell cycle regulation]] | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[[wnt signaling, notch signaling, transcription regulation, GO:0051726, GO:0009653, GO:0032502]] | \n", + "[[GO:0009653, GO:0006351, GO:0032502, MESH:D060449]] | \n", + "||
| T cell proliferation-0 | \n", + "[[cell signalling, protein interaction, GO:0007165, GO:0032502, regulatory role in immunity, GO:0030163, receptor-mediated signaling, GO:0016049, GO:0030154, GO:0006396]] | \n", + "[[GO:0009653, GO:0048468, cell signaling, receptor-mediated signaling, GO:0010468]] | \n", + "||
| T cell proliferation-1 | \n", + "[[cell signaling, immune regulation, GO:0007165, growth factor production and response, immune response and modulation, calcium homeostasis, GO:0000981, development and differentiation, GO:0005102, GO:0001816]] | \n", + "[[GO:0005126, GO:0007155, immunoreceptor-antigen complex binding, regulation of the ubiquitin-proteasome pathway, transcription factor regulator activity, gtp-binding protein binding, GO:0030154]] | \n", + "||
| Yamanaka-TFs-0 | \n", + "[[the enrichment test results reveal that the list of genes are all involved in stem cell pluripotency and early embryonic development. enriched terms include pluripotency, stem cell morphology, MESH:D047108, GO:0000981, GO:0016049, differentiation, cell proliferation.\\n\\nmechanism: the genes focus on the regulation of the pluripotency and early embryonic developmental program. they regulate various aspects such as transcription factors, cell growth, morphogenesis, differentiation and cell proliferation. by acting in concert, they maintain the pluripotency of stem cells and initiate the processes of early morphogenesis. it is hypothesized that these genes are part of a large regulatory network which facilitates the pluripotency of the progenitor cells and the successful orchestration of early embryonic development]] | \n", + "[[GO:0000988, embryonic stem cell differentiation, cell pluripotency, dna-binding, MESH:D005786, GO:0140110, transcription factor complex formation.\\nmechanism: these genes are known to be involved in the regulation of gene expression, and thus serve an important role in directing the biological activities associated with embryonic stem cell differentiation and pluripotency. they are likely to form complexes, interact with dna, and/or bind to components of the transcription machinery to regulate gene expression at the transcriptional level]] | \n", + "||
| Yamanaka-TFs-1 | \n", + "[[GO:0009792, GO:0048864, GO:0000981, GO:0009653]] | \n", + "[[GO:0048863, GO:0048468, embryonic stem cell differentiation, transcriptional regulation, pluripotency, transcription factor regulation.\\n\\nmechanism: the genes klf4, pou5f1, and sox2 act in concert to regulate the expression of developmental proteins that are involved in forming stem cells. this trio of transcription factors plays a key role in regulating cell differentiation and pluripotency, thus influencing the direction of embryonic stem cell development by regulating gene expression of proteins involved in stem cell formation]] | \n", + "||
| amigo-example-0 | \n", + "[[GO:0030198, GO:0007155, GO:0009653, cell signaling, cytoskeletal organization, GO:0030154, MESH:D002470]] | \n", + "[[GO:0008283, GO:0048729, motility regulation, vascular development, GO:0098868, UBERON:0002405]] | \n", + "||
| amigo-example-1 | \n", + "[[our term enrichment analysis suggests that the human genes jag2, spp1, jag1, vcan, olr1, col5a2, app, UBERON:0003010, postn, tnfrsf21, apoh, pglyrp1, vav2, fstl1, nrp1, s100a4, lrpap1, vtn, timp1, itgav, lum, pf4, cxcl6, col3a1, stc1, kcnj8, msx1, ptk2, prg2, pdgfa, serpina5, and vegfa are related to processes in growth and differentiation, including transcriptional network maintenance, cell adhesion and motility, GO:0006915, and extracellular matrix component formation.\\n\\nmechanism: \\nthese genes may be involved in a complex network of signaling pathways that regulate cell growth and differentiation, cell adhesion and migration, GO:0006915, and matrix component formation. they may be involved in the reception and transduction of growth and differentiation signals, could facilitate the assembly of extracellular matrix components to form the microenvironment necessary to prompt and]] | \n", + "[[GO:0001525, GO:0008283, GO:0016477, matrix remodeling, GO:0048771, jagged-mediated signaling, transcriptional regulation, GO:0030168, GO:0070527, immune regulation, extracellular matrix formation]] | \n", + "||
| bicluster_RNAseqDB_0-0 | \n", + "[[GO:0009653, GO:0032502, transcription regulation, cell signalling, GO:0006811]] | \n", + "[[GO:0016049, differentiation, migration, chromatin modulation, transcription regulation, cytoskeletal organization, intracellular trafficking, GO:0007155, GO:0007165, dna/rna metabolic processes, GO:0009653, GO:0001525, muscle growth, GO:0032502]] | \n", + "||
| bicluster_RNAseqDB_0-1 | \n", + "[[GO:0009653, neuronal growth, neuronal system development, cell-cell communication, cell signaling, GO:0009888, organ development]] | \n", + "[[chromatin regulation, GO:0048468, GO:0006412, GO:0006811, GO:0000981, GO:0043687]] | \n", + "||
| bicluster_RNAseqDB_1002-0 | \n", + "[[analysis of the gene list shows that they are all associated with sarcomere function, MESH:D009119, skeletal muscles and thermogenesis. the enriched terms include sarcomere function, MESH:D009119, UBERON:0001134, MESH:D022722, actin-myosin interaction, calcium handling, muscle development and differentiation, and mitochondrial function. \\n\\nmechanism: the underlying biological mechanism is associated with the activation of genes that are linked to the assembly, maintenance and contraction of the sarcomere, which is the fundamental unit of muscle contraction, as well as muscle development and differentiation, calcium handling, mitochondrial fluctuation, thermogenesis. this contributes to the generation of force within the skeletal muscles]] | \n", + "[[MESH:M0370791, GO:0007015, GO:0006936, z-disc formation, GO:0007097, muscle fiber organization, ion channel influx/efflux]] | \n", + "||
| bicluster_RNAseqDB_1002-1 | \n", + "[[skeletogenesis, MESH:D024510, GO:0048740, GO:0001501, GO:0006936, GO:0006412, GO:0009058, MESH:D009126]] | \n", + "[[MESH:D024510, GO:0048740, GO:0021675, calcium distribution, actin proteins, cardiac contractile proteins, sarcomeric proteins, membrane protein transport, ion channel proteins, enzyme regulation.\\nmechanism: this list of genes are likely to be involved in the regulation of muscle structures and contractions, organization of calcium distribution throughout the cell, nerve development, and support of membrane protein transport and enzymatic activities. these processes are important for maintaining muscle contraction and activity]] | \n", + "||
| endocytosis-0 | \n", + "[[GO:0007165, vesicle/lipid trafficking, cellular adhesion, nutrient regulation, cell metabolism, cytoskeletal organization, endocytosis/exocytosis, intercellular adhesion/motility]] | \n", + "[[GO:0006629, cell signaling, GO:0007049, cytoskeletal dynamics]] | \n", + "||
| endocytosis-1 | \n", + "[[membrane trafficking, GO:0007165, protein proteolysis, GO:0006629, receptor signaling, GO:0055088]] | \n", + "[[GO:0006897, intracellular signaling, GO:0016310, protein interactions, receptor trafficking]] | \n", + "||
| glycolysis-gocam-0 | \n", + "[[GO:0006096, aerobic glycolysis, GO:0006094]] | \n", + "[[GO:0006754, GO:0006096, MESH:D004734, MESH:M0496924]] | \n", + "||
| glycolysis-gocam-1 | \n", + "[[GO:0008152, GO:0006096, GO:0006098, GO:0006006, MESH:D004734]] | \n", + "[[metabolic pathway, GO:0006096, glucose oxidation, pyruvic acid production, GO:0006754]] | \n", + "||
| go-postsynapse-calcium-transmembrane-0 | \n", + "[[these genes appear to be involved in the development, functioning and regulation of the nervous system, specifically neurons and their associated pathways and processes. the terms \"neurotransmission\"; \"neuronal cell membrane regulation\"; \"neurotransmitter release\"; \"calcium signaling\"; \"neuronal ion channel regulation\"; and \"neuronal excitability regulation\" are significantly enriched in this gene set.\\n\\nmechanism: it appears that this gene set may be involved in a broad range of processes related to neurophysiology, including the regulation of neuronal membrane excitability and ion channels, neuronal cell membrane regulation, GO:0007269, and calcium signaling. these processes are all complex and interrelated, are likely to have a direct impact on neural development function]] | \n", + "[[summary: the enriched terms of the human genes atp2b1, atp2b2, cacna1c, cacng2, cacng3, cacng4, cacng5, cacng7, cacng8, chrna10, chrna7, chrna9, drd2, f2r, gpm6a, grin1, grin2a, grin2b, grin2c, grin2d, grin3a, grin3b, htr2a, itpr1, ncs1, p2rx4, p2rx7, plcb1, psen1, slc8a1, slc8a2, slc8a3, trpv1 include neuron development; neurotransmitter signaling; signal transduction; transmembrane transport; neural plasticity; ion transport; calcium signaling; glutamate receptor signaling; and synaptic signaling. \\n\\nmechanism: these genes are believed to act in concert to regulate and coordinate the various stages of neuron development, such as neurotransmitter signaling, GO:0007165, GO:0055085, neural]] | \n", + "||
| go-postsynapse-calcium-transmembrane-1 | \n", + "[[the term enrichment test reveals that the genes in the list are mainly involved in neuronal ion channels and calcium signalling pathways. enriched terms included calcium channel activity, GO:0005244, GO:0038023, GO:0015276, and g-protein coupled receptor activity. \\n\\nmechanism: the genes in the list form ion channels and g-protein coupled receptors within neuronal cells, which facilitates the communication of neurotransmitters between neurons. several of the genes are involved in calcium signalling pathways, which regulate various cellular pathways involved in the development and maintenance of neurons]] | \n", + "[[neuronal function, GO:0006811, ion channel regulation, neurotransmitter regulation, calcium regulation, potassium regulation, GO:0007268, membrane potential regulation]] | \n", + "||
| go-reg-autophagy-pkra-0 | \n", + "[[GO:0016049, GO:0048468, GO:0006915, GO:0006955, GO:0030163, GO:0006508]] | \n", + "[[this set of genes is associated with cellular functions related to metabolic homeostasis and activation of the pi3k/akt signaling pathway. the enriched terms associated with the genes include cell cycle regulation, protein kinase regulation, mitochondrial regulation, and mitochondrial stress response.\\n\\nmechanism: the metabolic homeostasis and activation of the pi3k/akt pathway are mediated by these genes, which affect the regulation of cell cycle, protein kinase regulation, mitochondrial regulation, and mitochondrial stress response. these genes have roles in regulating metabolic processes as well as responding to external stressors. their involvement in cell cycle regulation and protein kinase regulation ensures the healthy development and maintenance of the cell, while their role in mitochondrial regulation and mitochondrial stress response plays an important role in maintaining the cell's energy production]] | \n", + "||
| go-reg-autophagy-pkra-1 | \n", + "[[phosphatidylinositol signalling, vascular endothelial growth factor receptor signalling, progesterone-mediated oocyte maturation, nf-kb signaling, GO:0043526]] | \n", + "[[cell signaling, transcription regulation, GO:0006468, ras activation, akt activation, calcium-associated kinases, GO:0019722]] | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[[carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomal, GO:0005777, and catabolic processes; digit, skeletal, GO:0035108]] | \n", + "[[MESH:D009113, MESH:D009077, glycosyltransferase, MESH:D006821, GO:0070085, enzyme, MESH:D011506]] | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[[glycoside hydrolase (gh) activity, mucin biosynthesis, GO:0006031, MESH:D057056, lysosomal enzyme activity.\\nmechanism: glycoside hydrolase (gh) and lysosomal enzymes play important roles in the process of glycostasis, and are involved in a variety of metabolic activities such as the breakdown of polysaccharides, the synthesis of glycolipids and glycoproteins, and the degradation of other macromolecules. chitin and mucin biosynthesis also involve glycosylation and enzymatic modification of sugars and polysaccharides to form polymeric molecules. cysteine protease are involved in the hydrolysis of proteins, while lysosomal enzymes aid in the breakdown of molecules in the l]] | \n", + "[[the gene functions that were found to be enriched amongst this set of genes were predominantly related to carbohydrate metabolism, including glycosaminoglycan and glycosphingolipid biosynthesis as well as lysosomal enzyme activity.\\n\\nmechanism:\\nthe mechanism most likely lies in the pathway of glycoconjugation, which helps to regulate important processes such as cell adhesion, GO:0006955, and signal transduction. the pathway is integral to the proper formation and function of the extracellular matrix, which is important for cellular differentiation and tissue organization. the enriched terms found here likely represent genes that are involved in the biosynthesis and metabolism of various glycoconjugates, in addition to the regulation of lysosomal enzymes involved in the degradation of complex carbohydrates]] | \n", + "||
| ig-receptor-binding-2022-0 | \n", + "[[members of the immunoglobulin (ig) gene superfamily - specifically, igh, GO:0033984, MESH:C014609, GO:0042571, response and maintenance of the adaptive immune system at different levels, likely via antigen binding, signal transduction and b cell activation]] | \n", + "[[immunoglobulin heavy chain combination, immunoglobulin light chain combination, j-chain, antigen-specific receptor, t-lymphocyte receptor, regulation of immune function]] | \n", + "||
| ig-receptor-binding-2022-1 | \n", + "[[GO:0003823, b cell receptors, GO:0007596, GO:0005577, MESH:D001779, clec4d]] | \n", + "[[genes related to immunoglobulins, transcripts associated with immunoglobulin transcription and splicing, immunoglobulin gene expression, proteins involved in immunoglobulin regulation and processing, GO:0002637, GO:0002637, mhc class i antigen processing and presentation, cytokine-mediated signaling, GO:0002544, limit degranulation. \\n\\nmechanism: these genes are associated with immunoglobulin production, processing, and regulation. this includes genes related to immunoglobulins, transcripts involved in transcription and splicing, and proteins that are involved in the regulation and processing of immunoglobulins. additionally, genes related to mhc class i antigen processing, cytokine-mediated signaling, chronic inflammatory response, and limit degranulation are also expressed. these genes interact to form an integrated pathway that is involved in the regulation of the immune response and the formation of immunoglobulins]] | \n", + "||
| meiosis I-0 | \n", + "[[dna damage recognition, GO:0006281, GO:0006302, meiotic recombination, GO:0007059, GO:0035825, rad51 family proteins, dna end-protection, mus81-mms4 complex, muts family proteins, dna proofreading, spo11-associated pathway]] | \n", + "[[GO:0006260, GO:0006281, replication fidelity, GO:0007049, GO:0071897, dna prioritization]] | \n", + "||
| meiosis I-1 | \n", + "[[GO:0006281, GO:0006260, gene splicing]] | \n", + "[[this enrichment test on the list of human genes suggests a central role for dna damage repair and cell cycle regulation in the common functionalities of the genes. enriched terms found include \"dna repair\", \"cell cycle\", \"chromatin remodelling\", \"recombinational repair\", \"steroid hormone receptor\", \"centromere\", GO:0000724]] | \n", + "||
| molecular sequestering-0 | \n", + "[[GO:0000075, cell adhesion/motility complex, transcriptional complex, GO:0036211, rna processing complex]] | \n", + "[[GO:0019722, calcium buffering, GO:0006816, regulation of calcification, protection against calcium overload, calcium-v influx/efflux]] | \n", + "||
| molecular sequestering-1 | \n", + "[[calcium binding, apoptotic regulation, immune modulation, MESH:D018384, GO:0051726, stress-response regulation]] | \n", + "[[cell morphology regulation, GO:0008152, GO:0006915, GO:0006412, GO:0036211, GO:0006811, GO:0023052, stress response, GO:0006351, cell surface interactions, chromatin regulation]] | \n", + "||
| mtorc1-0 | \n", + "[[the human genes abcf2, acaca, acly, acsl3, actr2, actr3, add3, adipor2, ak4, aldoa, arpc5l, asns, atp2a2, atp5mc1, atp6v1d, MESH:D064096, bcat1, bhlhe40, btg2, bub1, cacybp, calr, canx, ccnf, ccng1, cct6a, cd9, cdc25a, cdkn1a, cfp, cops5, coro1a, cth, ctsc, GO:0038147, cyb5b, cyp51a1, dapp1, ddit3, ddit4, ddx39a, dhcr24, dhcr7, GO:0004146, ebp, edem1, eef1e1, egln3, eif2s2, elovl5, elovl6, eno1, eprs1, ero1a, etf1, MONDO:0100101, MONDO:0100102, fdxr, fgl2, MESH:D010649]] | \n", + "[[genes in this list are involved in various aspects of cellular metabolism, GO:0065007, and development.a number of the genes have roles in energy production and metabolism such as, atp2a2, aldoa, MONDO:0009214, fao1, fgl2, gapdh, gbe1, MONDO:0015408, glrx, MONDO:0005775, me1, phgdh, and pgm1. there is a strong presence of genes involved in protein synthesis and transport, including the ribosomal proteins, the eukaryotic translation factors and initiation factors (eif2s2, eif1e1, elovl5, and elovl6). this gene set is also enriched for a number of ubiquitin and ubiquitin-like proteins (ube2d3, ufm1, uso1, tomm40, hspd1, hspe1, sytl2, nherf1, and hk2). many of these genes are involved in regulation through multiple pathways including regulation of transcription (add3, actr2, actr3, cct6a, gga2, gdh2, mef2b, ykt]] | \n", + "||
| mtorc1-1 | \n", + "[[energy production, GO:0008152, protein biosynthesis and folding, cell regulation, MESH:D048788, protein turnover]] | \n", + "[[genes related to metabolism and biosynthesis (acly, aldoa, atp2a2, atp6v1d, cacybp, coro1a, dhcr24, MONDO:0100101, MONDO:0100102, gbe1, MESH:C066524, gsr, hmgcs1, hspa9, lgmn, me1, mthfd2l, nampt, pgm1, pgk1, psat1, psma3, psma4, psmg1, psmc2, psmc4, psmd12, psmd13, psmd14, stc1, stip1, and ufm1), protein folding/interaction (act2, actr2, actr3, add3, elovl5, eno1, ero1a, eif2s2, fgl2, insig1, itgb2, map2k3, mcm2, mcm4, nufip1, p4ha1, pdk1, pitpnb, pnp, psme3, sec11a, shmt2, slc2a1, slc2a3]] | \n", + "||
| peroxisome-0 | \n", + "[[peroxisome biogenesis, peroxisome formation, membrane protein trafficking, GO:0044255, mitochondrial-peroxisomal crosstalk]] | \n", + "[[protein homeostasis, peroxisome biogenesis, peroxisome assembly, peroxisome maintenance, protein regulation, GO:0050821]] | \n", + "||
| peroxisome-1 | \n", + "[[peroxisomal biogenesis, peroxisomal protein transport, oxidative damage resistance]] | \n", + "[[peroxisomal biogenesis, peroxisome assembly, peroxisome regulation, GO:0015031, membrane trafficking]] | \n", + "||
| progeria-0 | \n", + "[[cell structural element development, gene transcription, GO:0016070, GO:0006259, transcriptional regulation]] | \n", + "[[after performing the enrichment test on the genes zmpste24, banf1, MONDO:0010196, and lmna, we identified that all of the genes have a role in the regulation of nuclear and chromatin structures. the individual genes are involved in a wide range of processes in these two areas. this includes gene expression, GO:0006260, GO:0006338, GO:0000723, as well as cell cycle checkpoints.\\n\\nthe enriched terms are 'nuclear structure regulation'; 'chromatin structure regulation'; 'gene expression regulation'; 'dna replication regulation'; 'chromatin remodeling'; 'telomere maintenance'; and 'cell cycle checkpoint regulation'. \\n\\nmechanism: the underlying biological mechanism that our gene list points to is one involving the regulation of nuclear and chromatin structures. in order to maintain the stability of the genome and ensure its accurate transmission, molecules encoded by the four genes could be involved in key activities such as gene expression, GO:0006260, GO:0006338, GO:0000723, as well as cell cycle checkpoints]] | \n", + "||
| progeria-1 | \n", + "[[dna replication and repair, GO:0006334, GO:0000723, transcriptional regulation]] | \n", + "[[transcriptional regulation, GO:0006281, GO:0051726, GO:0030154]] | \n", + "||
| regulation of presynaptic membrane potential-0 | \n", + "[[GO:0007165, GO:0006811, regulation of neurotransmitter release]] | \n", + "[[MESH:D007473, MESH:D008565, synapse formation, GO:0007268, MESH:D009473, neuronal excitability, voltage-gated ion channels, MESH:D058446]] | \n", + "||
| regulation of presynaptic membrane potential-1 | \n", + "[[analysis of these genes show that they are involved in human neurological structure and function. enriched terms include neuron activity, GO:0005216, GO:0008066, GO:0004930, MESH:D005680, GO:0005267, MESH:D005680]] | \n", + "[[ion-channel function, neuron excitability, GO:0007268, MESH:D018079, MESH:D017470, MESH:D015221, MESH:D015222]] | \n", + "||
| sensory ataxia-0 | \n", + "[[MESH:D024510, neuronal development, GO:0015031, GO:0006629, GO:0009653]] | \n", + "[[GO:0006412, GO:0008152, ion channel transport, GO:0006936, MESH:D024510]] | \n", + "||
| sensory ataxia-1 | \n", + "[[GO:0015031, MONDO:0008090, GO:0048705, MESH:D024510, GO:0005783, mitochondrial protein transport, cytoskeletal organization]] | \n", + "[[nucleic acid metabolism, GO:0003676, GO:0050657, GO:0019538, GO:0005515, GO:0015031]] | \n", + "||
| term-GO:0007212-0 | \n", + "[[g alpha subunit signaling, gpcr activation and signaling, gpcr function, MESH:D019281]] | \n", + "[[g-protein coupled receptor (gpcr), g-protein subunit, MESH:D000262, MESH:D015220, MESH:D010770]] | \n", + "||
| term-GO:0007212-1 | \n", + "[[cellular signaling, g protein signaling pathway, calcium signaling pathway, GO:0007399, GO:0007268, phosphorylation cascade, nerve morphogenesis, indoleamine metabolism]] | \n", + "[[GO:0007165, cellular growth & differentiation, GO:0007010, endocrine system regulation, transcriptional regulation]] | \n", + "||
| tf-downreg-colorectal-0 | \n", + "[[nuclear receptor superfamily, transcription regulation, epigenetic regulation, GO:0051726, GO:0003677, GO:0006338, GO:0032502, cell signaling pathways, GO:0005652, GO:0016363]] | \n", + "[[genes such as hira, cebpb, e2f3, hmga1, znf263, tfdp1, trib3, bhlhe40, smarca4, slc26a3, nfe2l3, ssbp2, gtf3a, npm1, trip13, mef2c, nr3c2, foxm1, vdr, hand1, klf4, hexim1, tgif1, med24, tead4, smarcc1, scml1, MESH:D024243, myc, foxa2, bmal2, spib, nme2, phb1, cbx4, runx1, ppargc1a, polr3k, nr5a2, maf, nr1h4, sox9, dnmt1, cbfb, znf593, mta1, zbtb18 are all involved in the regulation of transcription, GO:0006338, GO:0003677, and epigenetics. of this group, genes involved in transcription are significantly enriched (e.g. hira, cebpb, e2f3,]] | \n", + "||
| tf-downreg-colorectal-1 | \n", + "[[transcriptional regulation, GO:0016569, GO:0009653, cardiovascular development, differentiation, MESH:M0464910, MESH:M0030450, GO:0048863]] | \n", + "[[GO:0016049, transcriptional regulation, GO:0006338, GO:0051726, GO:0006351, GO:0016569]] | \n", + "||
| ontological_synopsis | \n", + "EDS-0 | \n", + "[[GO:0032963, GO:0030198, GO:0004222, GO:0030206, GO:0008378, GO:0005509, GO:0008270, platelet derived growth factor binding, GO:0002020, GO:0035987, GO:0007266, GO:0007160, hypoxia response, epidrmis development, peptidyl-lysine hydroxyl]] | \n", + "[[collagen or extracellular matrix structural constituent, collagen metabolic process or biosynthetic process, proteoglycan metabolic process or biosynthetic process, GO:0006024, dna-binding transcription factor binding activity, GO:0001217, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, metal ion binding activity, GO:0003755, GO:0035987, GO:0004252, GO:1904028, protein peptidyl-prolyl is]] | \n", + "|
| EDS-1 | \n", + "[[GO:0030198, GO:0030199, GO:0043589, GO:0042060, GO:0043588, GO:0032964, GO:0006024, GO:0003755, GO:0035987]] | \n", + "[[GO:0030198, GO:0030199, GO:0032964, GO:0030166, GO:0006024]] | \n", + "||
| FA-0 | \n", + "[[analysis of the above genes shows that they are all involved in dna repair and involved in the fanconi anaemia nuclear complex, which is a critical part of the fanconi anaemia disease pathway. the list of enriched terms includes \"protein monoubiquitination\", \"dna repair complex\", \"fanconi anaemia nuclear complex\", \"double-strand break repair via homologous recombination\", \"response to intra-s dna damage checkpoint signaling\", \"telomere maintenance\", \"positive regulation of g2/m transition of mitotic cell cycle\", \"regulation of transcription by rna polymerase ii\".\\n\\nmechanism: the underlying biological mechanism is the fanconi anaemia pathway, where the defective genes of the path have the potential to lead to cancer or other fanconi anaemia-related illnesses. this dna repair pathway relies heavily on the fanconi anaemia nuclear complex, which involves the processes of monoubiquitination, involving the above genes, double-strbreak repair via homologous recombination. in addition, the regulation of telomere maintenance, positive regulation of g2/m transition of mitotic cell cycle regulation of transcription by rna polymerase ii are essential for proper dna repair]] | \n", + "[[GO:0006281, GO:0006513, GO:0043240, GO:0000785, GO:0005634, GO:0005829]] | \n", + "||
| FA-1 | \n", + "[[this group of genes are involved in a range of dna repair processes, including protein monoubiquitination and double-strand break repair via homologous recombination. they are all localized in different components of the cell (e.g. chromatin, GO:0005634, GO:0005829, GO:0005657, GO:0005694, etc.) and are part of several complexes/hierarchies (e.g. fanconi anaemia nuclear complex, GO:0033063, GO:0048476, GO:0033557, GO:0033593, etc.). enriched terms includes: dna repair; protein monoubiquitination; double-strand break repair via homologous recombination; regulation of dna metabolic process; negative regulation of double-stranded telomeric dna binding activity; response to gamma radiation; regulation of telomere maintenance; establishment of protein localization to telomere; and regulation of protein metabolic process.\\n\\nmechanism: these genes are involved in a range of complex and interrelated biochemical pathways, which utilize a variety of enzymatic activities (e.g. ubiqu]] | \n", + "[[GO:0006513, GO:0006281, GO:0003682, GO:0000400, GO:0003684, GO:0003697, GO:1990599, GO:0004520, GO:0006310, GO:0005524, GO:0006259, GO:0072757, GO:0051052, GO:0003691, GO:0000723, GO:0019219, GO:0051246, GO:0070200, GO:0016573, GO:0004402, gamma-tubulin binding activity, identical protein binding activity, jun kinase binding activity, rna polymerase ii-specific dna-binding transcription factor binding activity, GO:0061630, GO:0031386]] | \n", + "||
| HALLMARK_ADIPOGENESIS-0 | \n", + "[[GO:0005515, protein homodimerization, GO:0005524, GO:0003677, GO:0003824, MONDO:0016019]] | \n", + "[[protein binding activity, MESH:D010758, atp binding activity, gtp binding activity, GO:0022857, dna binding activity, receptor binding activity, GO:0004869, caspase binding activity, rna binding activity]] | \n", + "||
| HALLMARK_ADIPOGENESIS-1 | \n", + "[[protein homodimerization, GO:0019899, GO:0140657, GO:0005102, ligase binding, GO:0003924, GO:0046872, dna-binding, rna-binding, oxidase activity, MESH:D010758, GO:0120227, transportase activity, dehydrogenase activity, GO:0016791, GO:0016301, GO:0004175, GO:0022857, chemotactic receptor activity, GO:0017077]] | \n", + "[[protein binding activity, enzyme binding activity, atp binding activity, rna binding activity, gtp binding activity, identical protein binding activity, gtp-dependent protein binding activity, transition metal ion binding activity, GO:0016615, aldehyde dehydrogenase activity, GO:0008097, GO:0052650, fad binding activity, MESH:D010758, heme binding activity, GO:0003872, GO:0004609, GO:0003873, GO:0004144, GO:0003994, GO:0004784, GO:0004129, molybdenum ion binding activity]] | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[[receptor binding activity, signaling receptor binding activity, protein binding activity, dna-binding, GO:0016563, GO:0005125, GO:0008083, GO:0042605, enzyme binding activity, chemical binding activity, protein complex binding activity]] | \n", + "[[protein homodimerization, protein heterodimerization, GO:0042802, GO:0019901, dna-binding, rna-binding, GO:0017124, GO:0019958, GO:0008201, ubiquitin-protein ligase binding]] | \n", + "||
| HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[[enzyme binding activity, rna binding activity, protein binding activity, chemokine receptor binding activity, GO:0004712, GO:0042803, identical protein binding activity, GO:0008083, interleukin binding activity, cell-cell adhesion mediation, dna-binding transcription activity, GO:0015026, cytoplasmic factor activity, metal ion binding activity, polypeptide antigen transporter activity]] | \n", + "[[GO:0007155, GO:0005102, GO:0007165, GO:0001228, chemokine receptor binding activity, enzyme binding activity, GO:0008083, GO:0005125, degradation of redundant or damaged proteins and peptides, GO:0046983, metal ion binding activity, peptide antigen binding activity, GO:0004888, GO:0004712, GO:0042803, ubiquitin binding activity]] | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[[protein binding activity, enzyme binding activity, transcription factor binding activity, GO:0016787, GO:0004721, GO:0003714, GO:0003713, atp binding activity, GO:0004672, GO:0016563, GO:0003924, nad+ binding activity, ring-like zinc finger domain binding activity, GO:0061656, small protein activating enzyme binding activity, GO:0000224, GO:0062076, GO:0004383, GO:0004222, 17-beta-dehydrogen]] | \n", + "[[GO:0005215, GO:0005515, GO:0004672, GO:0038023, GO:0006351, GO:0044237, GO:0006974, GO:0007010, GO:0016787, GO:0046872, GO:0003924]] | \n", + "||
| HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[[protein binding activity, GO:0004672, GO:0006351, GO:0038023, enzymatic activity, GO:0016310, GO:0097472, GO:0003677, GO:0006351, postsynaptic organization, GO:0016887, nucleic acid binding activity, ubiquitin protein ligase binding activity, fad binding activity, MESH:D009249, GO:0061665, enzyme binding activity, GO:0022857, endopeptidase activator]] | \n", + "[[GO:0005515, GO:0016887, GO:0016563, GO:0003677, GO:0004674, GO:0022857, GO:0016787, GO:0061631, cis-regulatory region sequence-specific dna binding activity, GO:0061665, GO:0034594, GO:0007165, GO:0043027, GO:0003924, GO:0042803, nucleic acid binding activity, GO:0003713, GO:0003714, enzyme binding activity, calmodulin binding activity, metalloendope]] | \n", + "||
| HALLMARK_ANGIOGENESIS-0 | \n", + "[[GO:0030021, collagen binding activity, integrin binding activity, GO:0060090, identical protein binding activity, fibronectin binding activity, GO:0046983, heparan sulfate proteoglycan binding activity, GO:0007160, GO:0010810]] | \n", + "[[summary: the list of genes provided appear to be involved in a variety of unrelated processes, but when grouped by shared activities, several functions in common can be identified. these common functions include protein binding activity, GO:0060230, phospholipid binding activity, platelet-derived growth factor binding activity, GO:0046983, signaling receptor binding activity, collagen binding activity, atp activated inward rectifier potassium channel activity, voltage gated monoatomic ion channel activity, GO:0005249, GO:0016298, heparan sulfate proteoglycan binding activity, heparin binding activity, multiple growth factor activities, peptidoglycan binding activity, GO:0016019, platelet derived growth factor binding activity, non membrane spanning protein tyrosine kinase activity, GO:0005096, vascular endothelial growth factor binding activity, metal ion binding activity, small molecule binding activity, enzyme binding activity, retinoic acid binding activity, cxcr3 chemokine receptor binding activity, prostaglandin transmembrane transporter activity and sodium-independent organic anion transmembrane transporter activity. \\nmechanism: the genes in the list appear]] | \n", + "||
| HALLMARK_ANGIOGENESIS-1 | \n", + "[[GO:0007166, GO:0006468, GO:0045861, GO:0007160, GO:1902533, GO:0010604, transmem]] | \n", + "[[GO:0005515, GO:0006468, GO:0016477, GO:0008283, GO:0045861, GO:1902533, GO:0009966, GO:0010604, GO:0019901, GO:0008191, ion binding activity, small molecule binding activity, GO:0035987, GO:0005096, platelet-derived growth factor binding activity, GO:0046983, calcium ion binding activity, sympathetic nerve activity, GO:0051336]] | \n", + "||
| HALLMARK_APICAL_JUNCTION-0 | \n", + "[[GO:0098609, agonist binding activity, cytoplasmic matrix binding, protein homodimerization, GO:0005102]] | \n", + "[[GO:0007155, GO:0005178, gtp binding activity, collagen binding activity, atp binding activity, phospholipase binding activity, GO:0007160, GO:0050839, GO:0017124]] | \n", + "||
| HALLMARK_APICAL_JUNCTION-1 | \n", + "[[binding activities, GO:0003824, involvement in biological processes, structural roles]] | \n", + "[[extracellular matrix structure, GO:0038023, cell adhesion molecule binding activity, small gtpase binding activity, GO:0042803, identical protein binding activity, collagen binding activity, actin binding activity, atp binding activity, protein kinase binding activity, sh3 domain binding activity, integrin binding activity, GO:0005096]] | \n", + "||
| HALLMARK_APICAL_SURFACE-0 | \n", + "[[GO:0061024, protein organization, GO:0036211, GO:0015031, GO:0006897, GO:0007165, GO:0006915]] | \n", + "[[GO:0005480, cell structure maintenance, GO:0046872, GO:0016477, plasmamembrane transport, GO:0005515, GO:0043170, GO:0030296, endolemmal transport, GO:0016485, GO:0010467, GO:0006915, lipoprotein particle receptor catabolic process, peptide chain release, protein homodimerization, GO:0007165, GO:0048870, GO:1902600, GO:0000785, GO:0005654, GO:0031410, GO:0042552, GO:0044183]] | \n", + "||
| HALLMARK_APICAL_SURFACE-1 | \n", + "[[GO:0007155, protein folding and regulation, GO:0050801, MESH:D005786]] | \n", + "[[genes in this list are primarily involved in regulation of transcription, GO:0007165, membrane management, protein folding and binding, cell surface receptor signaling and adhesion, and cellular extravasation. enriched terms include: transcription, GO:0007165, protein-folding and binding, cell-surface receptor signaling, adhesion, GO:0045123, GO:0061024, extracellular matrix structural components, genetic expression, apoptotic pathways, and intracellular ion homeostasis. \\n\\nmechanism: genes on this list are primarily involved in several processes that coordinate essential cellular functions by dynamically managing activity of proteins at the surface of the cell, within underlying membrane layers, extracellularly and within dna. these genes manage the way cells communicate within their environment, interact with extracellular components, respond to stimuli, and extravasate. they code for proteins involved in transcription, GO:0007165, protein folding and binding, adhesion, apoptotic pathways, intracellular ion homeostasis, extracellular matrix structural components that have pleiotropic roles in modulating gene expression functioning of cellular components]] | \n", + "||
| HALLMARK_APOPTOSIS-0 | \n", + "[[dna binding activity, protein binding activity, enzyme binding activity, GO:0004197, identical protein binding activity, signaling receptor binding activity, calcium ion binding activity, protein kinase binding activity, GO:0000988, bh3 domain binding activity]] | \n", + "[[dna binding activity, GO:0046983, protein binding activity, enzyme binding activity, protein kinase binding activity, GO:0004197, GO:0003714, phosphoprotein binding activity, mhc class i protein binding activity, GO:0003700, signaling receptor binding activity, GO:0042803]] | \n", + "||
| HALLMARK_APOPTOSIS-1 | \n", + "[[calcium ion binding activity, protein binding activity, identical protein binding activity, chromatin dna binding activity, dna-binding transcription factor binding activity, ig domain binding activity, sh2 domain binding activity, bh3 domain binding activity, cyclin binding activity, rna binding activity, GO:0004197, metalloprotease inhibitor activity, phospholipid binding activity, lipopeptide binding activity, lysophosphatidic acid binding activity, sulfatide binding activity, atpase binding activity, pdz domain binding activity]] | \n", + "[[protein binding activity, identical protein binding activity, enzyme binding activity, GO:0003700, rna polymerase ii-specific transcriptional activity, GO:0004197, GO:0004896]] | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[[atp binding activity, GO:0016887, protein binding activity, signaling receptor binding activity, enzyme binding activity, GO:0042803, GO:0016791, GO:0000988, GO:0022857, ubiquitin-dependent protein binding activity, cholesterol binding activity, GO:0019871, phosphotyrosine residue binding activity]] | \n", + "[[atp binding activity, GO:0016887, cholesterol binding activity, GO:0022857, GO:0046982, GO:0000981, enzyme binding activity, GO:0016491, peptide antifungal protein binding activity, acyl-coa hydroxyacyltransferase activity, GO:0019145]] | \n", + "||
| HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[[GO:0140657, GO:0016887, GO:0008233, enzyme binding activity, GO:0003700, GO:0042803, identical protein binding activity, signaling receptor binding activity]] | \n", + "[[this gene list is associated with multiple functions in various metabolic processes, from binding and transporter activity to atpase activity, homodimerization activity, and various hydrolytic activities. enriched terms include: protein binding activity; atp hydrolysis activity; protein homodimerization activity; atpase binding activity; atpase-coupled transmembrane transporter activity; transcription regulatory region sequence-specific dna binding activity; and transmembrane transporter activity. mechanism: this set of genes acts as part of multiple metabolic processes, such as lipid and fatty acid metabolism, GO:0042632, GO:0140327, and hormone regulation. these genes facilitate enzymatic activity and activity in transporting molecules, such as fatty acids, MESH:D002784, MESH:D014815, hormones. the processes activities these genes are involved in suggest a coordination of metabolic cell stimulation processes]] | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[[atp binding activity, protein kinase binding activity, GO:0042803, GO:0003700, low-density lipoprotein particle binding activity, GO:0005041, GO:0030229, GO:0004602, GO:0004364, GO:0016491, GO:0004496, GO:0004631, GO:0047598, GO:0047024, MESH:D010758, GO:0060090, cholesterol binding activity, GO:0120020, isopentenyl]] | \n", + "[[atp binding activity, protein binding activity, GO:0007155, GO:0007165, GO:0006915, dna-binding, GO:0006695, cell structure organization, GO:0003985, GO:0008610, GO:0000988, GO:0015631, protein homodimerization]] | \n", + "||
| HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[[GO:0042632, MESH:D055438, GO:0005515, GO:0006351, GO:0010468, dna-binding, GO:0007165, negative regulation, positive regulation, GO:0016491, GO:0008610, GO:0003723, ldl particle binding, GO:0019901, phosphotransferase activity, acetyl-coa ligase activity, endopeptidase activity, etc]] | \n", + "[[GO:0006695, GO:0008610, positive regulation of transcription, GO:2001234, GO:0031647, regulation of cell adhesion/migration, atp binding activity, transcription factor binding activity, protein binding activity, protein kinase binding activity, signaling receptor binding activity, ion/metal binding activity, endopeptidase regulator activity, etc]] | \n", + "||
| HALLMARK_COAGULATION-0 | \n", + "[[the provided list of human genes are mainly involved in metabolism, adjustment of the immune system and coagulation, and development of cells and organs. in particular, they are found to be involved in binding activities and endopeptidase activities such as post-translational modification, transcription and regulation of protein. the enriched terms include calcium-dependent protein/phospholipid/lipoprotein binding activity, GO:0004197, protein homodimerization/homooligomerization activity, identical protein binding activity, and serine-type endopeptidase activity. \\n\\nmechanism: the expression and activities of these genes may play important roles in the development and metabolism of cells and organs by facilitating protein folding, GO:0043687, cell-matrix adhesion and crosstalk between proteins. the binding activities of these genes towards phospholipid, lipoprotein and other molecules mediate the interaction between cells and extracellular environment, and regulate blood coagulation and formation of extracellular matrix. the endopeptidase activities of these genes degrade and modulate proteins, which are essential for various biological processes]] | \n", + "[[protein binding activity, collagen binding activity, identical protein binding activity, integrin binding activity, phospholipid binding activity, atp binding activity, fibronectin binding activity, GO:0008237, GO:0004252, metaloendopeptidase activity, calcium ion binding activity]] | \n", + "||
| HALLMARK_COAGULATION-1 | \n", + "[[protein binding activity, domain specific binding activity, disordered domain specific binding activity, GO:0008233, GO:0004252, GO:0005125, signaling receptor binding activity, identical protein binding activity, GO:0004222, GO:0003924, receptor tyrosine kinase binding activity, GO:0004421, phospholipid binding activity, amyloid-beta]] | \n", + "[[the genes in this list are predicted to enable various calcium-dependent functions related to protein binding, GO:0019899, and peptidase activity, typically related to blood coagulation, GO:0007155, endodermal cell fate, and negative regulation of protein-regulating processes. these genes are involved in various activities across multiple cellular pathways, including cellular response to uv-a, GO:0030155, and blood coagulation. the enriched terms include “calcium-dependent functions”, “protein binding activity”, “enzme binding activity”, “peptidase activity”, “blood coagulation”, “cell adhesion”, “endodermal cell fate”, “negative regulation of protein-regulating processes”, “cellular response to uv-a”, and “regulation of cell adhesion”.\\n\\nmechanism: the mechanism underlying this list of genes is likely related to calcium-dependent regulation of proteins and peptides, which acts to control various cellular processes. calcium can act as a negative regulator of proteins, through calcium binding to proteins and preventing their activity, or as a]] | \n", + "||
| HALLMARK_COMPLEMENT-0 | \n", + "[[enriched functions observed in the genes include binding activitiy (for various ligands, such as dna, GO:0005562, MESH:C062738, calcium ions, heparin/heparan sulphate, MESH:D019204, c5l2 anaphylatiotaxin, MESH:M0028275, mhc, amyloid-beta, cytokine, opsonin, MESH:D005227, MESH:D011494, etc.), enzyme activity (such as deubiquitinase, lck, atpase, aminopeptidase, peptidase, etc.), GO:0044183, cysteine type endopeptidase inhibitor activity and endopeptidase activity, phospholipid binding activity, transcription factor activity and transcription regulatory region sequence-specific dna binding activitiy. the underlying mechanism could be related to signal transduction, functional process, dna/rna transcription, protein degradation and signalling pathways such as cell killing and apoptotic signalling pathways.\\n\\nsummary: enriched functions include multiple binding activities, GO:0003824, and transcription regulatory activities for signal transduction, functional processes, and signalling pathways. \\nmechanism: signal transduction, functional processes, dna/rna transcription, protein degradation,]] | \n", + "[[protein binding activity, GO:0001216, enzyme binding activity, metal ion binding activity, sh2 domain binding activity, GO:0004197, phosphoprotein binding activity, actin binding activity, cation binding activity, lipid binding activity, GO:0004252, GO:0008092, cell killing activity, protein kinase binding activity]] | \n", + "||
| HALLMARK_COMPLEMENT-1 | \n", + "[[enzyme binding activity, GO:0101005, GO:0004197, GO:0005102, GO:0019901, sh2 domain binding activity, GO:0004435, GO:0003924, GO:0004222, atpase binding activity, integrin binding activity, dna binding activity, lipoprotein receptor binding activity, GO:0007165, GO:0006915, MESH:D015850]] | \n", + "[[dna-binding, GO:0005543, GO:0005515, GO:0005102, GO:0019899, inhibitor activities, GO:0003924, GO:0046872, protein activities, GO:0023052, transcription regulation, GO:0006281, GO:0008219, GO:0006955]] | \n", + "||
| HALLMARK_DNA_REPAIR-0 | \n", + "[[the given list of human genes are primarily involved in dna binding, transcription and translational activities, rna binding, enzyme binding activities, and identical protein and nucleic acid binding activities. there is also evidence of involvement in activities such as transcription co-activator activity, nuclear localization, cytochrome-c oxidase activity, atp-dependent activities and endopeptidase activator activity. enriched terms include dna binding, GO:0003723, GO:0003887, GO:0046983, identical protein binding activity, transcription factor binding activity, GO:0003700, zinc ion binding activity, atp binding activity, protein binding activity]] | \n", + "[[dna binding activity, rna binding activity, enzyme binding activity, protein binding activity, calcium ion binding activity, GO:0140612, GO:0003713, zinc ion binding activity]] | \n", + "||
| HALLMARK_DNA_REPAIR-1 | \n", + "[[dna binding activity, rna binding activity, transcription activity, enzyme binding activity, GO:0042803]] | \n", + "[[dna binding activity, enzyme binding activity, GO:0016887, rna binding activity, protein binding activity, GO:0003887, GO:0004518, mrna regulatory element binding]] | \n", + "||
| HALLMARK_E2F_TARGETS-0 | \n", + "[[GO:0007049, GO:0006260, transcriptional regulation, post-transcriptional regulation, GO:0003682, GO:0140014, GO:0051169, GO:0046931]] | \n", + "[[chromatin binding activity, GO:0006260, GO:0006281, GO:0006351, GO:0016570, nuclear import/export, dna/rna binding, protein-macromolecule binding, GO:0051726, protein homodimerization, GO:0006200, GO:0000287, MESH:D011494, GO:0004518]] | \n", + "||
| HALLMARK_E2F_TARGETS-1 | \n", + "[[dna binding activity, protein binding activity, histone binding activity, GO:0016887, enzyme binding activity, GO:0006260, GO:0006306, chromatin binding activity, GO:0042803, GO:0003887, rna binding activity]] | \n", + "[[nuclear pore remodeling, GO:0065003, GO:0003677, transcriptional regulation, GO:0006260, GO:0006913, chromatin modification and repair, cell cycle progression, GO:0140014, GO:0019899, GO:0042393, protein homod]] | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[[extracellular matrix structural components, GO:0007160, protein domain specific binding activity, identical protein binding activity, GO:0048018, signaling receptor binding activity, metal ion binding activity, peptide hormone receptor binding activity, heparin binding activity, collagen binding activity, GO:0007165, GO:0005125]] | \n", + "[[protein binding activity, identical protein binding activity, collagen binding activity, integrin binding activity, heparin binding activity, phosphatidylinositol binding activity, cell adhesion molecule binding activity, extracellular matrix binding activity, signaling receptor binding activity, GO:0008009, gene transcriotion activity, metal ion binding activity]] | \n", + "||
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[[protein binding activity, identical protein binding activity, metal ion binding activity, ion binding activity, actin binding activity, small molecule binding activity, fibronectin binding activity, collagen binding activity, integrin binding activity, procollagen binding activity, cadherin binding activity, phosphatidylinositol-3,4,5-trisphosphate binding activity, substrate-binding activity, GO:0005096, GO:0004867, GO:0005006, GO:0005024, GO:0004896, platelet-derived growth factor binding activity, nucleotide-binding transcription factor activity]] | \n", + "[[GO:0005201, collagen binding activity, cell adhesion molecule binding activity, dna binding activity, gtp binding activity, GO:0042803, platelet-derived growth factor binding activity, platelet-derived growth factor binding activity, calcium ion binding activity, signaling receptor binding activity, identical protein binding activity]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[[binding activity, transport activity, GO:0003824, adhesion activity, intracellular signaling, GO:0006351, neuronal development]] | \n", + "[[dna binding activity, protein binding activity, enzyme binding activity, GO:0022857, transcription activity, GO:0003924, atpase binding activity, mrna binding activity, protein homodimerization, GO:0042169, GO:0016922, GO:0030165]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[[GO:0003677, GO:0051117, GO:0005515, GO:0016791, dehydrogenase activity, GO:0004016, GO:0055085, transcriptional regulation, GO:0007155, GO:0006915]] | \n", + "[[GO:0003677, GO:0000981, GO:0003723, protein binding/dimerization, transmembrane transporter, GO:0005509, GO:0019899, GO:0003924]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[[protein binding activity, dna-binding, domain binding activity, carbohydrate binding activity, enzyme binding activity, ligand binding activity, transmembr]] | \n", + "[[GO:0050839, GO:0003677, transfacmembrane receptor protein tyrosine kinase activity, ligand binding, ca2+ ion binding, GO:0005543, GO:0019899, GO:0016563, GO:0005243, GO:0003682, GO:0032794, GO:0048018, GO:0005242, GO:0004930, GO:0060089, calcium-dependent exonuclease activity, GO:0003779, GO:0007165, GO:0004672, GO:0016310, sh2 domain binding activity, heme binding activity, GO:0042803, hsp90 protein binding activity, GO:0017002, GO:0004957, ww domain binding activity, pdz domain binding activity, sh3 domain binding activity]] | \n", + "||
| HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[[dna-binding, GO:0016563, GO:0005515, membrane transporter activity, GO:0016787, GO:0016310, ligand-mediated activity]] | \n", + "[[GO:0008134, GO:0019899, GO:0005515, GO:0007155, ligand-gated ion transporter activity, GO:0001216, GO:0050839, protein domain specificity, GO:0030742, GO:0003677, GO:0019003, GO:0005525, GO:0051117, GO:0030165, GO:0005509, phosphotransfer, GO:0031490, GO:0001217]] | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[[GO:0006631, GO:0006629, GO:0005975, GO:0003677, GO:0003723, protein homodimerization, GO:0000287, GO:0005524, GO:0046872, GO:0047617, GO:0003995, fad binding activity, nadph binding activity, homodimerization activity, GO:0000774, GO:0015254, GO:0004497, 5alpha-androstane-3alpha,17beta-diol dehydrogenase activity, GO:0008170, identical protein binding activity, GO:0016860, enzyme binding activity, GO:0004674, GO:0042803, GO:0004351, GO:0004222, ubiquitin binding activity, dna-binding]] | \n", + "[[protein binding activity, identical protein binding activity, metal ion binding activity, atp binding activity;lipid transport activity, fatty acid binding activity, fad binding activity, pdz domain binding activity;transmembrane transporter activity, ubiquitin binding activity, nucleotide binding activity, GO:0004080, GO:0004738, enoyl-coa hydratase activity;amino-acid oxidase activity, GO:0003979, GO:0009055, GO:0004853, 5alpha-reductase activity, rna-binding]] | \n", + "||
| HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[[GO:0016491, enzyme binding activity, dna binding activity, GO:0004090, GO:0052650, GO:0015245, nadph binding activity, GO:0042803, atp binding activity, receptor ligand binding activity, nad+ binding activity, smad binding activity, rna polymerase ii-specific transcription factor activity, atp-dependent protease activity, GO:0016404, GO:0004672, ubiquitin conjugating]] | \n", + "[[GO:0003824, GO:0016491, protein binding activity, hydratase activity, GO:0003997, lipid binding activity, dna binding activity, ubiquitin binding activity, atp binding activity, flavine adenine dinucleotide binding activity, nadp+ binding activity, GO:0042803, smad binding activity, GO:0004466]] | \n", + "||
| HALLMARK_G2M_CHECKPOINT-0 | \n", + "[[GO:0003677, transcription binding, GO:0046872, GO:0005515, GO:0019899, MESH:D020558, GO:0003682, GO:0042826, GO:0046983, sumo-dependent ubiquitination, GO:0003723, GO:0005524, GO:0042054, GO:0008017, GO:0010997, boxh/aca snorna binding, GO:0043515, GO:0070840, m7gpppn-cap structure binding, GO:0008270, GO:0003697, GO:0038024, GO:0006200, GO:0051536, GO:0005884]] | \n", + "[[dna binding activity, rna binding activity, protein kinase binding activity, protein folding activity, enzyme binding activity, transcription factor binding activity, chromatin binding activity, protein domain specific binding activity, nucleic acid binding activity, atp binding activity, identical protein binding activity, GO:0140110, GO:0046983, histone binding activity, anaphase-promoting complex binding activity, cytoplasmic release activity, metal ion binding activity, GO:0016887, histone deacetylase binding activity, telomere binding activity]] | \n", + "||
| HALLMARK_G2M_CHECKPOINT-1 | \n", + "[[GO:0005515, GO:0003677, GO:0006351, GO:0019904, GO:0042054, GO:0004402, GO:0004674, GO:0030374, GO:0005049, GO:0016887, zinc ion binding activity, GO:0140037, GO:0036310, sumo polymer binding activity, nuclear receptor binding activity, dna topoisomerase binding activity, GO:0010997, GO:0000774, GO:0005096, microtubule binding activity, dna replication origin binding activity, GO:0000987, rna polymerase ii-specific transcription]] | \n", + "[[GO:0005515, GO:0003677, GO:0008134, MESH:D019098, GO:0003723, GO:0006260, GO:0051726, GO:0003682, GO:0010467, GO:0006457, regulation of chromosome structure, GO:0019904, GO:0005524, GO:0019900, GO:0035402, GO:0031267, MESH:M0518050, protein homodimerization, GO:0043130, atp-dependent dna/dna annealing]] | \n", + "||
| HALLMARK_GLYCOLYSIS-0 | \n", + "[[GO:0003676, GO:0005515, GO:0005524, metabolic activity, GO:0016310, MESH:D010084, GO:0005975, GO:0005125, GO:0008083]] | \n", + "[[the list of genes represent a range of molecular, metabolic, and protein regulatory processes, including atpase activity, glucose binding activity, GO:0004672, transcriptional activity and activity from receptors, transporters, and enzymes. the enriched terms are \"protein binding activity\"; \"atpase activity\"; \"transcriptional activity\"; \"receptor activity\"; \"transporter activity\"; \"enzyme activity\"; and \"glucose binding activity\".\\n\\nmechanism: the genes in the list encode proteins involved in a range of processes, such as structural support, GO:0007165, regulation of transcription, metabolic pathways and transport of molecules. the underlying biological mechanism is likely related to the coordinated expression of these genes in response to a particular stimulus, or to maintain cellular homeostasis]] | \n", + "||
| HALLMARK_GLYCOLYSIS-1 | \n", + "[[protein binding activity, identical protein binding activity, enzyme binding activity, atp binding activity, transcription activation activity, dna-binding transcription activity, heparin binding activity, cytoplasmic protein binding activity, signalling receptor binding activity, cytoskeletal protein binding activity, GO:0042803, GO:0060422, rna binding activity, GO:0140677, GO:0004689, phosphotransferase activity, heme binding activity, calcium ion binding activity]] | \n", + "[[enzyme binding activity, identical protein binding activity, dna binding activity, GO:0042803, heparin binding activity, atp binding activity, protein kinase binding activity, phosphatase binding activity, cyclin binding activity, protein phosphatase binding activity, GO:0004722, actin binding activity, lbd domain binding activity, actin filament binding activity, GO:0008083, chromatin binding activity, hyaluronic acid binding activity, GO:0004197, ubiquitin binding activity, cyclosporin a binding activity, mannose-binding activity, heparan sulfate binding activity, heme binding activity, GO:0016887, transition metal ion binding activity, GO:0031545, GO:0016615, GO:0004148, GO:0004784, transcription core]] | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[[GO:0007155, GO:0007165, epithelial-mesenchymal interaction, GO:0006898, GO:0001525, GO:0001843]] | \n", + "[[protein/lipid binding activity, GO:0003700, GO:0010468, GO:0051246, positive/negative regulation of cellular component organization, GO:0030036, GO:0030833, GO:0001525, GO:0090630, GO:0019219, GO:0007160]] | \n", + "||
| HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[[GO:0003700, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, chromatin binding activity, receptor binding activity, GO:0005096, gtpase binding activity, phospholipid binding activity, calcium ion binding activity, zinc ion binding activity, identical protein binding activity, apolipoprotein binding activity, phosphotyrosine residue binding activity, very-low-density lipoprotein particle binding activity, phosphatidylcholine binding activity, phosphatidylethanolamine binding activity, adenyl ribonucleotide]] | \n", + "[[acetylcholine binding activity, GO:0003990, GO:0005096, rna polymerase ii-specific dna-binding transcription factor binding activity, GO:0003714, GO:0017053, GO:0007165, GO:0006351, GO:0007155, GO:0016477, GO:0001525, GO:0035556, GO:0019219, GO:0006468]] | \n", + "||
| HALLMARK_HEME_METABOLISM-0 | \n", + "[[identical protein binding activity, dna binding activity, rna binding activity, GO:0000988, GO:0003714, GO:0016564, GO:0016563, GO:0016791, protein kinase binding activity, GO:0006865, GO:0006811, heme binding activity, oxygen binding activity, protein-fructose gamma-glutamyltransferase activity, GO:0042803, lamin binding activity, chromatin binding activity and ubiquitin ligase activity]] | \n", + "[[dna-binding, rna-binding, GO:0019899, GO:0019901, GO:0019903, protein homodimerization, GO:0048729, GO:0006468]] | \n", + "||
| HALLMARK_HEME_METABOLISM-1 | \n", + "[[transcription activity, dna binding activity;rna binding activity, protein kinase binding activity, atp binding activity, protein binding activity, identical protein binding activity, GO:0042803, GO:0004197, GO:0015075, protein domain specific binding activity, GO:0032452, GO:0004674, GO:0016564, GO:0061630, lamin binding activity, GO:0004521, GO:0038023, GO:0004602, phosphoprotein binding activity, molecule adaptation, enzyme binding activity, protein phosphatase binding activity, GO:0004418, ubiquitin conjugating enzyme binding activity, GO:0004842, ap-2 adapt]] | \n", + "[[GO:0003677, GO:0005515, GO:0016310, GO:0003824, GO:0005215, MESH:M0496924, vesicular pathways, cytoskeletal pathways, GO:0046872, GO:0003723, GO:0030544, GO:0042802, GO:0008013, phosphatidylinositol-4 binding, GO:0035612, rna polymerase ii dna binding, GO:0042393, GO:0019901, tyrosine-protein kinase activity, GO:0061630, GO:0003713, fibronectin leucine-rich-repeat sense-specific binding, endothelial differentiation-specific factor binding, fatty-acid binding, heme-binding, GO:0051537, GO:0050661, GO:0070742, MESH:D012330]] | \n", + "||
| HALLMARK_HYPOXIA-0 | \n", + "[[dna-binding transcription activity, enzyme binding activity, protein binding activity, ligand-binding activity, atp binding activity, nadp binding activity, metal ion binding activity, carbohydrate binding activity, signaling receptor binding activity, GO:0003714, GO:0001217, GO:0008160, heparin binding activity, n-acetylglucosamine n-sulfotransferase activity, MESH:D006497]] | \n", + "[[this is a list of genes of known or suspected functions in a variety of processes, ranging from dna binding and transcription regulation to enzyme binding, metabolic activity, GO:0005102, and structural protein formation. commonly enriched terms include dna binding, transcription regulation, GO:0019899, and protein binding. mechanism: a variety of processes are involved in these gene functions, including dna replication and repair, protein folding and conformational change, receptor binding and signal transduction, metabolic activity, structural protein formation]] | \n", + "||
| HALLMARK_HYPOXIA-1 | \n", + "[[dna binding activity, rna binding activity, protein binding activity, GO:0004672, GO:0019887, GO:0016407, GO:0016301, GO:0008233, GO:0004197, GO:0004252, ubiquitin binding activity, GO:0042803, GO:0000988, GO:0016563, GO:0016564, apolipoprotein binding activity, phosphatase binding activity, disordered domain specific binding activity, chromatin binding activity, GO:0016303, GO:0030701, GO:0004693, GO:0004396, actinin binding activity, 14-3-3 protein binding activity, gtp binding activity, MESH:D009584]] | \n", + "[[dna-binding transcription activity, GO:0003714, GO:0016564, GO:0016563, rna polymerase ii-specific, protein binding activity, GO:0042803, platelet-derived growth factor binding activity, GO:0030291, GO:0046982, GO:0004197, protein kinase binding activity, GO:0019887, GO:0004725, cyclin binding activity, GO:0004693, GO:0035403, phosphatidylinositol-3-kinase activity, nad+]] | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[[ligand binding, GO:0019899, GO:0005102, MESH:M0518050, GO:0003700, rna-binding, protein homodimerization, protein-kinase binding activity, identical protein binding activity, GO:0004896, c-c chemokine binding activity, GO:0004197, GO:0022857, gtp binding activity, protease binding activity]] | \n", + "[[GO:0005096, dna-binding transcription activator/repressor activity, protein binding activity, ligand binding activity, identical protein binding activity, bh3 domain binding activity, phosphatidylinositol binding activity, GO:0016787, atp binding activity, atpase-coupled intramembrane lipid transport activity, amyloid-beta binding activity, hsp90 protein binding activity, s100 protein binding activity, cadherin binding activity, GO:0038023, GO:0005125, GO:0005021, GO:0004896, identical protein binding activity, GO:0008233, heat shock protein]] | \n", + "||
| HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[[dna-binding, transcriptional activity, GO:0006355, GO:0005515, protein homodimerization, GO:0003924, GO:0005102, ligand-activated transcription, GO:0019900, GO:0002020, GO:0004674, GO:0004175, cystein-type endopeptidase activity, GO:0005102, GO:0061630, GO:0005125, GO:0008083, leukemia inhibitory factor activity, 5'-deoxyn]] | \n", + "[[dna-binding transcription activity, protein kinase binding activity, small gtpase binding activity, interleukin-binding activity, GO:0004896, signaling receptor binding activity, rna binding activity, gtp binding activity, GO:0004197, identical protein binding activity, protein domain specific binding activity, GO:0046982]] | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[[GO:0038023, binding activity, MESH:D016207, MESH:M0496065, MESH:D008074, MESH:D010455, MESH:D011506, GO:0019900, GO:0005524]] | \n", + "[[cytokine binding activity, protein binding activity, kinase binding activity, signaling receptor binding activity, GO:0004675, cell adhesion molecule binding activity, interleukin-receptor activity, GO:0004725, tir domain binding activity, ubiquitin protein ligase binding activity, GO:0008284, GO:0032768, GO:0009966, GO:0090276, GO:0045597, GO:0010604, GO:0098542, GO:0009612, GO:0001819, GO:0031349]] | \n", + "||
| HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[[GO:0004896, cxcr chemokine receptor binding activity, interleukin-binding activity, GO:0006952, GO:0010605, GO:0051247]] | \n", + "[[cytokine binding activity, GO:0004896, GO:0008083, cell adhesion molecule binding activity, chemokine (c-x3-c) binding activity, GO:0006952, signaling receptor binding activity, GO:0000988, identical protein binding activity, phosphatidylinositol binding activity, heparin binding activity, lipid binding activity, c-c chemokine binding activity, dna binding activity, GO:0005096, sh3 domain binding activity, ephrin receptor binding activity, transforming growth factor beta receptor binding activity, ubiquitin-like protein ligase binding activity, enzyme binding activity, calcium-dependent protein binding activity, protease binding activity]] | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[[protein binding activity, GO:0005125, GO:0004930, dna-binding transcription activity, lipopolysaccharide binding activity, atp binding activity, integrin binding activity, GO:0048018, GO:0022857, signaling receptor binding activity, extracellular atp-gated channel activity, phosphatidylinositol- 3-kinase activity, metallod]] | \n", + "[[GO:0004930, GO:0005125, GO:0003700, GO:0005216, receptor binding activity, GO:0008083, cell adhesion molecule binding activity, signalling receptor binding activity, GO:0003714, enzymatic activity, phospholipid binding activity, peptide hormone receptor binding activity, GO:0003924]] | \n", + "||
| HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[[GO:0038023, binding activity, GO:0003824, GO:0008083, GO:0005215, GO:0000988]] | \n", + "[[atp binding activity, chemokine/chemokine receptor/chemokine receptor binding activity, cytokine/cytokine binding activity/cytokine receptor activity, dna binding activity/dna-binding transcription factor activity, GO:0004930, identical protein binding activity, ion transport/ion transporter activity, peptide/peptide receptor binding activity, phospholipid binding activity, GO:0019887, signaling receptor binding activity, GO:0000988, GO:0022857]] | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[[signaling receptor binding activity, GO:0003713, regulation of transcription, dna-binding activity, rna binding activity, metal ion binding activity, identical protein binding activity, GO:0042803]] | \n", + "[[immunologic processes, GO:0098609, GO:0006952, cellular response, positive regulation, rna polymerase ii specific, GO:0003677, GO:0003723, protein homodimer]] | \n", + "||
| HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[[GO:0098542, GO:0006955, GO:0046718, GO:0032020, GO:0019882, GO:0019221, GO:0045087, GO:0007166, GO:0030225, GO:0032722, GO:0001961, cell-cell adhesion mediated by plasma membrane cell adhesion molecules]] | \n", + "[[GO:0003713, rna binding activity, dna binding activity, identical protein binding activity, GO:0061630, zinc ion binding activity, GO:0042803, double-stranded rna binding activity, heparin binding activity, GO:0030701, GO:0004175, cxcr chemokine receptor binding activity, tap binding activity, peptide antigen binding activity, gtp binding activity, GO:0033862, GO:0004197, amyloid-beta binding activity, macrophage migration inhibitory factor binding activity, GO:0004550, GO:0016064, GO:0140374, GO:0071345, GO:0046597, positive regulation of]] | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[[the list of genes are discovered to be enriched in terms like dna binding activities, GO:0042803, GO:0000988, GO:0004672, GO:0004725, GO:0016887, enzyme binding activity, phosphatidylinositol phosphate binding activity, GO:0030528, GO:0008009, and cytokine receptor activity.\\n\\nmechanism: the biological mechanism underlying the enriched terms is most likely associated with cell and immune response. these genes are involved in various processes related to cell signaling, detection, recognition, GO:0006351, and expression. through these processes, the genes regulate important functions such as cell adhesion, GO:0005515, GO:0019899, GO:0005125, and transcription factor activation. in addition, several of these genes are also involved in apoptotic and other cell regulation pathways]] | \n", + "[[protein binding activity, enzyme binding activity, dna-binding transcription activity, GO:0006200, protein homodimerization, kinase regulation, protein dimerization.\\nmechanism: these genes are likely involved in the regulation of gene expression cell signaling pathways, enabling an array of signaling activities that help to maintain cellular homeostasis]] | \n", + "||
| HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[[binding activity, GO:0003824, protein activity, GO:0000981]] | \n", + "[[GO:0016887, dna binding activity, gtp binding activity, peptide antigen binding activity, GO:0004252, dna-binding transcription activity, GO:0005125, GO:0008009, GO:0004896, GO:0038023, GO:0004930, rna binding activity, enzyme binding activity, GO:0046983, phosphorylation-dependent protein binding activity, GO:0019887, GO:0140311, toll-interleukin receptor (tir) domain binding activity, signaling receptor binding activity, and]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[[protein binding activity, transmembrane activity, GO:0003700, sequence-specific double-stranded dna binding activity, GO:0004930, identical protein binding activity, calcium ion binding activity, scaffold protein binding activity, transcription cis-regulatory region binding activity]] | \n", + "[[GO:0004930, GO:0042803, calcium ion binding activity, sodium:potassium:chloride transporter activity, GO:0004683, platelet-derived growth factor activity, GO:0005007, cytoskeletal protein binding activity, GO:0015171, n6-threonylcarbamylade adenine dinucleotide synthetase activity, GO:0043273, intracellular transport activity, signal transduction activity, GO:0016887, GO:0004175, GO:0016491, GO:1990817, GO:0004958, beta-caten]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[[dna-binding activity, transcription activity, calcium ion binding activity, atp-binding activity, protein binding activity, GO:0004930, cell death regulation, GO:0009653, GO:0042445]] | \n", + "[[the list of genes is significantly enriched for dna-binding activities, calcium ion binding activities, identical protein-binding activities, GO:0046982, GO:0016887, and g protein-coupled receptor activities.\\n\\nmechanism:\\nthe underlying biological mechanism likely involves a complex, dynamic interaction between various proteins, MESH:D004798, and ions, driven by a variety of dna-binding, calcium-binding, and atp-binding activities, resulting in the recruitment of additional proteins to form heterodimers, thereby leading to protein synapsis cell signaling]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[[cell adhesion molecule binding activity, atpase-coupled intramembrane transport, GO:0004222, GO:0042803, signal receptor binding activity, GO:0003700, MESH:D006493]] | \n", + "[[atp binding activity, atpase-coupled intramembrane transport, GO:0048018, dna-binding transcription regulation, protein domain binding activity, enzyme binding activity, GO:0005125, GO:0007165, GO:0007155, GO:0016477, GO:0030154, MESH:D048788]] | \n", + "||
| HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[[GO:0005125, protein domain specific binding activity, protein kinase binding activity, cell adhesion molecule binding activity, signaling receptor binding activity, GO:0004222, GO:0001217, rna binding activity, gtpase binding activity, structural proteins, atp binding activity]] | \n", + "[[receptor binding activity, identical protein binding activity, GO:0001216, enzyme binding activity, protein domain specific binding activity, protein kinase binding activity, ligand binding activity, atp binding activity, cytoskeletal protein binding activity, cell adhesion molecule binding activity, GO:0004930, transmembrane transporter binding activity, GO:0008233, dna binding activity, GO:0004252, histone binding activity, signal transduction activity]] | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[[protein binding activity, cytoskeleton binding activity, GO:0005096, atpase binding activity, GO:0042030, adenyl ribonucleotide binding activity, calmodulin binding activity, cadherin binding activity, gamma-tubulin binding activity, integrin binding activity, kinetochore binding activity, molecular function adaptor activity, GO:0042803, protein kinase binding activity, protein phosphatase binding activity, sh2 domain binding activity, sh3 domain binding activity, small gtpase binding activity, beta-catenin binding activity, beta-tubulin binding activity, dynein complex binding activity, identical protein binding activity, phosphatidylcholine binding activity, protein domain specific binding activity, protein tyrosine kinase binding activity]] | \n", + "[[actin binding activity, atp binding activity, atpase binding activity, GO:0098632, dynein complex binding activity, gamma-tubulin binding activity, gtp binding activity, gtpase binding activity, guanyl ribonucleotide binding activity, GO:0003924, GO:0005085, kinetochore binding activity, GO:0060090, GO:0140677, myosin binding activity, phosphatidylcholine binding activity, GO:0019904, GO:0042803, GO:0004672, GO:0004674, small gtpase binding activity]] | \n", + "||
| HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[[MESH:D020558, atpase, tubulin binding activity, microtubule binding activity, actin filament binding activity, kinesin binding activity, dynein binding activity, g protein-coupled receptor binding activity]] | \n", + "[[this set of genes are involved in activities, processes and signaling pathways related to intracellular motion such as transport within cells (microtubule/kinesin/dynein binding, GO:0005096, GO:0008092, motor protein activity), cell cycle activities (centrosome duplication, GO:0019899, protein homodimerization, GO:0019902, GO:0003682, GO:0043515, GO:0005516, formin binding, atpase/atp hydrolysis regulatory activity), and cell-cell signaling (jun kinase kinase kinase activity, map-kinase scaffolding, GO:0042608, GO:0045296, GO:0051879, GO:0097016, GO:0005680, GO:0051059, rna binding).\\n\\nmechanism: these genes enable a wide range of activities and processes related to intracellular motion and cell-cell signaling that are either directly or indirectly connected to the assembly, MESH:M0030663, and disassembly of cytoskeletal structures, MESH:D014404, and cellular organelles. these activities can promote cell cycle progression, GO:0008283, and/or cell-cell signaling]] | \n", + "||
| HALLMARK_MTORC1_SIGNALING-0 | \n", + "[[enzyme binding activity, acid binding activity, molecule transport, adapter binding activity, receptor binding activity, dna binding activity, protein binding activity, GO:0003824, GO:0016787, GO:0016491, anion binding activity, GO:0008233, GO:0140657, thioredoxin activity, translocation, GO:0061630, cysteine endopeptidase activity, GO:0004738, GO:0004618, magnesium ion binding activity, GO:0004340, GO:0003924]] | \n", + "[[protein binding activity, dna binding activity, enzyme binding activity, GO:0060090, GO:0140677, GO:0042803, domain binding activity, GO:0016491, protein kinase binding activity, phosphatidylinositol binding activity, GO:0016504, GO:0003714, nuclear androgen receptor binding activity, nf-kappab binding activity, ubiquitin protein ligase binding activity, phosphotyrosine residue binding activity, GO:0016564, GO:0003743, peptidyl-proinalyl cistrans isomerase activity]] | \n", + "||
| HALLMARK_MTORC1_SIGNALING-1 | \n", + "[[protein binding activity, identical protein binding activity, GO:0008233, GO:0003824, GO:0005884, dna-binding, rna-binding, GO:0016922, MESH:D054875, anion binding activity, atp binding activity, GO:0016887, protein kinase binding activity, phosphotyrosine residue binding activity, e3 ubiquitin-protein ligase binding activity, mdm2 binding activity, GO:0060090, GO:0140677, GO:0098772, GO:0003713, GO:0003714, GO:0016564, GO:0042803, k63]] | \n", + "[[protein-protein interaction, atp binding activity, GO:0042803, GO:0016887, protein kinase binding activity, ubiquitin protein ligase binding activity, GO:0060090, anion binding activity, chemical oxidoreductase activity, protein domain specific binding activity, gtp binding activity, dna binding activity, rna binding activity, transcription regulation activity, GO:0007165, chromatin binding activity, phospholipid binding activity, GO:0004017, lipoprotein particle binding activity, GO:0008233, actin filament binding activity, fad binding activity, steroid hydrolase activity, rna stem-loop binding activity, GO:0022857, nf-kappab binding activity, coenzyme a binding activity, protein n-terminal phospho-seryl-prolyl pept]] | \n", + "||
| HALLMARK_MYC_TARGETS_V1-0 | \n", + "[[GO:0003677, GO:0003723, GO:0003682, GO:0006351, GO:0006412, GO:0045292, atpase binding activity, enzyme binding activity, GO:0044183, ubiquitin protein ligase, MESH:C021362, nf-kappab binding activity, GO:0140693, nucleic acid binding activity, heparan sulfate binding activity, biopolymer binding activity, GO:0060090, GO:0140678, g-protein beta-subunit binding activity, molecular sequence recognition, complementary rna strand recognition, mrna 3'-utr]] | \n", + "[[GO:0003723, GO:0044183, dna binding/recognition, protein homodimerization, GO:0003678, GO:0019904, MONDO:0000179, GO:0042393, cytoplasmic protein binding, GO:0005524, GO:0006281]] | \n", + "||
| HALLMARK_MYC_TARGETS_V1-1 | \n", + "[[rna binding activity, identical protein binding activity, mrna 3' utr binding activity, GO:0000900, dna binding activity, ubiquitin protein ligase binding activity, protein domain specific binding activity, GO:0006457, dna replication origin binding activity, dna-binding transcription factor binding activity, GO:0042803]] | \n", + "[[GO:0003677, GO:0003723, GO:0019904, GO:0003682, GO:0019899, protein folding chaperone activities, atp binding activity, mrna 3'-utr binding activity, identical protein binding activity, GO:0004869, GO:0140693, GO:0140713, heparan sulfate binding activity, peptidyl-prolyl isomerase activity, cyclin binding activity, GO:0004693, nuclear localization sequence binding activity, magnetic ion binding activity, histone methyltransferase binding activity, mrna 5'-utr binding activity, GO:0033677, MESH:D012321]] | \n", + "||
| HALLMARK_MYC_TARGETS_V2-0 | \n", + "[[GO:0006351, GO:0006351, GO:0008284, GO:0071824, GO:0019219, rna binding activity, GO:0010468, GO:0006364]] | \n", + "[[rna-binding, GO:0036211, GO:0015031, cell signaling, GO:0006412, genetic information regulation, protein bridging, chromatin regulation, transcription regulation, GO:0003676, mitochondrial functions]] | \n", + "||
| HALLMARK_MYC_TARGETS_V2-1 | \n", + "[[rna binding activity, dna binding activity, protein binding activity, GO:0006364, GO:0019538, GO:0006351, transcription coregulator binding activity, GO:0022402, GO:0003682, mitochondria regulation, cyclin binding activity, cyclin-dependent protein serine/threonine kin]] | \n", + "[[rna binding activity, ribosomal rrna processing, mrna and/or rrna catabolism/stability, regulation of transcription/translation, regulation of signal transduction and metabolism processes, regulation of cell cycle/proliferation, protein modification/regulation, GO:0005634, GO:0005829, GO:0005840, GO:0005739]] | \n", + "||
| HALLMARK_MYOGENESIS-0 | \n", + "[[GO:0008092, GO:0005201, GO:0044325, ion channel regulator, GO:0003779, GO:0005096, GO:0051879, GO:0017046, GO:0003677, signalling receptor binding, GO:0042802, GO:0048306, GO:0019899, GO:0005509, GO:0005524, GO:0006200, GO:0051117, GO:0004017, GO:0008195, GO:0051015, microfilament binding, GO:0003872, GO:0043138, GO:0004517, MESH:D009243]] | \n", + "[[calcium ion binding activity, identical protein binding activity, actin filament binding activity, GO:0042803, signaling receptor binding activity, atp binding activity, gtp binding activity, dna binding activity, GO:0019887]] | \n", + "||
| HALLMARK_MYOGENESIS-1 | \n", + "[[GO:0005509, GO:0004129, GO:0003677, GO:0005524, GO:0003779, abnormal growth and development, GO:0002020, structural constituent]] | \n", + "[[calcium binding activity, enzyme binding activity, dna binding activity, atp binding activity, GO:0042803, protein domain-specific binding activity, gtp binding activity, actin binding activity, GO:0008160, small gtpase activator activity, transmembrane transporter binding activity, GO:0004016, c3hc4-type ring finger domain-binding activity, GO:0060090, GO:0005096]] | \n", + "||
| HALLMARK_NOTCH_SIGNALING-0 | \n", + "[[GO:0036211, MESH:D005786, signal transduction regulation, dna-templated transcription regulation, GO:0007219, GO:0016567, GO:0031146, GO:0045893]] | \n", + "[[this list of genes is associated with several biological processes related to the regulation of gene expression, such as notch receptor processing, amyloid-beta formation, proteolysis, regulation of cell differentiation, canonical wnt signaling pathway, protein ubiquitination, scf-dependent proteasomal ubiquitin-dependent protein catabolic process, and positive regulation of transcription by rna polymerase ii. the underlying biological mechanism is likely related to the role of these genes in transcription and post-transcriptional gene regulation. enriched terms include: gene expression regulation, GO:0007220, GO:0034205, GO:0006508, GO:0045595, GO:0060070, GO:0016567, GO:0031146, GO:0045944]] | \n", + "||
| HALLMARK_NOTCH_SIGNALING-1 | \n", + "[[GO:0006351, GO:0036211, MESH:D054875, GO:0065007, GO:0007219, GO:0031146, wnt, GO:0016567, GO:0043543, GO:0004879, GO:0003714, transcription corepressor binding activity, GO:0006351, rna polymerase ii-specific dna-binding transcription repressor activity, GO:0045893, GO:0000122, GO:0045737, GO:0010604, GO:0010628, negative regulation of cell different]] | \n", + "[[GO:0016567, GO:0031146, GO:0007219, GO:0036211, GO:0010468, GO:0030335, GO:0008284, GO:0045596]] | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[[GO:0006118, GO:0020037, GO:0005515, GO:0016491, atpase activity & binding activity, GO:0060090, acyl binding activity, GO:0003954, gtp binding activity, iron-sulfur cluster binding activity, fad binding activity, MESH:D010758, GO:0019395, rna binding activity, 4 iron, 4 sulfur cluster binding activity, ubiquitin protein ligase binding activity, GO:0004129, proton-transporting atp synthase activity, lipoic acid binding activity, mhc class i protein binding activity, angiostatin binding activity, deltarasin binding activity, ubiquitin protein binding activity, nadp binding activity]] | \n", + "[[acetyl-coa transferase activity, GO:0003995, aldehyde dehydrogenase activity, atpase binding activity, GO:0004129, GO:0009055, GO:0004300, fad binding activity, GO:0003924, heme binding activity, identical protein binding activity, lipid binding activity, metal ion binding activity, GO:0003958, GO:0016491, GO:0004738, pro]] | \n", + "||
| HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[[GO:0140657, GO:0009055, GO:0008553, ubiquitin protein ligase binding activity, MESH:D014451, heme binding activity, protein homodimerization, mhc class i protein binding activity, metal ion binding activity, angiostatin binding activity, mitochondrion targeting sequence binding activity, GO:0015227, rna binding activity, 4 iron, 4 sulfur cluster binding activity, GO:0000295, GO:0004129, fatselytranstransferase activity, GO:0003925, acyl-coa c-acetyltransferase activity, GO:0004774, GO:0003994, GO:0004095, GO:0003958, acetate coa-transfer]] | \n", + "[[GO:0009055, protein homodimerization, GO:0003924, GO:0000295, phosphoprotein binding activity, mitochondrial respiratory chain activity, proton-transporting atp synthase activity, mitochondrial ribosome binding activity]] | \n", + "||
| HALLMARK_P53_PATHWAY-0 | \n", + "[[GO:0003700, protein binding activity, protein kinase binding activity, GO:0042803, enzyme binding activity, GO:0098631, signaling receptor binding activity, actin binding activity, cyclin binding activity, GO:0005198, GO:0030695]] | \n", + "[[dna binding activity, rna polymerase ii-specific dna-binding transcription factor binding activity, transcription regulation, protein binding activity, enzyme binding activity]] | \n", + "||
| HALLMARK_P53_PATHWAY-1 | \n", + "[[dna binding activity, rna binding activity, rna polymerase binding activity, GO:0004672, GO:0042803, protein kinase binding activity, GO:0000988, GO:0003924, GO:0098631, cell signaling receptor binding activity, enzyme binding activity, heme binding activity, collagen binding activity, GO:0004392, GO:0060090, GO:0004527, GO:0042803, g protein-coupled receptor binding activity, GO:0022857, identical protein binding activity, GO:0016787, GO:0008083]] | \n", + "[[GO:0007165, MESH:D005786, GO:0005515, GO:0019899, GO:0016791, GO:0000988, GO:0007155, growth factor binding. \\nmechanism: these genes are involved in the regulation of gene expression and cellular processes by modulating signal transduction, binding proteins, and enzymes, as well as activating phosphatase activity, transcription factor activity and growth factor binding]] | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[[GO:0006351, GO:0016563, atpase-coupled ion transport, GO:0004672, GO:0008233, dna binding activity, GO:0017156, GO:1903530]] | \n", + "[[atp binding activity, GO:0019829, GO:0016477, GO:0044249, GO:0071333, GO:0090398, GO:0042742, GO:0005789, e-box binding activity, GO:0015149, GO:0002551, GO:0043303, GO:0008233, GO:0008607, GO:0045597, positively regulation of cellular biosynthetic process, positively regulation of glycolytic process, positively regulation of insulin secretion, positively regulation of macromolecule metabolic process, positively regulation of type b pancreatic cell development, positive regulation of cellular]] | \n", + "||
| HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[[transcription regulation, GO:0098609, GO:0007165, GO:0045047, GO:0030041, GO:0051594, GO:0060291, GO:1903561, GO:0030027, GO:0005881, GO:0043195, GO:0005829, GO:0030425, MESH:D012319, dna-templated trans]] | \n", + "[[GO:0098609, GO:0032502, differentiation, UBERON:0000061, transcription regulation, MESH:D012319, GO:0007165, GO:0043170, protein expression, cell signaling, protein production]] | \n", + "||
| HALLMARK_PEROXISOME-0 | \n", + "[[molecular binding activity, GO:0003824, GO:0005215, domain binding activity, GO:0006869, GO:0015031, GO:0006259, GO:0016070]] | \n", + "[[after term enrichment analysis on the gene summaries, the following terms were found to be enriched: atp binding activity, atpase-coupled activity, GO:0042803, identical protein binding activity, enzyme binding activity, GO:0005319, GO:0016887, and metal ion binding activity.\\n\\nmechanism: the enriched terms suggest a biological mechanism that involves energy production and transport, GO:0007165, and protein interactions and formation of protein complexes. these processes are necessary for various cellular processes such as metabolism, GO:0007585, GO:0098754, GO:0040007]] | \n", + "||
| HALLMARK_PEROXISOME-1 | \n", + "[[genes involved in this list are primarily associated with the metabolic or structural processes needed for cellular development and homeostasis. enriched terms include fatty acid metabolism, protein homodimerization, MESH:D010084, dna and rna binding, enzyme/acyl-coa/gtpase binding/hydrolase activity, transport/export/import, and regulation of transcription by rna polymerase ii. mechanism: these genes act together to provide a plethora of functions that are integral to the growth, maintenance and protection of cells. fatty acids are transported, oxidized, and bound to proteins or phospholipids in the membrane, proteins interact with atp and gtp and undergo homodimerization, transcriptional activity is regulated by heterodimerizing with transcription factor proteins]] | \n", + "[[cell metabolic process, GO:0090304, GO:0005515, GO:0003677, GO:0016485, GO:0042446, GO:0006694, GO:0005524, GO:0006200, protein homodimerization, GO:0019901, GO:0003714, GO:0003712, cyclin binding activity, rna binding activity, protein phosphatase binding activity, sulphatide binding activity, magnesium ion binding activity, GO:0043621, MESH:M0518050, protein transmembrane]] | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[[protein binding activity, GO:0016301, GO:0005048, GO:0005102, GO:0051726, apoptosis regulation, GO:0007165, rna binding activity, GO:0004721, GO:0004620, GO:0003924, 1-phosphatidylinositol phospholipase activity, phosphotyrosine residue binding activity, GO:0000774, guanyl ribonucleotide binding activity, GO:0004869, GO:0051219, GO:0044325, GO:0008092, GO:0050750, GO:0003713, GO:0050681, nuclear receptor coactiv]] | \n", + "[[cellular process regulations, GO:0003824, protein and peptide regulation, protein domain modification]] | \n", + "||
| HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[[the genes in this list are involved in several biological functions, including signal transduction, GO:0006915, cellular response to stimuli, response to dna damage, GO:0051726, and regulation of protein phosphorylation and ubiquitination. the terms \"protein phosphorylation\"; \"ubiquitination\"; \"signal transduction\"; \"cellular response to stimulus\"; \"dna damage response\"; \"regulation of cell cycle\"; \"intrinsic apoptosis\"; and \"scaffold protein\" are all statistically over-represented.\\n\\nmechanism: signaling pathways and cellular processes are intricately regulated and require the coordinated participation of different proteins. by performing a term enrichment analysis, we see that the genes in this list are involved in a variety of molecular pathways, including signal transduction, GO:0006915, cellular response to stimuli, response to dna damage, GO:0051726, and regulation of protein phosphorylation and ubiquitination. this suggests that the gene products help coordinate these pathways by forming complexes, binding to signaling molecules, or carrying out the necessary enzyme activities. this suggests the underlying biological mechanism may involve interplay between specific gene products, MESH:D011506, signaling molecules to ensure efficient functioning of the cell]] | \n", + "[[GO:0007165, GO:0019900, GO:0003924, GO:0004721, transcription factor activation, GO:0004620, GO:0005102, MESH:D054875, MESH:D000107, GO:0006915, GO:0016477, negative regulation of proliferation]] | \n", + "||
| HALLMARK_PROTEIN_SECRETION-0 | \n", + "[[protein binding activity, GO:0003924, gtp-dependent protein binding activity, snare binding activity, enzyme binding activity, protein kinase binding activity, clathrin binding activity, GO:0006897, retrograde transport, GO:0006893, GO:0006888, GO:0006622]] | \n", + "[[protein binding activity, atp binding activity, gtp-dependent protein binding activity, GO:0003924, signal sequence binding activity, clathrin binding activity, small gtpase binding activity]] | \n", + "||
| HALLMARK_PROTEIN_SECRETION-1 | \n", + "[[protein binding activity, activity, GO:0042803, enzyme binding activity, scaffold protein binding activity, snare receptor activity, syntaxin binding activity, GO:0016887, GO:0008553, GO:0008320, metal ion binding activity, protein foldinactivity, GO:0003924, protein kinase binding activity, phosphat]] | \n", + "[[atp binding activity, GO:0042803, smarc protein binding activity, GO:0003924, gtp binding activity, GO:0005096, enzyme binding activity, GO:0004197, protein domain specific binding activity, phosphatidylinositol-4-phosphate binding activity, protein kinase binding activity, GO:0008320, calcium-dependent protein binding activity, metal ion binding activity, dopaminergic receptor binding activity, ubiquitin-like protein ligase binding activity, GO:0005484, phosphatidylinositol-3,4,5-trisphosphate binding activity, phosphatidylinositol-3,5-bisphosphate binding activity, signaling receptor binding activity, GO:0005198, syntaxin binding activity, GO:0005484]] | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[[oxidative stress defense, GO:0098754, dna/rna binding, GO:0006351, GO:0098609, GO:0016043, GO:0019722, GO:0006468, GO:0010731, GO:0004392, GO:0019511, GO:0061621, GO:0005886, GO:0006750, GO:0006082]] | \n", + "[[the human genes provided are mostly involved in redox homeostasis, GO:0006952, and cell organization. there is also involvement in processes related to the maintenance of the blood-brain barrier, GO:0009650, and metabolism of hormones, MESH:D008055, and glucose. there are an abundance of terms related to transmembrane transport, MESH:D010088, heme and iron metabolism, GO:0019511, and gluthathione metabolism.\\n\\nmechanism:\\nredox homeostasis is regulated by a network of enzymatic and substrate-dependent processes. these processes include cellular antioxidant defense, removal of superoxide radicals and peroxides, GO:0061691, and regulation of the balance between oxidant production and scavenging. transport genes are employed to promote transmembrane transport of xenobiotics and lipids, like abcc1, atox1, and glrx. iron and heme metabolism is facilitated by genes like ftl, hmox2, and mpo. peptidyl-proline hydroxylation is regulated by genes like egln2 and mgst1, while glutathione metabolism is controlled by genes like g]] | \n", + "||
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[[MESH:D004734, oxidative stress response, GO:0042803, protein phosphatase 2a binding activity, GO:0004601, GO:0004602, GO:0047499, GO:0003954, chromatin dna binding activity, GO:0004861, GO:0004784, GO:0047184, GO:0015038, GO:0015035, phosphatidylinositol binding activity, GO:0004096, heme binding activity]] | \n", + "[[GO:0045454, GO:0019899, protein homodimerization, GO:0015035, GO:0004602, GO:0003954, atp binding activity, identical protein binding activity, transition metal ion binding activity, GO:0016209, heme binding activity, ubiquitin-specific protease binding activity, GO:0047499, heparin binding activity, GO:0004601, GO:0004784, GO:0008811, GO:0004096]] | \n", + "||
| HALLMARK_SPERMATOGENESIS-0 | \n", + "[[GO:0003723, GO:0031491, transcription and regulation, GO:0003677, GO:0004672, protein folding and chaperoning, metabolic regulation, MESH:D054875]] | \n", + "[[GO:0140677, GO:0004672, cellular component activity, binding activity, GO:0008233, nucleosome binding activity, ion binding activity, phosphatase binding activity, GO:0051726, apoptosis regulation, GO:0007155, GO:0007399, transcription regulation, GO:0015031, GO:0009988, MESH:D005786]] | \n", + "||
| HALLMARK_SPERMATOGENESIS-1 | \n", + "[[GO:0019899, GO:0005515, ligand binding, GO:0005509, GO:0000166, GO:0008134, GO:0003677, GO:0005525, GO:0042562, GO:0006200, GO:0004672, GO:0003723, GO:0008047, GO:0044183, GO:0003682, GO:0019903, GO:0019212, GO:0008233, GO:0022890]] | \n", + "[[all of the genes are involved in regulation of various metabolic processes and signaling pathways, with most of them associated with binding activities and regulation of protein activities. enriched terms include: protein binding activity, atp binding activity, protein-folding chaperone binding activity, chromatin binding activity, GO:0046976, transcription corepressor binding activity, GO:0004672, GO:0060090, enzyme binding activity, GO:0140677, GO:0098632, GO:0004888, gtp binding activity, signaling receptor binding activity, ribonucleoprotein complex binding activity, myosin light chain binding activity, GO:0017116, GO:0003689, GO:0051131, peptide alpha-n-acetyltransferase activity. mechanism: the genes are involved in various metabolic processes and signaling pathways, by regulating protein activities through different binding activities and histone methyltransferase activity. some of these activities regulate certain processes based on gtp binding, while others are involved in cell-cell adhesion, transmembrane signaling and chaperone-mediated protein complex assembly]] | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[[GO:0007165, regulation of transcription, GO:0051246, regulation of macromolecule metabolism, GO:0050794, interaction with transcription factors, interaction with smad proteins]] | \n", + "[[GO:0005524, GO:0048185, GO:0046332, protein phosphatase/kinase activity, smad signaling, bmp signaling, GO:0006351, MESH:D012319, GO:0005515, GO:0007165, GO:0007049, GO:0008152, GO:0007155]] | \n", + "||
| HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[[tgf binding activity, dna-binding transcription factor binding activity, smad binding activity, GO:0019211, GO:0004674, GO:0004869, GO:0061631, myosin binding activity, r-smad binding activity, beta-catenin binding activity, cadherin binding activity, gtp binding activity, i-smad binding activity, GO:0003924, GO:0003714, GO:0042803, nucleic acid binding activity, serine-type endope]] | \n", + "[[dna-binding activity, transcription regulation, GO:0035556, GO:0004674, smad binding activity, positive/negative regulation of rna/protein metabolic process, GO:0006468, receptor tyrosine kinase binding activity, GO:0007165, GO:0042803, GO:0061630, GO:0031326, GO:0009966, GO:0006357, GO:0090092]] | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[[dna binding transcription factor, GO:0005102, GO:0019899, GO:0005126, growth factor, transmembrane receptor]] | \n", + "[[the list of genes provided are involved in a broad set of functions related to gene transcription or regulation of transcription factors, cell signaling, binding activities and metabolic processes. the enriched terms for this gene set include dna-binding transcription factor activity, rna polymerase ii transcription regulatory region sequence-specific binding, GO:0003924, chemokine receptor binding activity, signaling receptor binding activity, protein kinase binding activity, enzyme binding activity, identical protein binding activity and protease binding activity.\\n\\nmechanism: the underlying biological mechanism for this list of genes is likely related to control of gene expression, as well as control of protein interactions that mediate cell signaling and metabolic processes. additionally, the functions related to binding activities suggest many of the genes are involved in cell-to-cell communication and cell adhesion]] | \n", + "||
| HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[[GO:0000988, rna polymerase ii-specific, dna-binding, identical protein binding activity, enzyme binding activity, signaling receptor binding activity, GO:0004672, GO:0005125, GO:0008083, GO:0098631, GO:0022857, GO:0016791, gtp binding activity, GO:0140657]] | \n", + "[[GO:0001216, transcription regulatory region sequence-specific dna-binding, gtp binding activity, enzyme binding activity, identical protein binding activity, signal receptor binding activity, GO:0016791, protein kinase binding activity, GO:0005125, GO:0008083]] | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[[GO:0006457, GO:0003723, transcription activator, GO:0003677, GO:0051082, GO:0003720, GO:0003676, GO:0044325, GO:0005524, GO:0006402, translation regulation, GO:0003755, GO:0035925]] | \n", + "[[rna binding activity, dna binding activity, protein binding activity, GO:0140693, identical protein binding activity, dna-binding transcription factor binding activity, GO:0042803, atpase binding activity, GO:0016887, enzymatic activity, GO:0003713, GO:0008494, protein phosphatase binding activity, peptidyl-prolyl primase activity, transcription cis-regulatory region sequence-specific activity]] | \n", + "||
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[[atp binding activity, GO:0016887, enzyme binding activity, identical protein binding activity, GO:0060090, GO:0140678, nucleic acid binding activity, GO:0046983, protein folding chaperone binding activity, ribosome binding activity, rna binding activity, snare binding activity, transcription corepressor binding activity, transcription regulator]] | \n", + "[[enzyme binding activity, rna binding activity, protein binding activity, transmembrane transporter binding activity, dna binding activity, protein kinase binding activity, box h/aca snorna binding activity, protein phosphatase binding activity, telomerase rna binding activity, GO:0042803, GO:0046982, transcription factor binding activity, atp binding activity, GO:0016887, GO:0003724, GO:0003756, ubiquitin protein ligase binding activity, GO:0004518, adenyl ribonucleotide binding activity, heat shock protein binding activity]] | \n", + "||
| HALLMARK_UV_RESPONSE_DN-0 | \n", + "[[genes included in this set are involved in various cellular functions such as enzyme binding activity, GO:0003924, lipoprotein binding activity, GO:0004620, and other related activities. common enriched terms across these genes include protein binding activity, smad binding activity, dna-binding activity, phosphotyrosine residue binding activity, GO:0003824, GO:0003924, and enzymatic inhibitor activity. mechanism: these genes are likely to be involved in regulation and control of cellular functions and processes through various proteins. this regulation and control is likely being done through interaction of the proteins encoded by these genes with other proteins and structurally with dna, as well as through the enzymatic activities of the encoded proteins]] | \n", + "[[gtp binding activity, enzyme binding activity, dna-binding transcription factor binding activity, phosphotyrosine residue binding activity, cyclin binding activity, receptor-ligand interaction, protein-protein interaction, smad binding protein, nf-kappab binding protein, growth factor binding protein]] | \n", + "||
| HALLMARK_UV_RESPONSE_DN-1 | \n", + "[[dna binding activity, GO:0000988, protein binding activity, smad binding activity, GO:0005096, MESH:C062738]] | \n", + "[[GO:0001216, rna polymerase ii-specific activity, nf-kappab binding activity, microtubule binding activity, actin binding activity, identical protein binding activity, smad binding activity, GO:0005243, GO:0005388, receptor binding activity, GO:0005096, histone binding activity, ap-1 transcription factor binding activity, vitamin d receptor binding activity, cytoplasmic protein binding activity, GO:0004930, platelet-derived growth factor binding activity, enzyme binding activity, protease binding activity, phospholipid binding activity, GO:0004672, GO:0004674, intracellular protein binding activity]] | \n", + "||
| HALLMARK_UV_RESPONSE_UP-0 | \n", + "[[GO:0005515, GO:0003677, binding activity, receptor binding activity, GO:0004672, GO:0007155, GO:0023052, GO:0010468]] | \n", + "[[protein binding activity, atp binding activity, rna binding activity, dna binding activity, receptor binding activity, enzyme binding activity, GO:0005548, GO:0098609, GO:0007268, GO:0097190, GO:0005138, GO:0042110, overall cellular metabolism, MESH:D005786]] | \n", + "||
| HALLMARK_UV_RESPONSE_UP-1 | \n", + "[[gtp binding activity, dna binding activity, GO:0016563, protein kinase binding activity, GO:0004175]] | \n", + "[[enzyme binding activity, GO:0016787, GO:0016740, GO:0038023, dna binding activity, rna binding activity, GO:0000988, protein binding activity]] | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[[the genes summarized above are all involved in developmental processes, such as organizing and regulating cell adhesion, components of the wnt pathway and regulation of gene expression. the enriched terms for these genes would be development-related terms, such as cell adhesion, GO:0060070, GO:0006468, GO:0016567, GO:0006351, GO:0006476, GO:0006351, and protein stability.\\n\\nmechanism: the underlying biological mechanism involves the involvement of many of these genes in the wnt pathway, which is a conserved signaling pathway involved in cell-cell communication and a variety of developmental processes. another mechanism involves the regulation of gene expression and the binding of dna-binding transcription factors, as well as protein ubiquitination and deacetylation which also control gene expression]] | \n", + "[[protein binding activity, GO:0003700, rna polymerase ii-specific dna-binding transcription factor binding activity, notch binding activity, pdz domain binding activity, GO:0042813, ubiquitin protein ligase binding activity, beta-catenin binding activity, GO:0003713, histone deacetylase binding activity, GO:0048019, transcription corepressor binding activity, GO:0060090, GO:0004407, cholesterol binding activity]] | \n", + "||
| HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[[GO:0005515, transcription regulation, GO:0051726, GO:0007165, response pathways]] | \n", + "[[GO:0007165, GO:0010468, GO:0006351, GO:0001932, GO:0031647, GO:0016477, GO:0008283, GO:0032502, GO:0006508]] | \n", + "||
| T cell proliferation-0 | \n", + "[[signaling receptor binding activity, protein kinase binding activity, GO:0061630, GO:0035556, GO:0001816, GO:0010467]] | \n", + "[[protein binding activity, enzyme binding activity, protein kinase binding activity, interleukin binding activity, phosphorylation-dependent protein binding activity, GO:0001216, GO:0042803, nucleic acid binding activity, GO:0005001, GO:0048018, GO:0004725, GO:0005125, cytoskeletal protein binding activity, cytokin receptor activity, GO:0030335]] | \n", + "||
| T cell proliferation-1 | \n", + "[[GO:0048018, phosphotyrosine residue binding activity, cytoskeletal protein binding activity, GO:0005574]] | \n", + "[[cation binding activity, diacylglycerol binding activity, enzyme binding activity, GO:0046982, receptor binding activity, protein kinase binding activity, phosphorylation-dependent protein binding activity, phosphotyrosine residue binding activity, GO:0005001, protease binding activity, cytoskeletal protein binding activity, phosphatidylinositol 3-kinase binding activity, GO:0061630, GO:0004888, GO:0043621, GO:0004697, zinc ion binding activity, transmembrane atp-gated monoatomic cation channel activity, purin]] | \n", + "||
| Yamanaka-TFs-0 | \n", + "[[transcription repressor and activator activities, rna polymerase ii-specific, nucleic acid binding activity, GO:0009889, GO:0009966, GO:0010468, GO:0045765, and protein-dna complex organization, GO:0042127]] | \n", + "[[dna-binding, GO:0000988, rna polymerase ii-specific, nucleic acid binding activity, transcription cis-regulatory region binding activity, GO:0010468, GO:0009889]] | \n", + "||
| Yamanaka-TFs-1 | \n", + "[[dna-binding, GO:0016563, GO:0016564, GO:0000988, rna binding activity, ubiquitin protein ligase binding activity, GO:0010628, GO:0010629, GO:0009889, GO:0045765, GO:0060828, GO:0009966, transcription cis-regulatory region binding activity, GO:0045944, GO:0003130, GO:0001714]] | \n", + "[[GO:0006351, GO:0010468, dna-binding, GO:0000785, GO:0005829, GO:0005654, GO:0005667, GO:0009966, GO:0045944, GO:0001714]] | \n", + "||
| amigo-example-0 | \n", + "[[GO:0005515, GO:0060230, GO:0005543, MESH:M0518050, GO:0050804]] | \n", + "[[the list of genes provided is involved in multiple processes related to cell adhesion, growth factor binding, protein phosphorylation, tissue development, and regulation of cholesterol homeostatis and transcytosis. the underlying biological mechanism likely involves multiple pathways, including cellular response to lipopolysaccharide, cell-matrix adhesion, and negative regulation of low-density lipoprotein. enriched terms include cell adhesion, cell surface receptor signaling, collagen binding activity, GO:0019838, GO:0042157, GO:1902533, GO:0046983, GO:0006468, regulation of bmp signaling, GO:0042127, GO:0010468, GO:0009966, regulation of very-low-density lipoproten particle clearance, GO:0045056]] | \n", + "||
| amigo-example-1 | \n", + "[[GO:0005515, GO:0043167, GO:0008009, GO:0019838, signal receptor binding, GO:0019902, GO:0016477, GO:0086009, GO:0007165, GO:0065007, GO:0006952]] | \n", + "[[GO:0051246, GO:0001952, GO:0042127, GO:0042981, GO:0043269, GO:0030193, GO:0007166, GO:0050804, GO:0005201, GO:0007160, organ development and differentiation, regulation of hormone pathways]] | \n", + "||
| bicluster_RNAseqDB_0-0 | \n", + "[[GO:0005509, double-stranded dna-binding, cell adhesion and migration, transcriptional regulation]] | \n", + "[[genes in this list are involved in a range of activities, including calcium ion binding activity, metal ion binding activity, protein domain specific binding activity, identical protein binding activity, dna-binding transcription factor activity, and several others. the underlying biological mechanism appears to be related to structural support and regulation of cellular processes. enriched terms include: metal ion binding, GO:0005509, GO:0005515, GO:0000988, dna-binding, GO:0042802, domain specific protein binding]] | \n", + "||
| bicluster_RNAseqDB_0-1 | \n", + "[[metal ion binding activity, protein binding activity, rna binding activity, GO:0019208, GO:0005243, GO:0042803, calcium ion binding activity, MESH:C086554]] | \n", + "[[GO:0001216, protein kinase binding activity, metal ion binding activity, calcium ion binding activity, transcription co-regulator activity, responsive to stimuli]] | \n", + "||
| bicluster_RNAseqDB_1002-0 | \n", + "[[UBERON:0001134, GO:0006936, GO:0016567, GO:0045010, calcium-dependent signaling, GO:0010468, GO:0006468, GO:0043687, GO:0042692, GO:0060537, MONDO:0020121, muscle organelle organization]] | \n", + "[[GO:0051015, GO:0000146, GO:0051371, GO:0003785, GO:0005523, GO:0017022, GO:0031432, GO:0004111]] | \n", + "||
| bicluster_RNAseqDB_1002-1 | \n", + "[[actin binding activity, GO:0007015, muscle alpha-actinin binding activity, GO:0006936, GO:0060415, GO:0071689, GO:0004672, protein phosphatase binding activity, GO:0043502, tropomyosin binding activity, troponin binding activity, troponin complex activities]] | \n", + "[[calcium-dependent protein binding activity, atp binding activity, actin filament binding activity, actin monomer binding activity, transmembrane transporter binding activity, GO:0016567, GO:0061630, tropomyosin binding activity, identical protein binding activity, GO:0008375, protein phosphatase 1 binding activity, zinc ion binding activity, troponin c binding activity, troponin i binding activity, actin binding activity, tropomyosin binding activity, GO:0001216, sequence-specific double-stranded dna binding activity]] | \n", + "||
| endocytosis-0 | \n", + "[[protein signaling, GO:0006468, GO:0016567, GO:0015031, GO:0030030, GO:0006897, GO:0006898, GO:0035091, GO:0001766, GO:0097320]] | \n", + "[[GO:0004674, lysophosphatidic acid binding activity, sulfatide binding activity, GO:0016790, cadherin binding activity, GO:0032456, sh3 domain binding activity, GO:0051260, macropinosome formation, GO:0031623, transferring transport, t cell receptor binding activity, GO:0005085, GO:0044351, GO:0001773, GO:0007520, GO:0018105, GO:0010468, vascular endothelial growth factor receptor signalling pathway, GO:0051128, GO:0007042, GO:0045807, GO:0051090]] | \n", + "||
| endocytosis-1 | \n", + "[[GO:0006897, GO:0005515, GO:0006869, GO:0016567, GO:0042632, GO:0035727]] | \n", + "[[GO:0006468, GO:0051260, cell signaling, GO:0005480, GO:0016567, endocytosis/exocytosis, GO:0005102, GO:0010468, vesicle buddying, GO:0007165, GO:0050727, GO:0035556, gtp-dependent pathways, receptor signaling, canonical inflammasome signaling]] | \n", + "||
| glycolysis-gocam-0 | \n", + "[[GO:0019538, enzymatic activity, protein transcription, cell metabolism, carbohydrate phosphorylation and metabolism, protein homeostasis, cell signaling, GO:0008104, cell homeostasis, cellular energy production]] | \n", + "[[protein binding activity, atp binding activity, peptidoglycan binding activity, GO:0051156, GO:0002639, GO:0010595, GO:0006002, GO:0061615, GO:0030388, GO:0046166, fructose binding activity, GO:0004332, MONDO:0009295, GO:0004807, disordered domain specific binding activity, GO:0004866, GO:0046835, GO:0072655, maintenance of protein location in]] | \n", + "||
| glycolysis-gocam-1 | \n", + "[[GO:0003824, GO:0031625, protein homodimerization, GO:0016310, GO:0006096, GO:1904659, GO:0070061, GO:0004332, GO:0004618, GO:0004619, GO:0004396, peptidoglycan binding activity, GO:0003872, GO:0004807, GO:0004347, GO:0021762, binding activity of sperm to zona pellucida, GO:0030388, GO:0019725, GO:0046716, GO:0071456, GO:0016525, UBERON:2005050]] | \n", + "[[protein binding activity, atp binding activity, ubiquitin protein ligase binding activity, fructose binding activity, GO:0042803, GO:0004618, GO:0004619, GO:0004807, GO:0004396, GO:0004332, GO:0004634, GO:0003872, GO:0004347, GO:0006096, GO:0006002, GO:0046166, GO:0046835, GO:0072655, GO:0072656, GO:0071456, negative regulation of]] | \n", + "||
| go-postsynapse-calcium-transmembrane-0 | \n", + "[[GO:0097553, GO:1990034, GO:0071318, GO:0007186, GO:0035235, GO:1990454, GO:0017146, GO:0014066, GO:1900274, GO:0099509, GO:2000300, GO:0032680, GO:0005245, GO:2000311, GO:0080164]] | \n", + "[[GO:0005262, GO:0005245, regulation of intracellular calcium concentrations, GO:0098960, GO:2000311, g protein-coupled receptor signaling, GO:0070588, GO:0015276]] | \n", + "||
| go-postsynapse-calcium-transmembrane-1 | \n", + "[[GO:0006816, regulation of calcium]] | \n", + "[[GO:0005261, acetylcholine-gated channel activity, GO:0022849, nmda selective glutamate receptor activity, GO:0005245, GO:1990454, GO:0035235, GO:0071318, regulation of]] | \n", + "||
| go-reg-autophagy-pkra-0 | \n", + "[[these genes are involved in several cellular activities, primarily in their roles in signal transduction pathways, GO:0036211, protein folding and stability, GO:0051726, and apoptosis. the terms enriched are: signaling receptor activity; protein phosphorylation; regulation of macromolecule biosynthetic process; autophagy; g2/m transition of mitotic cell cycle; chromosome segregation; cytoplasmic stress granule; torc1 signaling; defense response; anoikis; protein folding chaperone; histone acetylation; i-kappab kinase/nf-kappab signaling; k63-linked polyubiquitin modification-dependent protein binding activity.\\n\\nmechanism: these genes participate in a variety of biological processes, including signal transduction pathways, GO:0036211, GO:0051726, apoptosis and dna-templated transcription, answering to different external and internal stimuli as well as aiding in cell survival and death. the enriched terms involve protein-protein interactions and modifications, as well as involvement in akt/pi3k, tor, and nf-kb pathways that are essential for cell signaling, typical in response to bacterial infection and the activation of pro-survival mechanisms]] | \n", + "[[protein kinase binding activity, GO:0004672, GO:0004674, GO:0001934, GO:0010556]] | \n", + "||
| go-reg-autophagy-pkra-1 | \n", + "[[protein binding activity, metal ion binding activity, protein kinase binding activity, GO:0030295, protein folding chaperone activity, GO:0042803, chromatin binding activity, GO:0003713, GO:0016410, GO:0016538, GO:0016303, card domain binding activity, heat shock protein binding activity, muramyl dipeptide binding activity, 14-3-3 protein binding activity, rna polymerase iii cis-regulatory region sequence-specific dna binding activity]] | \n", + "[[the genes listed above are involved in a variety of processes, including negative and positive regulation of transport, GO:0051246, cell surface receptor signaling, and regulation of gene expression. these genes also have a variety of functions, including protein kinase binding activity, chromatin binding activity, GO:0030295, and metal ion binding activity. the enriched terms that describe these genes include: protein binding activity; protein kinase binding activity; signal transduction; positive and negative regulation of transport; chromatin binding activity; and protein serine/threonine kinase activity.\\n\\nmechanism: these gene products are part of, or act upstream of a variety of signaling pathways, all of which are involved in cell growth, MESH:D008283, and response to environmental stimuli. the pathways typically involve post-translational modifications of target proteins by phosphorylation, as well as formation or breakdown of protein-containing complexes. these signaling pathways ultimately affect gene expression and determine the type of output which a particular cell will produce]] | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[[the genes in this list share functions involving glycoprotein and carbohydrate metabolic processes and structural functions related to extracellular matrix organization. enriched terms include: dihydroceramidase activity, GO:0017040, GO:0061463, GO:0004134, GO:0004135, GO:0004556, hyaluronic acid binding activity, GO:0004415, GO:0004568, GO:0008843, clathrin heavy chain binding activity, GO:0008422, GO:0004348, GO:0004336, GO:0004553, GO:0008375, GO:0004563, identical protein binding activity, syndecan binding activity, heparan sulfate proteoglycan binding activity, GO:0003796, GO:0004567]] | \n", + "[[the genes in the list are involved in many processes relating to glycan metabolism and synthesis, such as glycoside catabolic process, GO:0006027, GO:0019377, GO:0005980, and sucrose catabolic process. other enriched terms are dihydroceramidase activity, hyaluronic acid binding activity, GO:0004415, GO:0030212, GO:0046373, GO:0004571, GO:0006487, and protein homodimerization activity.\\n\\nmechanism: glycan metabolism and synthesis involves several enzymes with diverse activities such as alpha-glucosidases, MESH:D043323, MESH:D001617, MESH:D001619, n-acetylglucosaminyltransferases. these enzymes hydrolyze transfer carbohydrate building blocks to form modify carbohydrates for a variety of cellular functions]] | \n", + "||
| hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[[GO:0006516, GO:0006027, heparan sulfate catabolism, glucoside catabolism, GO:0036508, GO:0006517, GO:0005975, GO:0006869, GO:0030214, receptor signaling, GO:0031589, GO:0009313, GO:0004672, GO:0008283, GO:0019915, GO:0050885, GO:0042742, GO:0005989, GO:0008344, GO:0007605, GO:0006487, GO:0006281, GO:0071451, peptidyl-serine]] | \n", + "[[GO:0005975, GO:0046477, GO:0006516, oligo-saccharide catabolic process, GO:0006869, GO:0015144, GO:0046982, protein domain specific binding activity, GO:0006629, GO:0016139, GO:0030214, GO:0006032]] | \n", + "||
| ig-receptor-binding-2022-0 | \n", + "[[immunoglobulin receptor binding activity, antigen binding activity, fc-gamma receptor i complex binding activity, GO:0004715, phosphotyrosine residue binding activity, peptidoglycan binding activity, phosphatidylcholine binding activity. mechanism: the genes listed appear to be involved in the regulation of the immune response. they likely aid in the recognition of pathogens, binding to the appropriate receptors, triggering a signal for an immune response. they may also play a role in enabling the recognition of self-antigens inhibiting a response to them]] | \n", + "[[immunoglobulin receptor binding activity, antigen binding activity, GO:0004715, phosphatidylcholine binding activity, phosphotyrosine residue binding activity]] | \n", + "||
| ig-receptor-binding-2022-1 | \n", + "[[antigen binding activity, immunoglobulin receptor binding activity, GO:0098542, GO:0002253, fc-gamma receptor i complex binding activity, GO:0004715, peptidoglycan binding activity, phosphatidylcholine binding activity, GO:0007229, GO:0038187, mannose binding activity, phosphotyrosine residue binding activity, GO:0051130, GO:0045657, protection of host from foreign agent]] | \n", + "[[GO:0042803, GO:0007160, phosphorylation-dependent signaling, GO:0019901, GO:0034988, GO:0030098, GO:0098609, GO:0001784, GO:0042834, integrin signaling, GO:0006909]] | \n", + "||
| meiosis I-0 | \n", + "[[these genes are involved in processes related to dna binding, repair, replication, recombination, and regulation thereof. the enriched terms would be: dna binding, GO:0003690, dna damage repair, GO:0006310, GO:0005515, meiotic recombination, GO:0007059, GO:0000278, GO:0071173, GO:0051289, GO:0003682, resolution of meiotic recombination intermediates. \\nmechanism: the underlying biological mechanism is that these proteins work together to maintain genomic stability, regulate gene expression, promote proper cell division, germline cell development, meiosis]] | \n", + "[[GO:0003677, atp dependent activity, GO:0003682, GO:0005634, protein export, transcriptional regulation, GO:0003690, GO:0003697, GO:0006281, GO:0004518, MESH:D011995, GO:0007059, GO:0000278, intrinsic apoptotic signaling, regulation of telomere maintenance.\\nmechanism: the genes identified are likely playing roles in a variety of dna metabolic pathways, including dna repair, double-stranded dna break repair, homologous recombination, transcriptional regulation, and mitotic cell cycle processes. these pathways likely enable cellular replication and maintenance of genomic integrity, as well as control of gene expression and apoptosis]] | \n", + "||
| meiosis I-1 | \n", + "[[GO:0140013, dna binding activity, GO:0006259, GO:0035825, telomere attachment, GO:0000785, GO:0000795, GO:0005694, GO:0005737]] | \n", + "[[GO:0003677, GO:0003690, GO:0042802, GO:0006259, GO:0006302, GO:0007131, meiotic chromosome segregation and pairing, GO:0007283, GO:0000712, GO:0051026, GO:0016925, GO:0007130]] | \n", + "||
| molecular sequestering-0 | \n", + "[[calcium ion binding activity, identical protein binding activity, GO:0004252, GO:0140314, calcium-dependent protein binding activity, arginine binding activity, GO:0140313, enzyme binding activity, GO:0019887, nf-κb binding activity, nuclear localization sequence binding activity, oxysterol binding activity, rage receptor binding activity, ubiquitin protein ligase binding activity, actin binding activity, rig-i binding activity, GO:0003713, zinc ion binding activity, GO:1903231]] | \n", + "[[calcium ion binding activity, identical protein binding activity, GO:0140311, ubiquitin protein ligase binding activity, cellular response, GO:0001932, GO:0010359, GO:0097214, GO:0010468, GO:0035456]] | \n", + "||
| molecular sequestering-1 | \n", + "[[protein binding activity, GO:0140313, GO:0000988, GO:0019887, calcium ion binding activity, dna-binding activity, ubiquitin protein ligase binding activity, tumor necrosis factor binding activity, regulatory pathway activity]] | \n", + "[[GO:0005515, GO:0046872, GO:0043167, GO:0010468, GO:0001932, cell death pathways, GO:0009059, GO:0046907, cellular response to infection and inflammation]] | \n", + "||
| mtorc1-0 | \n", + "[[enzyme binding activity, acid binding activity, molecule transport, adapter binding activity, receptor binding activity, dna binding activity, protein binding activity, GO:0003824, GO:0016787, GO:0016491, anion binding activity, GO:0008233, GO:0140657, thioredoxin activity, translocation, GO:0061630, cysteine endopeptidase activity, GO:0004738, GO:0004618, magnesium ion binding activity, GO:0004340, GO:0003924]] | \n", + "[[protein binding activity, dna binding activity, enzyme binding activity, GO:0060090, GO:0140677, GO:0042803, domain binding activity, GO:0016491, protein kinase binding activity, phosphatidylinositol binding activity, GO:0016504, GO:0003714, nuclear androgen receptor binding activity, nf-kappab binding activity, ubiquitin protein ligase binding activity, phosphotyrosine residue binding activity, GO:0016564, GO:0003743, peptidyl-proinalyl cistrans isomerase activity]] | \n", + "||
| mtorc1-1 | \n", + "[[cytoskeleton protein binding, phosphatase binding activity, GO:0016491, cell development and signaling activity, dna binding activity, cellular transporter activity, protein kinase binding activity]] | \n", + "[[protein binding activity, GO:0005215, dna binding activity, rna binding activity, atp binding activity, peptide activity, GO:0003824, enzyme binding activity, phosphoprotein binding activity, GO:0016563, GO:0016787, GO:0016491, GO:0004017, identical protein binding activity, GO:0060090, GO:0007165, signal receiving activity, GO:1901987, metabolism regulation, cell growth control]] | \n", + "||
| peroxisome-0 | \n", + "[[peroxisome biogenesis, protein import into peroxisome, GO:0000425, GO:0000268, GO:0140036, GO:0006631, protein homodimerization, enzyme binding activity, GO:0050821, GO:0043335]] | \n", + "[[peroxisome biogenesis, atp binding activity, GO:0016887, ubiquitin-dependent protein binding activity, GO:0016558, GO:0050821, GO:0043335, GO:0000425, GO:0006625, protein tetramerization.\\n\\nmechanism: these gene functions are involved in a complex process involving the biogenesis and maintenance of peroxisomes, which are subcellular organelles that contain a variety of enzymes involved in metabolic processes. this process entails the function of multiple proteins working together to ferry important proteins into the peroxisomal membrane, where these proteins will become functional components of the organelle]] | \n", + "||
| peroxisome-1 | \n", + "[[GO:0016558, GO:0050821, GO:0042127, protein-lipid binding, GO:0007031, GO:0008611, GO:0001881, GO:0006631]] | \n", + "[[protein binding activity, GO:0016558, peroxisome matrix targeting signal-2 binding activity, GO:0042803, GO:0008611, GO:0006631, GO:0008285, GO:0000425, GO:0032994, microtubule-based peroxisome localization.\\nmechanism: based on the functions that these genes carry out, it is likely that the genes are involved in a mechanism whereby proteins are imported into the peroxisome matrix, and the peroxisome matrix is organized, stabilized, and/or maintained in order to carry out fatty acid metabolism and pexophagy. the receptor recycling and microtubule-based localization also likely play a role in this mechanism]] | \n", + "||
| progeria-0 | \n", + "[[GO:0003677, GO:0005515, GO:0046872, cellular response to radiation, hypoxia, and starvation, GO:0042981, GO:0032204, GO:0010835, GO:0045069]] | \n", + "[[protein binding activity, dna binding activity, metal ion binding activity, GO:0003678, GO:0042803, GO:0071480, GO:0010836, GO:0007084, GO:0045071, GO:0032392, GO:0006259, GO:0009267, GO:1902570, GO:0042981, GO:0071456, GO:0032204, GO:0004222, GO:0050688, with a positive effect]] | \n", + "||
| progeria-1 | \n", + "[[dna damage and repair, GO:0005515, GO:0046872, homodimerization, GO:0006915, MESH:D016922, GO:0001666]] | \n", + "[[GO:2000772, dna binding and metabolic processes, dna helicase and metal ion binding activities, protein localization to nucleolus and regulation of apoptotic processes appear to be enriched terms common to the three genes given.\\n\\nmechanism: the three genes appear to be involved in similar nucleic acid binding and regulation activities that enable the maintenance and regulation of cellular processes. this suggests an underlying molecular mechanism in which these genes interact directly to modulate a variety of cellular processes related to senescence, GO:0003677, GO:0008152, GO:0006915]] | \n", + "||
| regulation of presynaptic membrane potential-0 | \n", + "[[GO:0005216, GO:0016917, GO:0008066, GO:0007186, GO:0007214, GO:0006836, GO:0005249, GO:0005248, GO:0007193]] | \n", + "[[voltage-gated potassium/sodium channel activity, GO:0015276, transmembrane transporter binding activity, GO:0004930, GO:0004971, GO:0015277, GO:0035235, GO:1902476, GO:0007214, GO:0019228, GO:0042391, GO:0007268, regulation of]] | \n", + "||
| regulation of presynaptic membrane potential-1 | \n", + "[[GO:0005216, membrane potential regulation, GO:0015276, g protein-coupled receptor signaling, GO:1902476, GO:0007214, GO:0071805]] | \n", + "[[GO:0005216, GO:0015276, membrane potential regulation, GO:0005249, GO:0005248, GO:0008066, GO:0004890, GO:0055074, GO:0022851, ionotropic glutamate receptor signaling, GO:1902476, GO:0051932, GO:0048167, negative regulation of smooth muscle apoptotic process, GO:0051924, GO:0086009, GO:0035249, GO:0060292, GO:0006836, GO:0050804, GO:0034220, GO:0051205, GO:0060079]] | \n", + "||
| sensory ataxia-0 | \n", + "[[dna-binding, rna polymerase ii-specific activity, GO:0046872, GO:0031625, GO:0045944, GO:0002639, GO:1901184, GO:0033157, monoatomic cation]] | \n", + "[[transcription regulation, GO:0031625, GO:0003677, GO:0006027, GO:0043583, GO:0045475, GO:0007399, GO:0006457, GO:0043066, GO:0010595, GO:0002639, GO:0034214, GO:0050974, GO:0006812, GO:0015886, GO:0071260, GO:0042552, GO:0098742, GO:0006839, GO:0019226, GO:0008380, GO:0003774, GO:0061608, nuclear localization sequence binding activity, GO:0006607, GO:0003887, GO:0006284, gap-filling, protein ubiquitination.\\n\\nmechanism: analysis of the given list of genes suggests that there]] | \n", + "||
| sensory ataxia-1 | \n", + "[[transcription regulation, nucleic acid metabol]] | \n", + "[[MESH:D015533, dna-binding, rna polymrease ii-specific, dna binding activity, GO:0034214, GO:0061608, protein folding chaperone binding activity, GO:0016567, cell aggregration, GO:0098609, GO:0042552, GO:0005886, GO:0034220, GO:0030218, GO:0015886, mitochondrial transport.\\nmechanism: the eighteen human genes are involved in a variety of complex biological processes, from transcriptional regulation, through to cellular adhesion and the transport of macromolecules, including proteins, nucleic acids and heme. there is likely significant cross-talk between these various processes, particularly at the level of dna binding proteins, transcription activators, and nuclear receptor activities. this suggests that these genes are likely playing a role in the coordination of cellular processes to facilitate proper neural development and maintenance of peripheral nerve function]] | \n", + "||
| term-GO:0007212-0 | \n", + "[[g protein-coupled receptor binding activity, GO:0003924, enzyme binding activity, GO:0042803, signaling receptor binding activity, GO:0004016, g-protein beta/gamma-subunit complex binding activity, signaling receptor binding activity, clathrin light chain binding activity, sequence-specific double-stranded dna binding activity, GO:0004672, nf-kappab binding activity, protein kinase a catalytic subunit binding activity, GO:0004674]] | \n", + "[[GO:0007186, GO:0051480, GO:0006357, GO:1901214, GO:0006915, GO:0006171, GO:0006468]] | \n", + "||
| term-GO:0007212-1 | \n", + "[[GO:0004672, g-protein activity, g-protein beta/gamma- subunit complex binding activity, atpase binding activity, GO:0004016, protein-folding chaperone binding activity, signal receptor binding activity, GO:0071333, GO:0007165, negative regulation of nf-kappa b transcription factor activity, GO:2000394, GO:0007212, cellular response to prostaglandin e, GO:0007204]] | \n", + "[[GO:0007186, GO:0043087, GO:0060170, GO:0006171, GO:0005783, membrane localization, transcriptional regulation, GO:0007212, GO:0006874, GO:0046039, GO:0098843, protein kinase activity. \\n\\nmechanism:\\nthe g protein-coupled receptor signaling pathway is a general pathway that mediates the effects of hormones, neurotransmitters other extracellular signals in cells across a variety of tissues organs. signaling through gpcrs involves activation of g proteins, which in turn activate or inhibit effector enzymes ion channels. the commonality among these genes is that they are involved in mechanisms of gpcr signaling downstream processes such as regulation of gtpase activity, camp synthesis regulation of calcium ion concentration. the genes may also participate in membrane localization, transcriptional regulation postsynaptic endocytic zone functions. other associated activities]] | \n", + "||
| tf-downreg-colorectal-0 | \n", + "[[GO:0003677, GO:0003723, GO:0003682, GO:0008134, GO:0003713, GO:0016564, MESH:M0518050, GO:0019899]] | \n", + "[[transcription activation/repression, GO:0007165, GO:0006351, GO:0007049, MESH:D012319, GO:0003682, GO:0008270, GO:0016575, protein ligase/cofactor binding]] | \n", + "||
| tf-downreg-colorectal-1 | \n", + "[[GO:0006351, dna-binding, rna polymerase ii-specific, transcription activator/transcription repressor, cis-regulatory region sequence-specific, GO:0001221, GO:0006355, GO:0006337, GO:0009966]] | \n", + "[[dna-binding transcription, GO:0016563, rna polymerase ii-specific, GO:0016564, positive/negative regulation of transcription, GO:0006351, GO:0010468, nucleic acid binding activity, sequence-specific double-stranded dna binding activity, protein kinase binding activity]] | \n", + "
| prompt_variant | \n", + "model | \n", + "method | \n", + "geneset | \n", + "v1 | \n", + "v2 | \n", + "jaccard_index | \n", + "
|---|---|---|---|---|---|---|
| 0 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "EDS-0 | \n", + "[[GO:0032964, GO:0030198, GO:0010712, GO:0043687, GO:0006493, GO:0006508, GO:0008270]] | \n", + "[[GO:0032964, matrix maturation, GO:0031012, MESH:D006023, MESH:D015238, zinc finger proteins, proteolytic subunits, MESH:D057057, MESH:M0465019]] | \n", + "0.07 | \n", + "
| 1 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "EDS-1 | \n", + "[[GO:0032964, GO:0061448, GO:0030198, GO:0030166]] | \n", + "[[GO:0032964, GO:0030198, GO:0006457, GO:0006955]] | \n", + "0.33 | \n", + "
| 2 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "FA-0 | \n", + "[[GO:0006281, GO:0035825, GO:0006302, chromosome stability \\n\\nhypotheses: the enriched terms suggest that the common function of these genes is dna repair, specifically in the context of homologous recombination and double-strand break repair. the genes are part of a complex network involved in maintaining chromosome stability, which is critical for preventing mutations and malignant transformation. mutations in these genes have been linked to various forms of cancer and the fanconi anemia disorder. understanding the mechanisms by which these genes function in dna repair could provide insights into cancer development and potential therapeutic targets]] | \n", + "[[GO:0006281, GO:0035825, fanconi anemia pathway]] | \n", + "0.40 | \n", + "
| 3 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "FA-1 | \n", + "[[GO:0006281, fanconi anemia pathway, GO:0035825, MESH:M0443452, genome maintenance, GO:0006302]] | \n", + "[[GO:0006281, GO:0035825, MESH:D051856, rad51 family proteins, chromosome stability maintenance\\n\\nmechanism: these genes are involved in dna damage repair and maintenance of genome stability, particularly through homologous recombination and the formation of the fanconi anemia complementation group proteins. the rad51 family proteins and chromosomal stability maintenance are also important in these processes]] | \n", + "0.22 | \n", + "
| 4 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ADIPOGENESIS-0 | \n", + "[[GO:0005739, GO:0006119, GO:0022900, GO:0006091, MESH:M0496924, GO:0006631, GO:0006099, GO:0006635]] | \n", + "[[mitochondrial function, GO:0008152, GO:0006118, GO:0006631, redox reactions]] | \n", + "0.08 | \n", + "
| 5 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ADIPOGENESIS-1 | \n", + "[[mitochondrial function, GO:0070469, energy production, GO:0006629, GO:0006869, GO:0005515, GO:0016049, GO:0051301, antioxidant enzyme. \\n\\nmechanism/]] | \n", + "[[mitochondrial function; energy metabolism; lipid metabolism; electron transport chain. \\n\\nmechanism: these genes likely contribute to the production and regulation of energy in the form of atp through processes including beta-oxidation of lipids, GO:0006119, and electron transport chain activity. dysfunction or dysregulation of these genes may lead to mitochondrial dysfunction and impaired energy metabolism, which have been implicated in various diseases including neurodegenerative disorders, MONDO:0004995, MONDO:0005066]] | \n", + "0.00 | \n", + "
| 6 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[[chemokine signaling pathway, cytokine-cytokine receptor interaction, GO:0006955, GO:0042110, GO:0050776, GO:0006954, GO:0050900]] | \n", + "[[GO:0005125, GO:0042110, GO:0042379, GO:0002429, GO:0032623, GO:0032609, GO:0002504, GO:0050776, GO:0030217, GO:0050900, GO:0060333, GO:0001819, GO:0002685, GO:0070098, GO:0050852]] | \n", + "0.16 | \n", + "
| 7 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[[MESH:D018925, MESH:D016207, t cell-mediated immunity, interferon signaling, GO:0006954, tgf-beta signaling, toll-like receptor signaling, tnf signaling]] | \n", + "[[GO:0008009, cytokine signaling, GO:0019882]] | \n", + "0.00 | \n", + "
| 8 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[[protein kinase activity; membrane transport; enzyme catalysis\\n\\nmechanism: these genes are involved in signal transduction and cellular metabolism, with a focus on protein kinase activity, GO:0055085, and enzyme catalysis. they play roles in the transport of various molecules across biological membranes, including fatty acids, sugars, and ions. they are also important in regulating cellular responses to extracellular stimuli, such as growth factors, MESH:D006728, and cytokines. additionally, they catalyze metabolic reactions and contribute to various metabolic pathways]] | \n", + "[[GO:0004672, GO:0031344, GO:0008285, GO:0010468, regulation of cellular protein localization and movement]] | \n", + "0.00 | \n", + "
| 9 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[[GO:0004672, GO:0008134, GO:0005515, GO:0007165, GO:0003824]] | \n", + "[[GO:0004672, GO:0008134, GO:0006810, enzymatic activity, GO:0006511, GO:0061024, GO:0042445, GO:0016567]] | \n", + "0.18 | \n", + "
| 10 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ANGIOGENESIS-0 | \n", + "[[GO:0031012, GO:0007155, tissue development and regeneration, growth factor signaling, endothelial-specific signaling, cytokine signaling]] | \n", + "[[GO:0030198, GO:0007155, GO:0030199, GO:0006029, GO:0045765, GO:0009611]] | \n", + "0.09 | \n", + "
| 11 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ANGIOGENESIS-1 | \n", + "[[ecm organization, GO:0031589, GO:0016477]] | \n", + "[[GO:0030198, GO:0007155, GO:0007088, protein kinase activity regulation, GO:0070848, cellular response to transforming growth factor beta stimulus\\n\\nmechanism: the genes listed are involved in the organization of the extracellular matrix and cell adhesion. specifically, they play roles in binding to and regulating the spacing of collagen fibrils, inhibiting proteases, promoting cell-cell and cell-matrix interactions, and regulating mitosis and protein kinase activity. growth factors and transforming growth factor beta are also involved in signal transduction pathways that are regulated by these genes]] | \n", + "0.00 | \n", + "
| 12 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-0 | \n", + "[[GO:0005884, GO:0007155, GO:0007010, GO:0008360, GO:0007165]] | \n", + "[[GO:0007155, GO:0007010, GO:0005925, GO:0070160]] | \n", + "0.29 | \n", + "
| 13 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-1 | \n", + "[[GO:0070160, GO:0031012, GO:0005604, GO:0007155, adhesion junction, GO:0007160]] | \n", + "[[GO:0070160, GO:0007155, GO:0008014, integrin, GO:0007165, adhesion g-protein coupled receptor (gpcr), GO:0015629, UBERON:4000022, protein tyrosine kinase (ptk), GO:0016303, map kinase, MESH:D016212]] | \n", + "0.12 | \n", + "
| 14 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_SURFACE-0 | \n", + "[[GO:0007155, GO:0007165, GO:0061024, GO:0015031]] | \n", + "[[GO:0007166, GO:0007169, GO:1901796, GO:0019048, GO:0045785, GO:0043408, GO:2000145, GO:0032956, GO:0051897, GO:0048015, GO:0010810, GO:0030334, regulation of cell growth\\n\\nmechanism and hypotheses: the enriched terms suggest a common mechanism involving transmembrane signaling pathways, with a focus on cell adhesion, migration, and growth regulation. several of the genes are involved in the regulation of the mapk signaling pathway, which is known to play a central role in cellular processes such as proliferation, differentiation, and apoptosis. pathway analysis of these genes may further elucidate the specific regulatory mechanisms at play]] | \n", + "0.00 | \n", + "
| 15 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_SURFACE-1 | \n", + "[[GO:0007155, GO:0007165, GO:0007154]] | \n", + "[[GO:0007160, GO:0006811, GO:0007165, GO:0098631, insulin regulation, GO:0016485]] | \n", + "0.12 | \n", + "
| 16 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_APOPTOSIS-0 | \n", + "[[GO:0006915, GO:0008219, GO:0043067, GO:0097153, binding of proteins involved in cell death.\\n\\nmechanism: the majority of the genes on the list are involved in apoptotic processes or regulate cell death. many of these genes belong to the bcl-2 protein family, which regulate apoptosis by either inhibiting or promoting cell death. other gene products, such as the caspases, also play a crucial role in the apoptotic process by cleaving proteins involved in cell death, ultimately leading to cell death. the enrichment of this theme in the gene list suggests that the regulation of apoptosis and programmed cell death is a significant biological mechanism that the genes in the list are involved in]] | \n", + "[[GO:0006915, GO:0008219, GO:0007165]] | \n", + "0.33 | \n", + "
| 17 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_APOPTOSIS-1 | \n", + "[[apoptosis regulation, cytokine signaling, growth factor regulation]] | \n", + "[[GO:0097153, GO:0042981, positive regulation of dna fragmentation, GO:0043067, GO:0010941, GO:1901796, GO:0006974, GO:0070613]] | \n", + "0.00 | \n", + "
| 18 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[[GO:0140359, long-chain fatty-acid metabolism, GO:0008203, GO:0006629, GO:0006637]] | \n", + "[[GO:0006869, GO:0008203, GO:0006631, peroxisomal biogenesis, GO:0004448, GO:0008146]] | \n", + "0.10 | \n", + "
| 19 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[[peroxisome biogenesis, GO:0006631, GO:0006699, GO:0008203, GO:0140359, GO:0016491, atp-binding cassette, GO:0005490]] | \n", + "[[GO:0007031, GO:0001676, GO:0006699, GO:0008202, GO:0008203, GO:0001523, GO:0006635, alpha-oxidation, GO:0006720, lipid metabolic process \\n\\nmechanism: these genes function in a variety of processes involved in lipid metabolism and peroxisome biogenesis. peroxisomes are intracellular organelles involved in many metabolic pathways, including fatty acid beta-oxidation, which our enriched terms suggest is a common theme among these genes. additionally, these genes are involved in the synthesis of bile acids, steroid hormones, and retinoids, highlighting the importance of lipid metabolism in cellular function]] | \n", + "0.12 | \n", + "
| 20 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[[GO:0006695, GO:0006633, GO:0006629, regulation of cholesterol levels, transport across cell membranes]] | \n", + "[[GO:0006629, GO:0006869, GO:0008610]] | \n", + "0.14 | \n", + "
| 21 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[[GO:0006695, GO:0006629, GO:0007165]] | \n", + "[[GO:0006695, GO:0006644, GO:0006633, GO:0016125]] | \n", + "0.17 | \n", + "
| 22 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_COAGULATION-0 | \n", + "[[GO:0006956, GO:0007596, GO:0006508, GO:0030198]] | \n", + "[[GO:0007596, extracellular matrix remodeling, GO:0030449]] | \n", + "0.17 | \n", + "
| 23 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_COAGULATION-1 | \n", + "[[blood coagulation cascade; complement activation, classical pathway; extracellular matrix disassembly; calcium ion binding. \\n\\nmechanism: these genes are involved in the regulation and activation of different pathways implicated in blood coagulation, GO:0006956, and extracellular matrix remodelling. blood coagulation involves the conversion of prothrombin to thrombin by coagulation factors, which leads to the formation of a fibrin clot. complement activation is a cascade resulting in the removal of damaged cells and pathogens. extracellular matrix disassembly and remodelling are implicated in cellular processes such as tissue repair, GO:0001525, metastasis. calcium-binding proteins play a vital role in signalling pathways regulation of enzymatic activities]] | \n", + "[[extracellular matrix breakdown, GO:0007596, protein inhibition]] | \n", + "0.00 | \n", + "
| 24 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_COMPLEMENT-0 | \n", + "[[GO:0006956, GO:0006955, GO:0030162, GO:0030168]] | \n", + "[[GO:0008233, GO:0007596, GO:0006956]] | \n", + "0.17 | \n", + "
| 25 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_COMPLEMENT-1 | \n", + "[[GO:0006956, GO:0007596, cytokine signaling, GO:0006468, GO:0006955, GO:0006954]] | \n", + "[[GO:0006956, GO:0007596, GO:0006955, GO:0030168, cytokine signaling, GO:0002685, response to virus.\\n\\nmechanism: these genes are involved in regulating different aspects of immune response, including complement activation, platelet activation, cytokine signaling, and leukocyte migration. they are also involved in blood coagulation, which can be activated during an immune response to prevent pathogen spread. the over-representation of these genes suggests that immune activation and regulation are key to the identified biological process]] | \n", + "0.44 | \n", + "
| 26 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_DNA_REPAIR-0 | \n", + "[[GO:0006281, transcription initiation, GO:0006396, GO:0009117]] | \n", + "[[GO:0006281, transcription initiation, GO:0009117]] | \n", + "0.75 | \n", + "
| 27 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_DNA_REPAIR-1 | \n", + "[[GO:0006270, GO:0006261, GO:0006297, transcription, dna-template-dependent, GO:0045893, GO:0000122, GO:0006281, GO:0000723, GO:0065004]] | \n", + "[[GO:0006281, transcription regulation]] | \n", + "0.10 | \n", + "
| 28 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_E2F_TARGETS-0 | \n", + "[[GO:0006260, GO:0006281, GO:0051726]] | \n", + "[[GO:0006260, GO:0006281, GO:0051276]] | \n", + "0.50 | \n", + "
| 29 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_E2F_TARGETS-1 | \n", + "[[GO:0006260, GO:0006281, dna polymerase, GO:0009117, GO:0006298, chromatin structure\\n\\nmechanism: the genes on this list primarily function in dna replication and repair. many of them are involved in dna polymerase activity, nucleotide metabolism, mismatch repair, and chromatin structure. it is likely that these genes work together in a coordinated manner to ensure accurate dna replication and repair, and that defects in these processes can lead to genetic instability and cancer development]] | \n", + "[[GO:0006260, GO:0006281, cell-cycle checkpoint regulation]] | \n", + "0.29 | \n", + "
| 30 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[[GO:0030198, GO:0030199, GO:0048251, GO:0071711, regulation of protein localization to extracellular matrix, GO:0043236, GO:0001968, GO:0005518]] | \n", + "[[GO:0030198, GO:0007155, GO:0005518, actin binding activity, GO:0007229, GO:0001501, GO:0005201, GO:0006936, GO:0005604, GO:0031012, GO:0008009, GO:0008083, GO:0016860, GO:0006508, GO:0005125]] | \n", + "0.10 | \n", + "
| 31 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[[GO:0030198, GO:0005518, GO:0051015, GO:0005125, GO:0007155, GO:0016477]] | \n", + "[[GO:0030198, GO:0006936, GO:0007155]] | \n", + "0.29 | \n", + "
| 32 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[[membrane-bound proteins, MESH:D004798, GO:0000981]] | \n", + "[[MESH:D002352, MESH:D004798, MESH:D008565, GO:0000981, receptors, MESH:D003598]] | \n", + "0.29 | \n", + "
| 33 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[[GO:0055085, cell signaling, GO:0004672, GO:1904659, GO:0006811]] | \n", + "[[GO:0006631, GO:0006811, GO:0010468]] | \n", + "0.14 | \n", + "
| 34 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[[membrane-associated protein complex, GO:0019899, GO:0034220, transcriptional regulation]] | \n", + "[[GO:0005515, GO:0007165, GO:0019899, GO:0005737, GO:0043687, GO:0006355, GO:0006915, GO:0045860, positive regulation of cell proliferation.\\n\\nmechanism/]] | \n", + "0.08 | \n", + "
| 35 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[[GO:0005515, GO:0003824, GO:0008134, GO:0006355, GO:0007165, cytokine signaling pathway, regulation of cell growth and differentiation]] | \n", + "[[GO:0007165, GO:0004672, g-protein coupled receptor signaling pathway, GO:0055085, GO:0035556, GO:0004721, GO:0006468, zinc ion binding. \\n\\nhypotheses: the enriched terms suggest that the genes in this list are involved in regulatory mechanisms that help to control intracellular signaling cascades and protein expression through phosphorylation and dephosphorylation of proteins, and zinc ion binding. additionally, these genes may play a role in transmembrane transport and regulation of ion channels]] | \n", + "0.07 | \n", + "
| 36 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[[GO:0006629, mitochondrial function, GO:0003824, GO:0006631, oxidation-reduction process, metabolism of carboxylic acid, GO:0006118, GO:0006082]] | \n", + "[[GO:0006631, GO:0005975, amino acid metabolism, mitochondrial function, oxidative stress response]] | \n", + "0.18 | \n", + "
| 37 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[[GO:0006629, oxidation-reduction process, energy production, metabolism of fatty acids, mitochondrial function, GO:0045333]] | \n", + "[[GO:0006631, energy production, mitochondrial function, GO:0006629, oxidation-reduction process, GO:0006637, GO:0006099, MESH:D014451, GO:0019752, GO:0015936, GO:0006084, GO:0022900]] | \n", + "0.29 | \n", + "
| 38 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-0 | \n", + "[[GO:0051301, GO:0006260, GO:0007059, GO:0000910]] | \n", + "[[GO:0051726, GO:0006260, GO:0006281]] | \n", + "0.17 | \n", + "
| 39 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-1 | \n", + "[[GO:0006270, GO:0007059, GO:0000075, GO:0007052, GO:0007346, GO:0065004]] | \n", + "[[GO:0006260, GO:0051726, GO:0006281, GO:0007059, GO:0000910]] | \n", + "0.10 | \n", + "
| 40 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_GLYCOLYSIS-0 | \n", + "[[GO:0070085, GO:0005975, fructose-bisphosphate metabolism, GO:0006098, GO:0006006, GO:0006012, GO:0006090, GO:0006089, GO:0019319, GO:0006011, GO:0052573, GO:0004332]] | \n", + "[[GO:0006096, GO:0005975]] | \n", + "0.08 | \n", + "
| 41 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_GLYCOLYSIS-1 | \n", + "[[GO:0006096, GO:0005975, GO:0007165, GO:1904659, GO:0033554]] | \n", + "[[GO:0052574, GO:0006006, protein kinase binding activity, GO:0006090, GO:0006024, GO:0015012, GO:0006098, GO:0006096, rna polymerase iii transcription initiation, GO:0051287, GO:0022618, GO:0030199, GO:0008408, GO:0042803, atp-binding cassette transporter activity]] | \n", + "0.05 | \n", + "
| 42 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[[GO:0007411, GO:0007155, transcriptional regulation, cell communication. \\n\\nhypotheses: \\nthese genes may be involved in regulating the formation of neural circuits and maintaining neural plasticity through dynamic regulation of gene expression and protein signaling. the enriched terms suggest that the neural development process involves complex regulation of cell-cell communication and adhesion, as well as transcriptional control of gene expression. axon guidance is critical for the proper formation of neural circuits, and dysregulation of this process may lead to neural disorders]] | \n", + "[[neuronal development, GO:0007155, GO:0007165, GO:0016477, GO:0010977, GO:0001525, MESH:D018121, transcriptional regulation]] | \n", + "0.20 | \n", + "
| 43 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[[GO:0007411, GO:0007155, transcription regulation, neuro-endocrine signaling, protein cleavage, cell migration.\\n\\nmechanism: these genes are involved in various aspects of neuronal development and signaling, including axon guidance, neuron migration, cell adhesion and communication, transcription regulation, and protein cleavage. these processes are critical for proper central nervous system development and function]] | \n", + "[[GO:0007155, GO:0007411, neuronal proliferation and differentiation, GO:0007165, GO:0001525]] | \n", + "0.22 | \n", + "
| 44 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_HEME_METABOLISM-0 | \n", + "[[GO:0006811, GO:0010468, protein turnover, GO:0061024]] | \n", + "[[GO:0006810, GO:0005488, MESH:D008565, MONDO:0018815, solute carrier (slc) family of transporters]] | \n", + "0.00 | \n", + "
| 45 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_HEME_METABOLISM-1 | \n", + "[[GO:0005515, GO:0003824, GO:0008152, GO:0006082, GO:0006810, GO:0006811, GO:0006820, GO:0044281, GO:0019538, GO:0006357, GO:0003924, GO:0016740, GO:0000166, GO:0003677, GO:0000988, GO:0006163, GO:0008643, GO:0050801, GO:0003723, GO:0019899]] | \n", + "[[GO:1904659, GO:0003723, GO:0003677, GO:0000988, GO:0006811, GO:0019899, GO:0042826, GO:0140657, GO:0003824, GO:0008270]] | \n", + "0.25 | \n", + "
| 46 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_HYPOXIA-0 | \n", + "[[GO:0006096, GO:0006006, GO:0006000, GO:0005975, MESH:D004734, GO:0045333, GO:0019318, GO:0019682, triose-phosphate metabolic process, GO:0006090, GO:0006754]] | \n", + "[[GO:0006096, GO:0006006, GO:0005515, transcription regulation]] | \n", + "0.15 | \n", + "
| 47 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_HYPOXIA-1 | \n", + "[[GO:0006006, insulin signaling pathway, GO:0051726, transcriptional regulation]] | \n", + "[[GO:0006096, GO:0016310, GO:0006006, GO:0051726, GO:0007165, transcriptional regulation, heparan sulfate biosynthesis]] | \n", + "0.38 | \n", + "
| 48 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[[cytokine, receptor, t-cell, GO:0006955, GO:0065007]] | \n", + "[[cytokine signaling, GO:0042110, GO:0042113, GO:0007159, GO:0030593, GO:0050900]] | \n", + "0.00 | \n", + "
| 49 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[[GO:0004896, GO:0002224, GO:0002685, GO:0002521, GO:0002682, GO:0046649, GO:0019221, GO:0007159, GO:0051249, positive regulation of leukocyte proliferation\\n\\nmechanism: these genes are involved in the immune system response and regulation, specifically in the activation, differentiation, and migration of leukocytes. they are also involved in cytokine-mediated signaling pathways and toll-like receptor signaling pathways. the enriched terms suggest that these genes are involved in the regulation of various aspects of immune system processes, including leukocyte proliferation and adhesion]] | \n", + "[[GO:0004896, GO:0007166, GO:0045321, GO:0050900, GO:0006955, GO:0006954, GO:0002250, GO:0070663, GO:0002521, GO:0042110, GO:0042113, GO:0046649]] | \n", + "0.16 | \n", + "
| 50 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[[cytokine receptor activity; signal transduction; jak-stat cascade; cytokine-mediated signaling pathway\\n\\nmechanism: the enriched terms suggest that the commonality in gene function is the involvement of cytokine receptors and signaling pathways, particularly the jak-stat cascade, in cytokine-mediated signaling. this pathway is activated by cytokine binding to their respective receptors, leading to activation of the jak family of tyrosine kinases, which then phosphorylate and activate stat transcription factors to induce gene expression changes and cellular responses. the presence of these genes in the list suggests a potential role in regulating immune responses and inflammation through cytokine signaling]] | \n", + "[[GO:0004896, GO:0050778, GO:0007155, GO:0019221, GO:0002687]] | \n", + "0.00 | \n", + "
| 51 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[[GO:0005126, GO:0002376, GO:0001817, GO:0050776, cytokine-mediated signaling pathway\\n\\nmechanism]] | \n", + "[[GO:0004896, GO:0019221, GO:0050776, GO:0050900, apoptosis regulation, GO:0006954, antimicrobial response]] | \n", + "0.09 | \n", + "
| 52 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[[cytokine signaling, GO:0004950, GO:0004930, GO:0050900, GO:0004908, GO:0002224, GO:0005164]] | \n", + "[[GO:0005125, GO:0008009, GO:0004930, GO:0050900, inflammation\\n\\nmechanism]] | \n", + "0.20 | \n", + "
| 53 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[[GO:0004896, GO:0004930, GO:0042379, GO:0006955, GO:0006954, GO:0019221, GO:0050900, GO:0002694, GO:0002682, GO:0001819, GO:0009617, GO:0032496, GO:0070555, GO:0034612, GO:0042110]] | \n", + "[[GO:0004896, GO:0004930, GO:0004950, GO:0004888, GO:0004896]] | \n", + "0.11 | \n", + "
| 54 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[[interferon-induced protein, GO:0051607, GO:0006955, nucleotide-binding domain, leucine-rich repeat-containing receptor signaling, GO:0005764, GO:0019882, cytokine]] | \n", + "[[interferon response, GO:0051607, GO:0006955]] | \n", + "0.25 | \n", + "
| 55 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[[GO:0140888, cytokine signaling pathway, GO:0045087, GO:0009615, GO:0006952]] | \n", + "[[GO:0140888, GO:0045087, GO:0051607, cytokine signaling, GO:0019882, ubiquitin-mediated proteolysis\\n\\nmechanism: these genes are involved in the innate immune response and antiviral activity, particularly in the interferon signaling pathway. they encode proteins that regulate cytokine signaling, antigen processing and presentation, and ubiquitin-mediated proteolysis. the functions of these genes suggest a coordinated response to viral infection, with the interferon signaling pathway acting as a central mediator of the antiviral response]] | \n", + "0.22 | \n", + "
| 56 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[[interferon signaling, immune response regulation, cytokine signaling, tnf-receptor superfamily, protein tyrosine phosphatase, ubiquitin-proteasome system, MONDO:0007435]] | \n", + "[[GO:0006955, GO:0019221, chemokine signaling pathway, GO:0019882]] | \n", + "0.00 | \n", + "
| 57 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[[GO:0006955, cytokine signaling, GO:0030163, GO:0000502, ubiquitin system, viral rna sensing, MESH:D018925, GO:0019882]] | \n", + "[[GO:0045087, GO:0051607, GO:0005125, GO:0009615, GO:0001817, GO:0051607, GO:0032481, type i interferon signaling pathway. \\n\\nmechanism/]] | \n", + "0.00 | \n", + "
| 58 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[[GO:0005509, GO:0055085, GO:0007155, GO:0004672, GO:0007186]] | \n", + "[[GO:0005509, GO:0005245, GO:0006811, GO:0015085, GO:0005388, GO:0019722, GO:0055074, GO:0048306]] | \n", + "0.08 | \n", + "
| 59 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[[cytokine signaling, g-protein coupled receptor signaling, GO:0019722, protein metabolism and processing]] | \n", + "[[GO:0005509, GO:0042981, GO:0055085, GO:0006811, GO:0006468]] | \n", + "0.00 | \n", + "
| 60 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[[receptor signaling pathway, GO:0006468, negative regulation of transcription, GO:0031396, GO:0071345, GO:0032880, GO:0070374]] | \n", + "[[GO:0044425, GO:0007165, GO:0003824]] | \n", + "0.00 | \n", + "
| 61 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[[signal transduction; cytokine activity; coagulation; ion transport; extracellular matrix organization. \\n\\nmechanism: the enriched terms suggest that the commonality in the function of these genes is related to signal transduction and regulation of various biological processes, such as coagulation, GO:0005125, GO:0030198, and ion transport. specifically, these genes are involved in regulating signaling pathways that are critical for these biological processes. there are several pathways known to contribute to these enriched terms, including the jak/stat, MESH:D016328, mapk/erk, and pi3k pathways. these pathways play important roles in cell signaling, GO:0006954, GO:0006955, other cellular processes]] | \n", + "[[cytokine signaling, growth factor signaling, coagulation and complement activation, enzymatic activity regulation]] | \n", + "0.00 | \n", + "
| 62 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[[GO:0008017, GO:0007010, regulation of protein activity, GO:0051301, GO:0019894, GO:0003779]] | \n", + "[[microtubule organization, GO:0007098, GO:0030036, GO:0051726, GO:0071539]] | \n", + "0.00 | \n", + "
| 63 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[[microtubule organization, GO:0140014, GO:0051301]] | \n", + "[[GO:0008017, GO:0008574, GO:0007098, GO:0051225, GO:0003774, GO:0007010]] | \n", + "0.00 | \n", + "
| 64 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-0 | \n", + "[[GO:0046034, GO:0006629, GO:0006006, GO:0006457, GO:0046907]] | \n", + "[[GO:0006457, GO:0006006, microtubule organization and biogenesis, GO:0000502, GO:0043043, GO:0042254]] | \n", + "0.22 | \n", + "
| 65 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-1 | \n", + "[[GO:0051087, GO:0005515, GO:0006457, GO:0043161]] | \n", + "[[GO:0008152, GO:0009117, GO:0006629, GO:0005975, GO:0006457, GO:0030163, GO:0010468, GO:0000988, GO:0003682]] | \n", + "0.08 | \n", + "
| 66 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-0 | \n", + "[[GO:0006413, GO:0042254, GO:0006260, GO:0006281, GO:0008380, GO:0009117]] | \n", + "[[GO:0042254, GO:0000394, GO:0006412, GO:0006412, GO:0006457, chaperonin-mediated protein folding]] | \n", + "0.09 | \n", + "
| 67 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-1 | \n", + "[[GO:0006413, GO:0006412, GO:0042254]] | \n", + "[[GO:0042254, GO:0006413, GO:0006414, GO:0006397]] | \n", + "0.40 | \n", + "
| 68 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-0 | \n", + "[[GO:0006396, GO:0042254, rrna maturation]] | \n", + "[[GO:0006364, ribosomal subunit biogenesis, GO:0003723, nucleolar function, GO:0006412]] | \n", + "0.00 | \n", + "
| 69 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-1 | \n", + "[[GO:0006364, nucleolar rna processing, GO:0042273, GO:0003723]] | \n", + "[[GO:0006364, GO:0005730, GO:0003723, ribosomal biogenesis, GO:0051726]] | \n", + "0.29 | \n", + "
| 70 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MYOGENESIS-0 | \n", + "[[GO:0003779, GO:0006936, sarcomere assembly, GO:0005509, GO:0005861, GO:0005523, MESH:D024510, GO:0005524, GO:0004672, GO:0005515, GO:0032982]] | \n", + "[[GO:0006936, muscle metabolism, GO:0007010]] | \n", + "0.08 | \n", + "
| 71 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MYOGENESIS-1 | \n", + "[[GO:0006936, GO:0005861, GO:0005509, GO:0003779, sarcomere organization and biogenesis]] | \n", + "[[GO:0005861, MESH:M0013780, MESH:D018995, GO:0006936, GO:0005509, sarcomere assembly, MESH:D024510]] | \n", + "0.33 | \n", + "
| 72 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-0 | \n", + "[[GO:0007219, GO:0016567, GO:0001709, GO:0016055]] | \n", + "[[GO:0007219, basic helix-loop-helix transcription factor activity, GO:0016567, GO:0016563, GO:0005102, GO:0097153, GO:0006468]] | \n", + "0.22 | \n", + "
| 73 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-1 | \n", + "[[GO:0007219, GO:0016567]] | \n", + "[[GO:0007219, GO:0016567, transcriptional regulation, GO:0001709]] | \n", + "0.50 | \n", + "
| 74 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[[GO:0006754, GO:0022900, GO:0005746, GO:0006119]] | \n", + "[[GO:0005739, GO:0006119, GO:0022900, MESH:D004734, GO:0031966, MESH:D024101]] | \n", + "0.25 | \n", + "
| 75 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[[GO:0005746, GO:0006119, mitochondrial metabolism, complex i-v, energy production]] | \n", + "[[GO:0005746, GO:0006754, GO:0022900, GO:0006119]] | \n", + "0.29 | \n", + "
| 76 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_P53_PATHWAY-0 | \n", + "[[GO:0006281, GO:0010468, GO:0008083]] | \n", + "[[cyclin family, GO:0006281, GO:0008083, GO:0004672, GO:0000988, zinc finger protein]] | \n", + "0.29 | \n", + "
| 77 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_P53_PATHWAY-1 | \n", + "[[GO:0006281, GO:0051726, GO:0007165, GO:0006915, MESH:D016207]] | \n", + "[[GO:0008083, transcriptional regulation, GO:0006915, GO:0006281]] | \n", + "0.29 | \n", + "
| 78 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[[GO:0006006, insulin signaling, pancreatic development, neuroendocrine regulation]] | \n", + "[[GO:0006006, insulin regulation, GO:0031016, GO:0006096, GO:0006094, GO:0030073, hormone regulation]] | \n", + "0.10 | \n", + "
| 79 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[[GO:0006006, pancreatic islet development, neuroendocrine differentiation, GO:0007269, MESH:D009473]] | \n", + "[[GO:0006006, GO:0030073, pancreatic islet development, neuroendocrine differentiation]] | \n", + "0.50 | \n", + "
| 80 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PEROXISOME-0 | \n", + "[[atp binding cassette transporter activity, GO:0006631, GO:0042445, GO:0008289, GO:0043574, GO:0005502]] | \n", + "[[GO:0140359, GO:0055085, atp-binding cassette, GO:0043574, GO:0006631, GO:0006839]] | \n", + "0.20 | \n", + "
| 81 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PEROXISOME-1 | \n", + "[[GO:0005777, GO:0006635, antioxidant response, mitochondrial carrier protein]] | \n", + "[[GO:0005777, GO:0006631, beta-oxidation, MESH:D018384, antioxidant defense mechanism, coenzyme a ligase, aldehyde dehydrogenase family, MESH:D009195]] | \n", + "0.09 | \n", + "
| 82 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[[GO:0004672, GO:0035556, GO:1902531, GO:0050794, GO:0003824, cytoskeletal regulation]] | \n", + "[[GO:0004672, intracellular signaling, GO:0050794]] | \n", + "0.29 | \n", + "
| 83 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[[GO:0004672, GO:0007165, GO:0006468, GO:0035556]] | \n", + "[[GO:0016301, GO:0006468, GO:0007165]] | \n", + "0.40 | \n", + "
| 84 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-0 | \n", + "[[GO:0005794, GO:0005480, GO:0005764]] | \n", + "[[GO:0005794, membrane trafficking, GO:0016192, GO:0015031, GO:0006906, GO:0035493, GO:0005793]] | \n", + "0.11 | \n", + "
| 85 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-1 | \n", + "[[golgi transport, GO:0016192, GO:0015031, GO:0008104, GO:0032880, GO:0006886, GO:0016197]] | \n", + "[[GO:0007030, GO:0006888, GO:0016192, GO:0007040, sorting nexin-containing complex, GO:0030665, GO:0032880]] | \n", + "0.17 | \n", + "
| 86 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[[GO:0016209, GO:0006749, GO:0016491]] | \n", + "[[antioxidant activity; redox regulation; catalytic activity, UBERON:0035930, such as water and oxygen. the over-representation of terms related to antioxidant activity, redox regulation, and responding to oxidative stress suggest that these genes are involved in maintaining the balance between oxidants and antioxidants in the body, help protect against oxidative damage]] | \n", + "0.00 | \n", + "
| 87 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[[GO:0016209, redox regulation, MESH:D018384]] | \n", + "[[oxidative stress response, antioxidant defense, regulation of reactive oxygen species, GO:0006749, superoxide anion radical metabolism, peroxiredoxin-mediated detoxification]] | \n", + "0.00 | \n", + "
| 88 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-0 | \n", + "[[GO:0051726, GO:0003677, GO:0003723, GO:0016301, transcription regulation, chromatin organization and modification]] | \n", + "[[GO:0008584, GO:0007283, GO:0097722, GO:0007340, GO:0048232, testicular germ cell proliferation\\n\\nmechanism and]] | \n", + "0.00 | \n", + "
| 89 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-1 | \n", + "[[GO:0005515, enzymatic activity, GO:0006811]] | \n", + "[[GO:0006811, GO:0006468, MESH:D054875, GO:0007283, receptor signaling]] | \n", + "0.14 | \n", + "
| 90 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[[growth factor signaling, transcriptional regulation, smad/tgf-beta signaling pathway, cellular differentiation]] | \n", + "[[tgf-beta signaling pathway, transcriptional regulation, GO:0007165, cell growth and differentiation]] | \n", + "0.14 | \n", + "
| 91 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[[GO:0005024, GO:0060395, GO:0030509]] | \n", + "[[tgf-beta signaling pathway, GO:0030509, GO:0071141, GO:0004674, GO:0008134, GO:0006468, GO:0030154, GO:0060348, GO:0042981, GO:0034436]] | \n", + "0.08 | \n", + "
| 92 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[[GO:0006955, cytokine signaling pathway, transcription regulation. \\n\\nmechanism: these genes are primarily involved in regulating the immune response through the cytokine signaling pathway. they also play a role in transcriptional regulation of genes involved in these pathways. overall, these genes are important in regulating the response to pathogens and maintaining immune homeostasis]] | \n", + "[[GO:0004950, GO:0005125, GO:0006955, GO:0006954, GO:0050900, GO:0007165]] | \n", + "0.12 | \n", + "
| 93 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[[cytokine signaling pathway, GO:0002682, GO:0006351, GO:0006355, GO:0050900, GO:0006954, GO:0050727, GO:0032496, GO:0002237, GO:0009615, GO:0045893, GO:0045892]] | \n", + "[[interleukin signaling, GO:0032602, GO:0006955]] | \n", + "0.00 | \n", + "
| 94 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[[GO:0044183, GO:0006457, GO:0006396, cellular stress response, GO:0006401]] | \n", + "[[endoplasmic reticulum stress response, GO:0006457, GO:0008380, GO:0006402, mrna localization, translation regulation, stress response]] | \n", + "0.09 | \n", + "
| 95 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[[GO:0006457, GO:0006396, GO:0006413, endoplasmic reticulum stress response, GO:0042254]] | \n", + "[[GO:0006457, GO:0061077, GO:0015031, GO:0006413, GO:0003723, MESH:D020365, GO:0042254, aminoacyl-trna synthesis, GO:0005783, MESH:D005786]] | \n", + "0.25 | \n", + "
| 96 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-0 | \n", + "[[GO:0006816, cytoskeletal organization, cell signaling, protein regulation]] | \n", + "[[GO:0030198, GO:0007155, GO:0006811, GO:0004672, transcription regulation, receptor signaling pathway]] | \n", + "0.00 | \n", + "
| 97 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-1 | \n", + "[[GO:0030198, GO:0007165, GO:0006811]] | \n", + "[[GO:0030198, GO:0030155, GO:0006468, positive regulation of cellular signaling pathway activity, GO:0022604, GO:0072659]] | \n", + "0.12 | \n", + "
| 98 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-0 | \n", + "[[GO:0006810, GO:0003824, regulation of transcription, GO:0016310, GO:0005515, GO:0006950, GO:0006915, GO:0006811, GO:0005524, GO:0007165, GO:0005975]] | \n", + "[[GO:0006810, GO:0008152, GO:0003824]] | \n", + "0.17 | \n", + "
| 99 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-1 | \n", + "[[GO:0008152, GO:0005515, GO:0007165, GO:0009165, GO:0006468, transcription factor activity\\n\\nmechanism: these enriched terms suggest that the commonality between these genes is their involvement in fundamental biological processes required for normal cell function. these include metabolism, signal transduction, and protein biosynthesis and regulation. the transcription factor activity term suggests that some of these genes may be transcriptional regulators, controlling the expression of other genes involved in these processes. overall, these genes likely work together to maintain cellular homeostasis and respond to internal and external cues]] | \n", + "[[GO:0003723, GO:0003677, GO:0000166, GO:0006396, GO:0006260]] | \n", + "0.00 | \n", + "
| 100 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[[wnt signaling pathway regulation, transcriptional regulation, GO:0051726]] | \n", + "[[GO:0016055, transcriptional regulation, cell cycle progression]] | \n", + "0.20 | \n", + "
| 101 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[[GO:0016055, GO:0008013, transcription regulation]] | \n", + "[[GO:0016055, GO:0051726, transcriptional regulation]] | \n", + "0.20 | \n", + "
| 102 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "T cell proliferation-0 | \n", + "[[GO:0006955, GO:0007165, GO:0001816, cell proliferation and differentiation, GO:0042981]] | \n", + "[[cytokine, MESH:D007378, MESH:D011948, GO:0005530, GO:0008180, GO:0000502, protein tyrosine phosphatase, MESH:D010770, GO:0000981]] | \n", + "0.00 | \n", + "
| 103 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "T cell proliferation-1 | \n", + "[[cytokine, GO:0006955, GO:0023052, receptor, t cell]] | \n", + "[[cytokine signaling, tnf-receptor superfamily, GO:0006955, GO:0007165, GO:0019882, cell proliferation and survival, protein phosphorylation and kinase activity]] | \n", + "0.09 | \n", + "
| 104 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "Yamanaka-TFs-0 | \n", + "[[MESH:D047108, stem cell pluripotency, MESH:D063646, cell cycle progression]] | \n", + "[[MESH:D047108, GO:0001709, cell cycle progression]] | \n", + "0.40 | \n", + "
| 105 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "Yamanaka-TFs-1 | \n", + "[[MESH:D047108, stem cell maintenance, GO:0010468]] | \n", + "[[MESH:D047108, GO:0048863, pluripotent stem cell, transcription factor regulation, homeobox protein]] | \n", + "0.14 | \n", + "
| 106 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "amigo-example-0 | \n", + "[[GO:0030198, GO:0007155, GO:0007229, GO:0051495, GO:0002576]] | \n", + "[[GO:0031012, GO:0007155, MESH:D011509, GO:0005202, integrin]] | \n", + "0.11 | \n", + "
| 107 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "amigo-example-1 | \n", + "[[GO:0030198, GO:0007155, GO:0006029, GO:0042339, GO:0007229, GO:0030168]] | \n", + "[[GO:0030198, GO:0007155, GO:0016477, GO:0009888, GO:0042246, signaling pathway regulation, GO:0030168]] | \n", + "0.30 | \n", + "
| 108 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_0-0 | \n", + "[[GO:0055085, GO:0006811, GO:0005524, zinc finger domain binding, GO:0007186, GO:0000988]] | \n", + "[[GO:0006351, GO:0005515, MESH:D016335, GO:0005509, MESH:D008565]] | \n", + "0.00 | \n", + "
| 109 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_0-1 | \n", + "[[GO:0019722, GO:0000988, GO:0055085]] | \n", + "[[calcium binding, receptor protein activity, GO:0000988, GO:0005515]] | \n", + "0.17 | \n", + "
| 110 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_1002-0 | \n", + "[[GO:0006936, GO:0007015, GO:0032972, GO:0005509, GO:0005861, GO:0005865, GO:0003779, GO:0045214, GO:0005523, GO:0017022, GO:0045932, skeletal muscle thin filament, cardiac muscle thin filament]] | \n", + "[[GO:0006936, GO:0005509, GO:0043269, GO:0032516, GO:0051015]] | \n", + "0.12 | \n", + "
| 111 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_1002-1 | \n", + "[[GO:0006936, GO:0051015, GO:0005523, calcium binding, myofibril assembly.\\n\\nmechanism: these genes are involved in the regulation and maintenance of muscle structure and the contraction cycle. they act through the interaction of actin and myosin filaments, with the regulation of calcium ions controlling muscle contraction. the proteins encoded by these genes are involved in ion channel regulation, protein binding and modification, and energy metabolism]] | \n", + "[[GO:0006936, GO:0005509, GO:0051015, GO:0043462, GO:0097009, GO:0006811]] | \n", + "0.22 | \n", + "
| 112 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "endocytosis-0 | \n", + "[[GO:0006897, intracellular trafficking, cytoskeleton reorganization]] | \n", + "[[GO:0006897, GO:0007010, GO:0007165, GO:0006629, GO:0060348, brain development. \\n\\nhypotheses: these genes may be involved in common pathways related to endocytic vesicle trafficking, cytoskeletal organization, and signal transduction. some of the genes are associated with lipid metabolism and bone and brain development, suggesting their potential roles in cellular processes related to these functions]] | \n", + "0.12 | \n", + "
| 113 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "endocytosis-1 | \n", + "[[GO:0006897, GO:0016192, intracellular signaling, GO:0015031, cytoskeletal organization]] | \n", + "[[GO:0006897, intracellular trafficking, cytoskeletal reorganization]] | \n", + "0.14 | \n", + "
| 114 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "glycolysis-gocam-0 | \n", + "[[glucose metabolism; glycolysis\\n\\nmechanism: these genes play a role in converting glucose to produce energy in the form of atp. hexokinase (hk1) and glucose phosphate isomerase (gpi) are involved in the initial steps of glucose metabolism, while phosphofructokinase (pfkm), MESH:D005634, and pyruvate kinase (pkm) are involved in glycolysis. triosephosphate isomerase (tpi1) and glyceraldehyde-3-phosphate dehydrogenase (gapdh) are also involved in glycolysis and produce atp by oxidizing glucose. phosphoglycerate mutase (pgam2) and enolase (eno3) are also involved in glycolysis and help convert glucose to pyruvate, which can then be converted to atp]] | \n", + "[[GO:0006096, GO:0006006, MESH:D004734]] | \n", + "0.00 | \n", + "
| 115 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "glycolysis-gocam-1 | \n", + "[[GO:0006096, GO:0005975, energy pathway]] | \n", + "[[GO:0006096, GO:0006006, GO:0004743, GO:0019682, GO:0006000, phosphoenolpyruvate metabolic process]] | \n", + "0.12 | \n", + "
| 116 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "go-postsynapse-calcium-transmembrane-0 | \n", + "[[GO:0006816, GO:0004970, n-methyl-d-aspartate receptor complex, GO:0043269, GO:0014069, GO:0007165]] | \n", + "[[GO:0006816, intracellular calcium homeostasis, ionotropic glutamate receptor regulation, nmda receptor subunits, sodium/calcium exchanger proteins, trp ion channel family]] | \n", + "0.09 | \n", + "
| 117 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "go-postsynapse-calcium-transmembrane-1 | \n", + "[[GO:0006816, GO:0005509, GO:0005216, GO:0005102, GO:0007268, GO:0030594]] | \n", + "[[GO:0005509, GO:0005262, GO:0004970, calcium-mediated signaling pathway, GO:0007268, GO:0031175, GO:0005216]] | \n", + "0.30 | \n", + "
| 118 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "go-reg-autophagy-pkra-0 | \n", + "[[summary: regulation of cellular processes, including cell growth and metabolism, GO:0006915, GO:0006955, and regulation of chromatin remodeling and transcription.\\n\\nmechanism: these genes function in various pathways involved in the regulation of cellular processes. akt1 and pik3ca are involved in the pi3k/akt/mtor signaling pathway, which regulates cell growth, MESH:D013534, and metabolism. casp3 is a protease involved in the execution-phase of cell apoptosis. ccny and cdk5r1 are involved in the regulation of cell division cycles and the development of the central nervous system. hspb1 plays an important role in cell differentiation, but its overexpression may promote cancer cell proliferation and metastasis while protecting cancer cells from apoptosis. irgm regulates autophagy formation in response to intracellular pathogens. kat5 is a histone acetylase that has a role in dna repair and apoptosis and is thought to play an important role in signal transduction. mlst8, rptor, and smcr8 are involved in the torc1 signaling pathway, which regulates protein synthesis and cell growth in response to nutrient and insulin levels. nod2 is a pattern recognition receptor that detects cytosolic nucleic acids and trans]] | \n", + "[[MESH:D002470, GO:0016301, GO:0009966, GO:0001558, GO:0042981, GO:0010506, GO:0032006]] | \n", + "0.00 | \n", + "
| 119 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "go-reg-autophagy-pkra-1 | \n", + "[[GO:0038202, GO:0032006, GO:0010605, activation of map3k7/tak1]] | \n", + "[[GO:0016049, GO:0004672, GO:0006955, GO:0007165, GO:0000988, neuronal development, GO:0006468]] | \n", + "0.00 | \n", + "
| 120 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[[GO:0005764, glycoside hydrolase activity, GO:0005975, GO:0016787, GO:0006027, GO:0005980, GO:0006689, GO:0015929, acid hydrolase activity, chitin catabolic process\\n\\nmechanism: these genes participate in the lysosomal degradation of various carbohydrate molecules, breaking them down into their component parts for further processing by the cell]] | \n", + "[[glycosyl hydrolase activity, degradation of carbohydrates, GO:0006032, GO:0030211, GO:0003796, GO:0030214]] | \n", + "0.00 | \n", + "
| 121 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[[GO:0004559, GO:0004415, lysosomal enzyme activity, GO:0016798, GO:0006487]] | \n", + "[[GO:0016787, GO:0044248, GO:0006027, GO:0005764]] | \n", + "0.00 | \n", + "
| 122 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "ig-receptor-binding-2022-0 | \n", + "[[immunoglobulin receptor binding activity, GO:0002253, GO:0098542, GO:0002922, b cell-mediated immunity]] | \n", + "[[GO:0019731, GO:0098542, GO:0002253, immunoglobulin receptor binding activity]] | \n", + "0.50 | \n", + "
| 123 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "ig-receptor-binding-2022-1 | \n", + "[[GO:0002250, GO:0002376, antigen binding activity, immunoglobulin receptor binding activity. \\n\\nmechanism: the enriched terms suggest that these genes are involved in the recognition and response to specific foreign antigens encountered by the immune system. antigen binding activity enables the binding of specific antigens, while immunoglobulin receptor binding activity allows for the activation and signaling of immune cells. together, these genes contribute to the adaptive immune response and immune system processes by recognizing and responding to diverse foreign antigens]] | \n", + "[[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253]] | \n", + "0.17 | \n", + "
| 124 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "meiosis I-0 | \n", + "[[meiotic recombination; homologous recombination; chromosome segregation during meiosis; double-strand break repair via homologous recombination.\\n\\nmechanism: these genes are all involved in the meiotic cell cycle process, specifically in events related to recombination, repair, and segregation of chromosomes during meiosis. the proteins encoded by these genes interact with each other to form protein complexes that are essential for proper meiotic division. the enriched terms indicate a strong association with meiotic recombination and double-strand break repair via homologous recombination. additionally, they suggest a role in chromosome segregation during meiosis]] | \n", + "[[GO:0140013, GO:0035825, GO:0007059, GO:0006281, GO:0000795]] | \n", + "0.00 | \n", + "
| 125 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "meiosis I-1 | \n", + "[[meiotic recombination, GO:0006281, GO:0035825, GO:0007059, GO:0006302, holliday junction, rad51, GO:0007127]] | \n", + "[[meiotic recombination, GO:0006281, GO:0007059, GO:0035825, holliday junction resolution, double-strand dna binding, GO:0007276, GO:0007130]] | \n", + "0.33 | \n", + "
| 126 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "molecular sequestering-0 | \n", + "[[GO:0005515, GO:0006955, intracellular transport\\n\\nmechanism/]] | \n", + "[[GO:0006955, GO:0051726, GO:0046907]] | \n", + "0.20 | \n", + "
| 127 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "molecular sequestering-1 | \n", + "[[GO:0006810, regulation of cell growth and survival, GO:0010468, GO:0006915]] | \n", + "[[GO:0051726, GO:0006955, GO:0005515]] | \n", + "0.00 | \n", + "
| 128 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "mtorc1-0 | \n", + "[[GO:0046034, GO:0006629, GO:0006006, GO:0006457, GO:0046907]] | \n", + "[[GO:0006457, GO:0006006, microtubule organization and biogenesis, GO:0000502, GO:0043043, GO:0042254]] | \n", + "0.22 | \n", + "
| 129 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "mtorc1-1 | \n", + "[[GO:0000502, GO:0030163]] | \n", + "[[GO:0000502, GO:1904659, GO:0008152, GO:0003676, GO:0044183, GO:0005524, GO:0005783, GO:0005739, GO:0006096, GO:0006631]] | \n", + "0.09 | \n", + "
| 130 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "peroxisome-0 | \n", + "[[peroxisome biogenesis, GO:0016558, peroxin]] | \n", + "[[peroxisome biogenesis, peroxisomal protein import, peroxin proteins, MONDO:0019234, neonatal adrenoleukodystrophy, MONDO:0019609, MONDO:0009959, MONDO:0008972, MONDO:0009958]] | \n", + "0.09 | \n", + "
| 131 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "peroxisome-1 | \n", + "[[peroxisome biogenesis, matrix protein import, MONDO:0009279, peroxin (pex) family]] | \n", + "[[peroxisome biogenesis, GO:0005777, GO:0017038]] | \n", + "0.17 | \n", + "
| 132 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "progeria-0 | \n", + "[[GO:0006998, chromatin organization and maintenance, dna repair and recombination]] | \n", + "[[GO:0005652, GO:0005635, GO:0006281]] | \n", + "0.00 | \n", + "
| 133 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "progeria-1 | \n", + "[[GO:0006325, GO:0006281, nuclear stability]] | \n", + "[[GO:0006997, GO:0006281, chromatin structure organization, GO:0000723]] | \n", + "0.17 | \n", + "
| 134 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "regulation of presynaptic membrane potential-0 | \n", + "[[GO:0007268, GO:0005216, neurological function]] | \n", + "[[GO:0005216, GO:0031175, GO:0007268, GO:0042391]] | \n", + "0.40 | \n", + "
| 135 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "regulation of presynaptic membrane potential-1 | \n", + "[[GO:0005216, GO:0048666, GO:0007268]] | \n", + "[[GO:0005267, chloride ion transmembrane transport, GO:0042391, GO:0034220, GO:0030594]] | \n", + "0.00 | \n", + "
| 136 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "sensory ataxia-0 | \n", + "[[MONDO:0015626, MONDO:0005244, MONDO:0007790, GO:0043209, GO:0006264, tetratricopeptide repeat, transporter protein\\n\\nmechanism: these genes are involved in myelin upkeep and various neurological diseases associated with defects in myelin sheath synthesis and functions. they play roles in mitochondrial dna replication and transport, as well as protein transportation across the nuclear membrane. the presence of tetratricopeptide repeat motifs in these genes suggests their roles in protein-protein interactions and chaperone functions]] | \n", + "[[MONDO:0015626, MONDO:0007790, MONDO:0005244, myelin sheath maintenance, GO:0006264]] | \n", + "0.50 | \n", + "
| 137 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "sensory ataxia-1 | \n", + "[[MONDO:0011890, MONDO:0007790, MONDO:0011527, GO:0043217, peripheral myelin sheath, n-acetyl-d-glucosamine residue degradation, MESH:D008565, GO:0007399, nervous system myelination, GO:0006260]] | \n", + "[[GO:0042552, GO:0007422, GO:0016567, er-associated protein degradation.\\n\\nmechanism/]] | \n", + "0.00 | \n", + "
| 138 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "term-GO:0007212-0 | \n", + "[[GO:0007186, GO:0007189, regulation of cyclic nucleotide metabolic process, regulation of camp metabolic process]] | \n", + "[[g-protein signaling, GO:0007165, neurotransmitter activity]] | \n", + "0.00 | \n", + "
| 139 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "term-GO:0007212-1 | \n", + "[[GO:0007186, GO:0019932, GO:0007212]] | \n", + "[[g-protein signaling pathway, GO:0030594, GO:1902531]] | \n", + "0.00 | \n", + "
| 140 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "tf-downreg-colorectal-0 | \n", + "[[transcriptional regulation, GO:0006338, GO:0000988, GO:0003700, rna polymerase ii regulatory region sequence-specific dna binding, zinc finger domain, GO:0042393, nucleosome binding.\\n\\nmechanism: the enriched functions suggest that the given set of genes are involved in transcriptional regulation and chromatin remodeling. transcription factors bind to specific dna sequences and regulate gene expression, while chromatin remodeling alters the structure of chromatin to allow or prevent access to the dna by transcriptional machinery. zinc finger domain-containing proteins are involved in dna binding, and histone binding proteins facilitate the formation of transcriptionally active or inactive chromatin structures. the enriched functions suggest the potential involvement of these genes in both gene activation and repression, which may have important implications in cellular differentiation, development, and disease]] | \n", + "[[transcription regulation, GO:0006338, GO:0003700]] | \n", + "0.22 | \n", + "
| 141 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "tf-downreg-colorectal-1 | \n", + "[[transcription regulation, chromatin structure alteration, cell cycle progression, GO:0003682]] | \n", + "[[GO:0003700, GO:0006355, GO:0006325, GO:0010468, transcription factor complex\\n\\nmechanism: these genes all play a role in regulating transcription, primarily at the level of dna binding and chromatin organization. they are involved in the regulation of gene expression and the formation of transcription factor complexes]] | \n", + "0.00 | \n", + "
| 142 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "EDS-0 | \n", + "[[GO:0030198, GO:0030199, GO:0006024]] | \n", + "[[GO:0030198, GO:0043062, GO:0030199, GO:0006486, GO:0008233, GO:0008270]] | \n", + "0.29 | \n", + "
| 143 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "EDS-1 | \n", + "[[GO:0030199, GO:0030198, GO:0032964]] | \n", + "[[GO:0032963, GO:0030198, GO:0031012]] | \n", + "0.20 | \n", + "
| 144 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "FA-0 | \n", + "[[fanconi anemia pathway, homologous recombination repair pathway, dna double-strand break repair]] | \n", + "[[GO:0006281, GO:0006325, GO:0006312, GO:0006302, GO:0035825, GO:0006260]] | \n", + "0.00 | \n", + "
| 145 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "FA-1 | \n", + "[[GO:0006281, GO:0006302, GO:0035825, mitotic cell-cycle checkpoint, GO:0006974]] | \n", + "[[fanconi anemia pathway, GO:0035825, GO:0006302]] | \n", + "0.33 | \n", + "
| 146 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ADIPOGENESIS-0 | \n", + "[[GO:0006631, GO:0006869, GO:0005746, GO:0006637, GO:0032000, GO:0016042, GO:0019216, GO:0033108, GO:0035336, GO:0033539, GO:0051791]] | \n", + "[[GO:0006629, GO:0006631, mitochondrial function, GO:0006119, GO:0006099, beta-oxidation of fatty acids, GO:0006084, GO:0006637, GO:0015980, GO:0005975]] | \n", + "0.11 | \n", + "
| 147 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ADIPOGENESIS-1 | \n", + "[[GO:0006119, GO:0006631, GO:0006457, GO:0030301, GO:0019915, stress response, GO:0045333, mitochondrial metabolism, energy generation, GO:0006986, GO:0046890, GO:0032368, GO:0033344, GO:0007517, GO:0006979, GO:0001666, regulation of fatty acid catabolic process, GO:0019216]] | \n", + "[[GO:0005740, GO:0006122]] | \n", + "0.00 | \n", + "
| 148 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[[GO:0042110, GO:0030098, GO:0019221, GO:0002682, GO:0050776]] | \n", + "[[GO:0002376, GO:0042110, GO:0019221, GO:0019882, GO:0030098, GO:0050900, GO:0050778, GO:0050777, GO:0001817]] | \n", + "0.27 | \n", + "
| 149 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[[GO:0005125, GO:0008009, GO:0034341, GO:0042110, GO:0050727]] | \n", + "[[GO:0042110, cytokine signaling, GO:0019882, GO:0006955, chemokine signaling, interferon signaling, GO:0030183, GO:0050900]] | \n", + "0.08 | \n", + "
| 150 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[[GO:0006351, regulation of transcription, GO:0006629, GO:0030163]] | \n", + "[[GO:0016567, GO:0036211, GO:0008134, GO:0045892, GO:0071535, GO:0031647, GO:0043161]] | \n", + "0.00 | \n", + "
| 151 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[[GO:0006508, GO:0004672, GO:0007010, GO:0006695, GO:0045944, GO:0043066]] | \n", + "[[regulation of transcription, GO:0005515, GO:0007155, GO:0007165, GO:0016126]] | \n", + "0.00 | \n", + "
| 152 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ANGIOGENESIS-0 | \n", + "[[GO:0030198, GO:0007267, GO:0043405, GO:0042127, GO:0030155, GO:0002576]] | \n", + "[[GO:0030198, GO:0070848, GO:1903010, GO:0042060]] | \n", + "0.11 | \n", + "
| 153 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ANGIOGENESIS-1 | \n", + "[[GO:0030198, GO:0001525, vascular development, GO:0030335, GO:0001938, GO:0017015, GO:0007155]] | \n", + "[[GO:0030198, GO:0001525, GO:0007155]] | \n", + "0.43 | \n", + "
| 154 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-0 | \n", + "[[GO:0098609, GO:0034332, GO:0002159, GO:0030198]] | \n", + "[[GO:0007155, GO:0007010, GO:0048041, regulation of actin cytoskeleton, GO:0051017, GO:0046847, GO:0035023]] | \n", + "0.00 | \n", + "
| 155 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-1 | \n", + "[[GO:0070160, GO:0007155, GO:0007154, GO:0022407, GO:0043542, GO:0030198, cell junction organization and biogenesis, GO:0032956, GO:0001525, GO:0010810]] | \n", + "[[GO:0007155, GO:0016477, GO:0048870, GO:0007229, GO:0008360, focal adhesion\\n\\nmechanism: the enriched terms suggest that the common function of these genes is involved in cell adhesion and migration. these processes are essential for various biological functions such as wound healing, inflammation, and embryonic development. integrin-mediated signaling pathway and focal adhesion are two crucial pathways in cell adhesion and migration, which are perturbed in many types of cancer and autoimmune diseases. these findings may shed light on the underlying mechanism and potential targets for drug development]] | \n", + "0.07 | \n", + "
| 156 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_SURFACE-0 | \n", + "[[GO:0051716, GO:0005515, GO:0035556, GO:0007155, GO:0055085, GO:0061024, GO:0015031]] | \n", + "[[GO:0007155, GO:0023052, GO:0006810]] | \n", + "0.11 | \n", + "
| 157 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_SURFACE-1 | \n", + "[[GO:0007155, GO:0016477, GO:0007165, GO:0038023, GO:0006468, GO:0008104, GO:0055085, GO:0003824]] | \n", + "[[GO:0007155, GO:0007186, GO:0010906, GO:0050796, GO:0070528, GO:0043406, GO:0050731, GO:0051897, GO:0061024, GO:0043066]] | \n", + "0.06 | \n", + "
| 158 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_APOPTOSIS-0 | \n", + "[[GO:0006915, GO:0043123, GO:0050855, GO:0001817, GO:0002697, GO:0050670, GO:0051249, GO:0050856, GO:0034097, GO:0032496]] | \n", + "[[GO:0006915, GO:0012501, regulation of cell death\\n\\nmechanism: these genes are involved in various processes that regulate cell death. they participate in the apoptotic process, the programmed cell death that occurs in multicellular organisms. apoptosis is a complex physiological process that is essential for development and homeostasis in healthy adult tissues. these genes also contribute to the regulation of cell death, preventing or promoting apoptosis under specific conditions]] | \n", + "0.08 | \n", + "
| 159 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_APOPTOSIS-1 | \n", + "[[cellular stress response, GO:0006915, GO:0006954, GO:0043067, negative regulation of nf-kappab transcription factor, GO:0043280]] | \n", + "[[GO:0097153, GO:0006915, GO:0006954, GO:0008285, GO:0050871, GO:0001819, GO:0045944, GO:0004672, GO:0046328, GO:0010803]] | \n", + "0.14 | \n", + "
| 160 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[[GO:0006695, GO:0006699, peroxisome biogenesis]] | \n", + "[[peroxisome organization; steroid metabolic process; cholesterol metabolic process; fatty acid metabolic process; lipid metabolic process\\n\\nmechanism: \\n\\nthese genes are involved in various metabolic pathways, especially those related to lipid and sterol metabolism. many of these genes are involved in the transport of lipids and cholesterol, including the abc transporters abca1, abca2, abca3, abca4, abca5, abca6, abca8, abca9, and abcg4. other genes such as cat, ch25h, crot, cyp7a1, GO:0033783, MESH:D013253, dhcr24, and hsd17b6 are involved in the synthesis, GO:0009056, and modification of cholesterol and sterols. \\n\\nadditionally, these genes are also involved in peroxisome biogenesis and function, with genes such as pex1, pex11a, pex11g, pex12, pex13, pex16, pex19, pex26, MESH:D010758]] | \n", + "0.00 | \n", + "
| 161 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[[GO:0006629, GO:0006869, GO:0005777, mitochondrial function]] | \n", + "[[GO:0006695, GO:0006629, GO:0007031, peroxisome biogenesis, GO:0008202, GO:0006635, GO:0006699, GO:0015908, GO:0006886]] | \n", + "0.08 | \n", + "
| 162 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[[GO:0016126, GO:0006695, GO:0030301, GO:0006629, GO:0008202, GO:0042632]] | \n", + "[[GO:0006695, GO:0006629, GO:0045540, GO:0019216, GO:0016126]] | \n", + "0.38 | \n", + "
| 163 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[[GO:0006695, GO:0006629, GO:0008203, GO:0016126, GO:0008299, GO:0042632, GO:0045540, GO:0019216]] | \n", + "[[GO:0006695, GO:0006694, GO:0006629]] | \n", + "0.22 | \n", + "
| 164 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_COAGULATION-0 | \n", + "[[GO:0007596, GO:0006956, GO:0030168, GO:0042730, GO:0042060]] | \n", + "[[GO:0030198, GO:0030574, GO:0007596, GO:0042730, GO:0002576, GO:0052547, GO:0045055, GO:0045862]] | \n", + "0.18 | \n", + "
| 165 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_COAGULATION-1 | \n", + "[[GO:0030198, GO:0007596, GO:0006508, GO:0006955]] | \n", + "[[GO:0007596, GO:0006955]] | \n", + "0.50 | \n", + "
| 166 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_COMPLEMENT-0 | \n", + "[[c1q binding, GO:0006958, GO:0010951, GO:0043154, GO:2001237, GO:1903051]] | \n", + "[[GO:0006956, GO:0002576, GO:0050776, GO:0009611, blood coagulation\\n\\nmechanism: genes involved in complement activation, platelet degranulation, regulation of immune response, response to wounding, and blood coagulation are enriched in this gene set. these functions are related to the prevention of thrombosis and regulation of the immune system]] | \n", + "0.00 | \n", + "
| 167 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_COMPLEMENT-1 | \n", + "[[GO:0006955, GO:0007596, GO:0030163, GO:0006508, GO:0010951, GO:0071345, GO:0010952, GO:0030194, GO:0030449]] | \n", + "[[GO:0006955, GO:0007596, GO:0006508, GO:0030168, GO:0006954, GO:0010952]] | \n", + "0.36 | \n", + "
| 168 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_DNA_REPAIR-0 | \n", + "[[GO:0006260, GO:0006281, GO:0006397, GO:0006351, GO:0042278]] | \n", + "[[GO:0006260, GO:0006281, dna binding and packaging, GO:0009117, GO:0006338]] | \n", + "0.25 | \n", + "
| 169 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_DNA_REPAIR-1 | \n", + "[[GO:0097747, GO:0003677, GO:0006397, GO:0006281]] | \n", + "[[GO:0006260, GO:0006281, transcription elongation, GO:0006396, GO:0009117, GO:0003682]] | \n", + "0.11 | \n", + "
| 170 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_E2F_TARGETS-0 | \n", + "[[GO:0006260, GO:0007049, GO:0051301, GO:0140014, GO:0006281]] | \n", + "[[GO:0006260, GO:0007049, GO:0007052, GO:0007059, GO:0007346, GO:0006281, GO:0006334]] | \n", + "0.33 | \n", + "
| 171 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_E2F_TARGETS-1 | \n", + "[[GO:0006260, GO:0006281, GO:0071897, GO:0006302, GO:0022616, GO:0006974, GO:0000075, dna damage recognition and signaling]] | \n", + "[[GO:0006260, GO:0006281, GO:0051726, GO:0007059]] | \n", + "0.20 | \n", + "
| 172 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[[GO:0030198, GO:0043062, GO:0042277, GO:0030199, GO:0007155, GO:0007229, GO:0043410, GO:0005125, GO:0043498, GO:0010646, GO:0071711, GO:0007166, GO:0008285, GO:0070374, GO:0043236, GO:0005509, GO:0030335]] | \n", + "[[GO:0030198, GO:0030199, GO:0032964, GO:0071711, regulation of growth factor signaling, regulation of bmp signaling, regulation of tgf-beta signaling]] | \n", + "0.14 | \n", + "
| 173 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[[GO:0030198, GO:0007155, GO:0005604, GO:0005581, GO:0007229, GO:0005925, GO:0005515, ecm-receptor interaction, GO:0030334, GO:0007010]] | \n", + "[[GO:0030198, GO:0007155, GO:0007229, GO:0030574, GO:0009888, GO:0016477, GO:0071711]] | \n", + "0.21 | \n", + "
| 174 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[[GO:0006811, GO:0006631, GO:0006006, GO:0032870, GO:0008203, drug binding]] | \n", + "[[GO:0005509, GO:0006816, GO:0005516, GO:0010857, GO:0055074, GO:0005262, GO:0030899]] | \n", + "0.00 | \n", + "
| 175 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[[GO:0006629, GO:0007165, transcriptional regulation]] | \n", + "[[GO:0006811, GO:0023051, transport of small molecules, GO:0072657, GO:0009966, GO:0008202, GO:0010817, GO:0048522, GO:0010468, GO:0043066, GO:0051246, GO:0071363]] | \n", + "0.00 | \n", + "
| 176 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[[GO:0006351, GO:0008152, GO:0008283, GO:0006955, GO:0007165]] | \n", + "[[GO:0005509, GO:0051302, GO:0042981, GO:0006816]] | \n", + "0.00 | \n", + "
| 177 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[[GO:0008152, GO:0007165, GO:0032502, GO:0006955, GO:0006351, GO:0019538, GO:0006810, GO:0001558, GO:0042981, GO:0006811]] | \n", + "[[GO:0051726, GO:0008283, GO:0006260, GO:0051301, cancer progression]] | \n", + "0.00 | \n", + "
| 178 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[[1. metabolic process \\n2. oxidation-reduction process \\n3. response to oxidative stress \\n4. lipid metabolic process \\n5. carbohydrate metabolic process \\n6. amino acid metabolic process \\n7. detoxification \\n8. fatty acid beta-oxidation \\n9. tca cycle \\n10. electron transport chain \\n11. glucose homeostasis \\n12. protein folding and stabilization \\n13. ion homeostasis]] | \n", + "[[GO:0006635, mitochondrial beta-oxidation of fatty acids, GO:0015980, GO:0008152, GO:0044255, GO:0006084, coenzyme metabolic process, GO:0001676, GO:0019752, GO:0006099]] | \n", + "0.00 | \n", + "
| 179 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[[GO:0006629, oxidative stress response, energy production]] | \n", + "[[GO:0006631, MESH:D004734, mitochondrial function, GO:0016042, oxidative stress response]] | \n", + "0.14 | \n", + "
| 180 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-0 | \n", + "[[GO:0022402, GO:0140014, GO:0007059, GO:0007052, GO:0000226, GO:0006260]] | \n", + "[[cdc20, cdc25a, cdc25b, cdc27, cdc45, cdc6, cdc7, cdk1, cenpa, cenpe, cenpf, chek1, cks1b, cks2, dbf4, e2f1, e2f2, e2f3, e2f4, espl1, exo1, fbxo5, gins2, h2ax, h2az1, h2az2, h2bc12, hmmr, hus1, ilf3, incenp, katna1, kif11, kif15, kif20b, kif22, kif23, kif2c, kif4a, kif5b, kpna2, kpnb1, lig3, mad2l1, map3k20, mcm2, mcm3, mcm5, mcm6, ne]] | \n", + "0.00 | \n", + "
| 181 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-1 | \n", + "[[GO:0006260, GO:0007049, GO:0006281, GO:0140014, GO:0007059]] | \n", + "[[GO:0051726, GO:0006260, chromosomal segregation, GO:0051276, GO:0006281]] | \n", + "0.25 | \n", + "
| 182 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_GLYCOLYSIS-0 | \n", + "[[1. glycosylation\\n2. glycolysis\\n3. pentose phosphate pathway]] | \n", + "[[GO:0006096, GO:0005978, glycosylation pathway]] | \n", + "0.00 | \n", + "
| 183 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_GLYCOLYSIS-1 | \n", + "[[GO:0006006, energy generation, GO:0016052, GO:0006096, GO:0006090, GO:0006099, GO:0022900, GO:0006119, GO:0006754]] | \n", + "[[GO:0008152, GO:0006796, molecular function regulation, GO:0033554, GO:0031323, GO:0019538, GO:0050794, GO:0044281]] | \n", + "0.00 | \n", + "
| 184 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[[GO:0030182, GO:0007411, GO:0016477, GO:0007155, GO:0008283]] | \n", + "[[GO:0007399, nervous system neuron differentiation, nervous system development and angiogenesis, GO:0045765, GO:0023056, GO:0048598]] | \n", + "0.00 | \n", + "
| 185 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[[GO:0007399, GO:0007165, GO:0007155]] | \n", + "[[GO:0031175, GO:0007411, GO:0051960, GO:0007165, GO:0007267]] | \n", + "0.14 | \n", + "
| 186 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_HEME_METABOLISM-0 | \n", + "[[GO:0006811, GO:0005515, GO:0008152]] | \n", + "[[GO:0015886, GO:0051536, [2fe-2s] cluster binding]] | \n", + "0.00 | \n", + "
| 187 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_HEME_METABOLISM-1 | \n", + "[[GO:0048821, GO:0045646, GO:0042541, GO:0015671, GO:0020037, GO:0005506, GO:0043496, GO:0046982]] | \n", + "[[gene expression regulation; metabolism; transport\\n\\nmechanism and hypotheses:\\nthe genes in this list are involved in various cellular processes, including gene expression regulation, GO:0008152, and transport. gene expression regulation may be a mechanism by which these genes function, possibly through the involvement of transcription factors such as foxo3 and klf3. metabolism may also be a key mechanism, as many of these genes are involved in metabolic pathways, such as fech and alas2 in heme synthesis, and gclc and gclm in glutathione metabolism. transport may also be a contributing mechanism, as several genes in this list, such as slc2a1 and slc6a9, are involved in membrane transport of various molecules. overall, the commonality in function among these genes may be attributed to their roles in regulating cellular metabolism and transporting molecules across various membranes]] | \n", + "0.00 | \n", + "
| 188 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_HYPOXIA-0 | \n", + "[[GO:0008152, GO:0006096, GO:0006979, GO:0080135, GO:1901031, GO:0046324, GO:0006006, GO:0005975, GO:0006974]] | \n", + "[[GO:0006110, GO:0051246, GO:0010628, GO:0030198, GO:0006006, GO:0009749, GO:0001558, GO:0008284, GO:0051094]] | \n", + "0.06 | \n", + "
| 189 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_HYPOXIA-1 | \n", + "[[glycolysis; gluconeogenesis; citrate cycle; pyruvate metabolism; atp production\\n\\nmechanism: these genes are enriched in functions related to energy metabolism, including glycolysis, GO:0006094, the citrate cycle, GO:0006090, and atp production. they are involved in various aspects of energy metabolism, such as glucose uptake and metabolism, GO:0005980, atp synthesis. the over-representation of these functions suggests that these genes may play a role in the regulation of energy metabolism at the cellular organismal level]] | \n", + "[[hk1, hk2, pfkl, pfkfb3, gys1, pklr, pgk1, tpi1, aldoa, eno2, pgam2, pgm2, fbp1, eno1, ndst1, ndst2]] | \n", + "0.00 | \n", + "
| 190 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[[il10ra, tnfrsf18, il18r1, il1r2, il1rl1, il2ra, il2rb, il4r, MESH:D016753, MESH:D018793, tnfrsf1b, tnfrsf21, tnfrsf4, tnfrsf8, tnfrsf9, tnfsf11, tnfsf10, ifngr1, ccr4, ctla4, cxcl10, icos, irf4, irf6, irf8, socs1, socs2, ager, cish, gata1, gbp4, spp1, bcl2, bcl2l1, bmpr2, ccnd2, ccne1, cd79b, galm, glipr2, gpx4, hk2, MESH:D016753, itga6, itgae, itih5, klf6, lif, lrig1, ltb, mxd1, myc]] | \n", + "[[il2ra, il1r2, il2rb, il10ra, ctla4, cd44, MESH:D016753, il1rl1, il18r1, icos, tnfrsf4, tnfrsf18, tnfrsf8, tnfrsf21, tnfsf11, tnfrsf9, tnfsf10, tnfrsf1b, cd48, tnfrsf4, cxcl10, MESH:D018793, selp, ccne1, MESH:D047990, socs1, socs2]] | \n", + "0.39 | \n", + "
| 191 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[[cytokine signaling pathway, GO:0006955, GO:0002682, GO:0006954, leukocyte migration and chemotaxis, GO:0002694, GO:0071347, GO:0032680]] | \n", + "[[GO:0006955, cell signaling, GO:0005125, GO:0008009, GO:0008083, GO:0007166, GO:0002250, GO:0030595, GO:0050900, GO:0006954]] | \n", + "0.12 | \n", + "
| 192 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[[GO:0006955, cytokine signaling pathway, GO:0060333, positive regulation of interleukin production, GO:0032729]] | \n", + "[[GO:0019221, GO:0002757, GO:0007259, GO:0002694, regulation of leukocyte migration and chemotaxis, GO:0035456, GO:0034341, GO:0070555, GO:0070671, GO:0070741, response to tumor necrosis factor. \\n\\nhypotheses: these genes are involved in activating immune responses and cytokine-mediated signaling pathways. the enrichment of terms related to leukocyte activation and chemotaxis suggests an increased focus on the recruitment of immune cells to sites of infection and inflammation. the involvement of genes related to cytokine signaling, such as jak-stat cascade, suggests that the activation of immune responses may be regulated by cytokines released in response to infection or inflammation. overall, these genes are likely involved in the regulation of immune system activation and inflammation]] | \n", + "0.00 | \n", + "
| 193 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[[GO:0005126, GO:0006955, GO:0050900, jak-stat signaling pathway, GO:0034341, GO:0002690, GO:0051249, GO:0001817, GO:0050863, GO:0019221, GO:1902105]] | \n", + "[[cytokine signaling, GO:0006954, GO:0006955, interleukin signaling, GO:0008009, jak-stat signaling, toll-like receptor signaling]] | \n", + "0.06 | \n", + "
| 194 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[[GO:0050900, cytokine signaling, GO:0002224, GO:0006954, GO:0032729, GO:0045087, GO:0032733, GO:0030595]] | \n", + "[[cytokine signaling, GO:0006955, GO:0006954]] | \n", + "0.22 | \n", + "
| 195 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[[cytokine signaling, chemokine signaling, GO:0050900, GO:0002250, GO:0045087]] | \n", + "[[GO:0004896, GO:0042379, GO:0050900, GO:0002694, GO:0050778, GO:0045088, GO:0005149, GO:0042110, GO:0006952, GO:0006954, GO:0002685, GO:0034097]] | \n", + "0.06 | \n", + "
| 196 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[[interferon signaling, GO:0045087, antiviral defense]] | \n", + "[[GO:0051607, GO:0045087, interferon signaling, type i interferon response, viral defense]] | \n", + "0.33 | \n", + "
| 197 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[[GO:0034341, GO:0002718, GO:0060333, GO:0045070, GO:0032897, innate immune response-activating signal transduction, GO:0060337, GO:0035457, antiviral mechanism by interferon-stimulated genes (isg)]] | \n", + "[[GO:0051607, GO:0002376, GO:0140888]] | \n", + "0.00 | \n", + "
| 198 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[[GO:0051607, GO:0035458, GO:0071357, GO:0045071, GO:0031323, GO:0002682, GO:0034097, GO:0034340]] | \n", + "[[GO:0060337, GO:0006955, GO:0002579, GO:0051607, GO:0046596, GO:0032481, GO:0045087, GO:0034341, GO:0032727, GO:0002504, GO:0002479, GO:0032728, GO:0071357, GO:0043331, GO:0016032, GO:0045859, GO:0006954, GO:0060333, GO:0038187]] | \n", + "0.08 | \n", + "
| 199 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[[interferon signaling, GO:0019882, GO:0045321]] | \n", + "[[GO:0019882, interferon response, GO:0001816, GO:0006954, GO:0002376, GO:0050776, GO:0006952, GO:0009615, response to interferon]] | \n", + "0.09 | \n", + "
| 200 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[[GO:0005509, contractile fiber part, GO:0006936]] | \n", + "[[GO:0005509, GO:0070588, GO:0051924, GO:0051899, GO:0042391, GO:0071277]] | \n", + "0.12 | \n", + "
| 201 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[[GO:0043167, GO:0007165, GO:0019222, GO:0050794, g protein-coupled receptor signaling, GO:0035556, GO:0031325, GO:0043066, metabolic process regulation, GO:0005509, GO:0034765, GO:0001932, GO:0043169, GO:0045859, GO:0051716]] | \n", + "[[GO:0006811, neurological signaling, tissue development.\\n\\nmechanism]] | \n", + "0.00 | \n", + "
| 202 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[[GO:0006955, GO:0007165, GO:0050794, cytokine signaling, GO:0006954, GO:0006935, GO:0008284, GO:0043066]] | \n", + "[[GO:0006955, cellular signaling, GO:0001525]] | \n", + "0.10 | \n", + "
| 203 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[[GO:0006955, GO:0006954, GO:0002694, GO:0001817, interleukin-10 signaling, tumor necrosis factor (tnf) signaling, GO:0006956, platelet activation and aggregation, eicosanoid synthesis]] | \n", + "[[1. immune response\\n2. inflammatory response\\n3. coagulation\\n4. positive regulation of endothelial cell migration \\n5. cell adhesion\\n6. positive regulation of cell migration \\n7. signal transduction \\n8. negative regulation of apoptotic process \\n9. regulation of angiogenesis \\n10. positive regulation of protein serine/threonine kinase activity \\n11. positive regulation of transcription from rna polymerase ii promoter \\n\\nmechanism: the enriched functions suggest that these genes play an important role in innate and adaptive immune responses, inflammatory processes, GO:0007596, cell adhesion and migration, GO:0001525, and signal transduction pathways. they could be involved in regulating the expression and activity of various immune cells, MESH:D016207, chemokines to modulate immunity inflammation. the coagulation-related genes may contribute to thrombotic disorders cardiovascular diseases by affecting blood clot formation fibrinolysis. the cell adhesion migration-related genes are potentially involved in tumor metastasis progression through facilitating cell invasion motility. the signal]] | \n", + "0.00 | \n", + "
| 204 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[[GO:0007018, GO:0007052, cell division, chromosome separation]] | \n", + "[[GO:0007052, GO:0007017, GO:0051301, GO:0007010, GO:0030029]] | \n", + "0.14 | \n", + "
| 205 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[[kinesin family members, microtubule formation and stabilization, spindle formation and assembly, GO:0000910, GO:0051726, gene expression and chromosome segregation]] | \n", + "[[GO:0007051, GO:0031023, GO:0007059, GO:0071173, GO:0051382, GO:0007052, GO:0000226, GO:0007098, GO:0007020, GO:0000075, GO:0007018, GO:0007346, GO:0000070, GO:0001578, GO:0008017, GO:0000910, GO:0030953]] | \n", + "0.05 | \n", + "
| 206 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-0 | \n", + "[[GO:0006457, GO:0050776, GO:0009117, GO:0006629, gluconeogenesis and glycolysis, mrna processing and splicing]] | \n", + "[[glycolysis; tca cycle; cholesterol biosynthesis; pentose phosphate pathway\\n\\nmechanism and hypotheses:\\nthe enriched terms suggest that these genes are involved in various aspects of cellular metabolism. glycolysis is the central pathway for glucose metabolism, converting glucose into pyruvate. the tca cycle is responsible for generating energy from the breakdown of carbohydrates, MESH:D005227, and amino acids. the cholesterol biosynthesis pathway is responsible for producing cholesterol, which is involved in membrane structure, steroid hormone synthesis, and bile salt production. the pentose phosphate pathway is involved in the production of nadph, which is critical for many cellular processes, including antioxidant defense and biosynthesis.\\n\\noverall, these genes are likely involved in regulating various aspects of cellular metabolism, including energy production, biosynthesis of important molecules like cholesterol and nadph, mediating the cellular response to oxidative stress]] | \n", + "0.00 | \n", + "
| 207 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-1 | \n", + "[[GO:0044237, protein regulation, transcriptional regulation, translation regulation, GO:0006281, stress response.\\n\\nmechanism: these enriched terms suggest that the identified genes are involved in several pathways, including maintaining cellular metabolism and homeostasis, regulating transcription and translation of proteins, repairing dna in response to damage, and responding to cellular stress]] | \n", + "[[GO:0051087, GO:0006457, co-factor binding, GO:0008152, GO:0005524]] | \n", + "0.00 | \n", + "
| 208 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-0 | \n", + "[[GO:0006412, GO:0006457, GO:1990904, u4/u6.u5 tri-snrnp, chaperone-mediated protein folding.\\n\\nmechanism: these genes are involved in protein synthesis and processing, including translation and ribosome biogenesis. many of them are also involved in protein folding and chaperone-mediated protein folding. the u4/u6.u5 tri-snrnp is also highly represented, indicating these genes may be involved in splicing]] | \n", + "[[GO:0006397, GO:0006413, GO:0042254]] | \n", + "0.00 | \n", + "
| 209 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-1 | \n", + "[[GO:0006396, GO:0006413, GO:0006446, GO:0042254, GO:0008380, GO:0006397]] | \n", + "[[GO:0006396, GO:0006412, GO:0042254, GO:0006402, GO:0043488, regulation of mrna splicing, GO:0043393, GO:0008380, GO:0006417, GO:0003723]] | \n", + "0.23 | \n", + "
| 210 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-0 | \n", + "[[GO:0042254, GO:0008033, GO:0006364, GO:0016072, GO:0009451, GO:0022613]] | \n", + "[[GO:0042254, GO:0006364, GO:0003723, GO:0005681, GO:0006413]] | \n", + "0.22 | \n", + "
| 211 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-1 | \n", + "[[GO:0042254, GO:0006364, GO:0000394, rna polymerase ii regulation, rna processing and modification]] | \n", + "[[GO:0006396, GO:0022613, GO:0042254, GO:0000166, GO:0003723, GO:0090304, GO:0042273, GO:0006364, GO:0065004]] | \n", + "0.17 | \n", + "
| 212 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MYOGENESIS-0 | \n", + "[[GO:0006936, GO:0006816, z-disc, UBERON:0002036, GO:0030017, MESH:D014335, GO:0005861, GO:0071689]] | \n", + "[[muscle filament sliding; sarcomere organization; muscle system process\\n\\nmechanism: the majority of the listed genes are involved in muscle contraction and development, specifically in the organization and structure of the sarcomere. the enriched terms - muscle filament sliding, GO:0045214, muscle system process - all relate to the mechanisms of muscle contraction the intricate process of sarcomere formation]] | \n", + "0.00 | \n", + "
| 213 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MYOGENESIS-1 | \n", + "[[UBERON:0001630, MESH:D009218, MESH:D000199, MESH:D014336, filament]] | \n", + "[[GO:0003012, GO:0006936, GO:0045214, GO:0030029]] | \n", + "0.00 | \n", + "
| 214 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-0 | \n", + "[[GO:0007219, GO:0045165, GO:0022008, GO:0030154, GO:0045893, GO:0043066, GO:0008285, GO:0043065, GO:0045747, GO:0016055, GO:0007268]] | \n", + "[[GO:0007219, GO:0008593, GO:0016055, GO:0030111, GO:0045944, GO:0045596, GO:0045597]] | \n", + "0.12 | \n", + "
| 215 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-1 | \n", + "[[GO:0051726, GO:0030154, GO:0001709, transcriptional regulation, GO:0016567]] | \n", + "[[GO:0007219, GO:0005515, GO:0000122, GO:0000988]] | \n", + "0.00 | \n", + "
| 216 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[[GO:0022900, GO:0045333, GO:0002082]] | \n", + "[[GO:0042773, mitochondrial atp synthesis coupled electron transport in respiratory chain, GO:0033108, GO:0006979]] | \n", + "0.00 | \n", + "
| 217 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[[GO:0006119, GO:0005746, GO:0070469, GO:0005739, MESH:D004734, GO:0031966, GO:0006099, GO:0006635, citrate cycle, GO:0098798, GO:0006754, GO:0051536]] | \n", + "[[GO:0003954, GO:0022900, GO:0042773, GO:0005743, GO:0007005, GO:0006119, GO:0033108, respiratory chain complex i, ii, iii, iv, v, vi, GO:0006743, GO:0006631]] | \n", + "0.05 | \n", + "
| 218 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_P53_PATHWAY-0 | \n", + "[[GO:0006974, GO:0051726, cell growth and proliferation]] | \n", + "[[GO:0051726, GO:0006915, GO:0008285, GO:0006974, negative regulation of cellular process.\\n\\nmechanism: the genes in this list are enriched in functions that regulate the cell cycle and cell death. specifically, they are involved in cell cycle arrest, apoptosis, negative regulation of cell proliferation, and response to dna damage stimulus]] | \n", + "0.33 | \n", + "
| 219 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_P53_PATHWAY-1 | \n", + "[[GO:0051726, GO:0006281, GO:0030330, GO:0000082, response to dna damage]] | \n", + "[[GO:0006974, GO:0051726, GO:0006915, GO:0006281, MESH:D002470, p53 signaling, checkpoint regulation, transcriptional regulation, GO:0006338]] | \n", + "0.17 | \n", + "
| 220 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[[pancreatic development, beta cell differentiation, GO:0030073, GO:0042593, GO:0006006]] | \n", + "[[GO:0030073, GO:0042593, GO:0003309, GO:0003323, pancreatic beta cell function, pancreatic islet cell development]] | \n", + "0.22 | \n", + "
| 221 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[[GO:0003323, GO:0030073, glucose regulation, diabetes-related pathways]] | \n", + "[[GO:0003323, GO:0030073, GO:0042593, GO:0031018, GO:0050796, GO:0006006, positive regulation of pancreatic beta cell differentiation, GO:0010827, regulation of insulin secretion by glucose]] | \n", + "0.18 | \n", + "
| 222 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PEROXISOME-0 | \n", + "[[GO:0006631, GO:0006805, steroid hormone biosynthesis]] | \n", + "[[GO:0140359, GO:0006631, GO:0006695, GO:0035357, GO:0005777]] | \n", + "0.14 | \n", + "
| 223 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PEROXISOME-1 | \n", + "[[GO:0006631, GO:0007031, GO:0015721, GO:0006282]] | \n", + "[[GO:0006631, GO:0006629, GO:0008202, GO:0030301, GO:0006641, GO:0008206, GO:0005777]] | \n", + "0.10 | \n", + "
| 224 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[[mapk cascade; pi3k-akt signaling pathway; regulation of cell proliferation\\n\\nmechanism: the enriched terms suggest that the common function of the listed genes is to regulate cellular processes related to signal transduction and cell cycle/apoptosis. the mapk cascade is a crucial signaling pathway that controls the expression of genes required for cellular proliferation, differentiation, and survival. pi3k-akt signaling pathway controls cell survival, GO:0040007, and metabolism. the enriched term \"regulation of cell proliferation\" suggests that the listed genes contribute to regulating the balance between cell growth and division. these genes could affect the rate of cellular proliferation, arresting or promoting the cell cycle or modulating apoptotic signal transduction]] | \n", + "[[GO:0016301, GO:0006468, GO:0010646, GO:0035556, regulation of map kinase activity\\n\\nmechanism: these genes are involved in several signaling pathways and primarily regulate protein kinase activity and phosphorylation. they are involved in the regulation of cell communication and intracellular signaling cascades, including the map kinase cascade]] | \n", + "0.00 | \n", + "
| 225 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[[GO:0033554, GO:0035556, GO:0006468, GO:0042981, GO:0080135]] | \n", + "[[GO:0007165, GO:0006468, GO:0008152, GO:0001558, GO:0042127, GO:0042981, GO:0045859, GO:0043408, GO:0032024, GO:0005975, GO:0010906, GO:0010604]] | \n", + "0.13 | \n", + "
| 226 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-0 | \n", + "[[GO:0016192, GO:0046907, GO:0006897, GO:0061024, GO:0008104, GO:0048193]] | \n", + "[[GO:0016192, endosome to golgi transport, GO:0006886, GO:0008104, GO:0015031, regulation of membrane organization and biogenesis]] | \n", + "0.20 | \n", + "
| 227 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-1 | \n", + "[[GO:0048193, GO:0005768, GO:0005764, GO:0006612, GO:0006886, GO:0042391, GO:0034765, GO:0005773]] | \n", + "[[GO:0006886, GO:0006891, GO:0007030, GO:0072583]] | \n", + "0.09 | \n", + "
| 228 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[[GO:0016209, GO:0051920, GO:0006749, GO:0006979, GO:0070301]] | \n", + "[[GO:0016209, redox regulation, GO:0006749, oxidation-reduction process, GO:0006979]] | \n", + "0.43 | \n", + "
| 229 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[[GO:0016209, regulation of iron ion binding, GO:0006979, GO:0048821, GO:2000378, GO:0006282, GO:0070301, GO:0050790, GO:0032092, regulation of thiol-dependent ubiquitinyl hydrolase activity, GO:0034599]] | \n", + "[[oxidative stress response, redox regulation, GO:0006749, GO:0016209, GO:0000302]] | \n", + "0.07 | \n", + "
| 230 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-0 | \n", + "[[GO:0007283, GO:0140013, GO:0007130, GO:0007281, GO:0097722, oocyte meiosis]] | \n", + "[[GO:0140013, GO:0007283, GO:0007059, GO:0051301, GO:0140014]] | \n", + "0.22 | \n", + "
| 231 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-1 | \n", + "[[GO:1903047, GO:0010971, regulation of spindle assembly checkpoint, GO:0034501, GO:0090234, GO:0051985, GO:0110028]] | \n", + "[[GO:0007052, GO:0007059, GO:0007094]] | \n", + "0.00 | \n", + "
| 232 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[[tgf-beta signaling pathway, GO:0030514, GO:0090287, GO:0030513, GO:0006351, GO:0006355, GO:0045893, GO:0000122]] | \n", + "[[GO:0030509, GO:0000122, GO:0045944, GO:0048705, GO:0007183, GO:0007179]] | \n", + "0.08 | \n", + "
| 233 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[[tgf-beta signaling pathway, GO:0030509, GO:0030513, GO:0030198, GO:0060391]] | \n", + "[[GO:0007179, GO:0030514, GO:0010990]] | \n", + "0.00 | \n", + "
| 234 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[[ccl2, ccl20, ccl4, ccl5, ccn1, ccnd1, ccrl2, cd44, cd69, cd80, cd83, cdkn1a, icam1, icoslg, ifih1, ifit2, ifngr2, GO:0043514, il15ra, MESH:D020382, il1a, il1b, GO:0070743, MESH:D015850, il6st, il7r, inhba, irf1, jag1, nfkb1, nfkb2, nfkbia, nfkbie, nr4a1, nr4a2, nr4a3, ptger4, MESH:D051546, rel, rela, relb, ripk2, stat5a, tlr2, tnf, tnfaip2, tnfaip3, tnfaip6, tnfaip8, tnfrsf9, tnfsf9, tnip1, tnip]] | \n", + "[[GO:0006955, GO:0006954, GO:0034097, GO:0050865, GO:0071624, GO:0032855, GO:0010552, GO:0051092, GO:0043406, GO:0007259, GO:0043065, GO:0004672]] | \n", + "0.00 | \n", + "
| 235 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[[cytokine signaling, GO:0000988, stress response, GO:0050776, GO:0006954]] | \n", + "[[GO:0006955, GO:0006954, GO:0032680, GO:0001816, GO:0032496, negative regulation of nf-kappab transcription factor activity.\\n\\nmechanism and]] | \n", + "0.10 | \n", + "
| 236 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[[GO:0006457, GO:0036503, upr signaling pathway]] | \n", + "[[GO:0006457, MESH:M0354322, ubiquitin-mediated proteolysis, GO:0034976, GO:0006986, GO:0006397, GO:0008380]] | \n", + "0.11 | \n", + "
| 237 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[[GO:0006457, GO:0006605, GO:0006396, GO:0006950, GO:0006417, GO:0016481, GO:0006986, GO:0006913, GO:0008380, GO:1903021, GO:0016032, GO:0032496, GO:0072659, GO:0017148, GO:0022613, negative regulation of transcription by rna polymerase]] | \n", + "[[GO:0006457, chaperone-mediated protein processing, GO:0015031, GO:0007029, GO:0006986]] | \n", + "0.11 | \n", + "
| 238 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-0 | \n", + "[[tgf-beta signaling pathway, GO:0030198, GO:0007155, GO:0030334, GO:0042127]] | \n", + "[[GO:0004672, GO:0003700, GO:0006355, GO:0035556, cytoplasmic membrane-bounded vesicle, receptor protein signaling pathway, GO:0007155, GO:0001932, GO:0007399, GO:0007498, GO:0045666]] | \n", + "0.07 | \n", + "
| 239 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-1 | \n", + "[[GO:0030198, GO:0030036, GO:0030155, GO:0007160, GO:0016477, GO:0007229, GO:0030199, GO:0035023, GO:0030178, basement membrane formation, GO:0014909]] | \n", + "[[GO:0030198, GO:0007165, GO:0008083, neural development, GO:0022008]] | \n", + "0.07 | \n", + "
| 240 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-0 | \n", + "[[GO:0006355, regulation of transcription, dna-templated; go:0044267, cellular protein metabolic process; go:0009968, GO:0009968]] | \n", + "[[GO:0033554, GO:0031323, GO:0051050, GO:0009966]] | \n", + "0.00 | \n", + "
| 241 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-1 | \n", + "[[GO:0006955, GO:0008104, GO:0051726]] | \n", + "[[GO:0008104, GO:0006950, GO:0042981, GO:0008283, GO:0006979, regulation of transcription, GO:0006974, GO:0007049, response to hypoxia.\\n\\nmechanism]] | \n", + "0.09 | \n", + "
| 242 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[[GO:0016055, GO:0007219, transcriptional regulation, GO:0030154, GO:0008283]] | \n", + "[[cellular response to wnt stimulus, GO:0090263, GO:0045746]] | \n", + "0.00 | \n", + "
| 243 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[[GO:0007219, GO:0045747, GO:0045746, GO:0045165]] | \n", + "[[GO:0016055, GO:0007219, GO:0005515, GO:0008134]] | \n", + "0.14 | \n", + "
| 244 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "T cell proliferation-0 | \n", + "[[cd28 co-stimulation, il-2 signaling, GO:0042110]] | \n", + "[[GO:0002376, GO:0042110, GO:0001816, GO:0046649, GO:0006955, GO:0007166]] | \n", + "0.12 | \n", + "
| 245 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "T cell proliferation-1 | \n", + "[[GO:0042110, GO:0051247, GO:0001817]] | \n", + "[[t cell activation; cytokine signaling; lymphocyte proliferation; immune response\\n\\nmechanism: these genes are all involved in the regulation and function of the immune system, specifically in t cell activation, GO:0046651, and cytokine signaling pathways. they play a role in immune responses to pathogens, MONDO:0007179, MONDO:0004992]] | \n", + "0.00 | \n", + "
| 246 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "Yamanaka-TFs-0 | \n", + "[[GO:0000988, transcriptional regulation, GO:0030154, GO:0008283, stem cell maintenance, MESH:D047108]] | \n", + "[[GO:0000988, GO:0003677, GO:0048863]] | \n", + "0.12 | \n", + "
| 247 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "Yamanaka-TFs-1 | \n", + "[[MESH:D047108, regulation of transcription, GO:0048863]] | \n", + "[[pluripotency, self-renewal, GO:0048863]] | \n", + "0.20 | \n", + "
| 248 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "amigo-example-0 | \n", + "[[GO:0030198, GO:0030199, GO:0001525, GO:0001568, GO:0030168, GO:0001666, GO:0001936]] | \n", + "[[extracellular matrix organization; angiogenesis; positive regulation of cell migration; positive regulation of endothelial cell migration; positive regulation of sprouting angiogenesis; positive regulation of angiogenesis; positive regulation of vascular endothelial cell migration; positive regulation of smooth muscle cell migration; positive regulation of vascular smooth muscle cell migration; positive regulation of tube formation; positive regulation of endothelial cell proliferation; positive regulation of vascular endothelial growth factor production. \\n\\nhypotheses: several of the genes in the list encode for extracellular matrix components or regulators of matrix organization, including col3a1, col5a2, lum, postn, and vcan. others, such as cxcl6, pdgfa, pf4, and vegfa, encode for angiogenic growth factors. itgav is a common denominator and is associated with integrin-mediated signaling that regulates cell adhesion, migration, angiogenesis. fgfr1 has also been shown to play a critical role in angiogenesis extracellular matrix organization by regulating downstream signaling pathways such as pi3k mapk]] | \n", + "0.00 | \n", + "
| 249 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "amigo-example-1 | \n", + "[[GO:0030198, GO:0030155, regulation of cell substrate adhesion, GO:0045785, GO:0043062]] | \n", + "[[GO:0030198, GO:0007155, GO:0001525, GO:0016477, GO:0030334, GO:0008284, GO:0043410]] | \n", + "0.09 | \n", + "
| 250 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_0-0 | \n", + "[[GO:0005509, GO:0050804, transcriptional regulation, GO:0050808]] | \n", + "[[GO:0030182, GO:0006811, GO:0000988, GO:0005509, GO:0007399, GO:0007267, synapse assembly and organization, g protein-coupled receptor signaling, GO:0003723, GO:0005515]] | \n", + "0.08 | \n", + "
| 251 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_0-1 | \n", + "[[GO:0007186, GO:0010468, GO:0007154, GO:0006355, GO:0005515, GO:0007155, GO:0001932, GO:0016055, GO:0030334, GO:0007165, GO:0043408, GO:0003677, GO:0006357, GO:0005543, GO:0051493, GO:0006811]] | \n", + "[[GO:0006396, GO:0008134, GO:0006355, GO:0003682, GO:0005634, GO:0003723, GO:0006397, transcriptional regulation, GO:0061629]] | \n", + "0.04 | \n", + "
| 252 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_1002-0 | \n", + "[[atp hydrolysis coupled calcium ion transport, GO:0030036, GO:0006936, GO:0033365, GO:0051147, GO:0014743, GO:0045214]] | \n", + "[[GO:0006936, GO:0045214, GO:0006941, GO:0060048]] | \n", + "0.22 | \n", + "
| 253 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_1002-1 | \n", + "[[GO:0006936, MESH:D024510, GO:0007519, GO:0055001, GO:0030239, GO:0007517]] | \n", + "[[GO:0006936, GO:0033275, GO:0031034, GO:0005509, GO:0045214, MESH:D024510]] | \n", + "0.20 | \n", + "
| 254 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "endocytosis-0 | \n", + "[[GO:0006897, GO:0016192, GO:0007041, GO:0007032, GO:0030163]] | \n", + "[[GO:0030301, GO:0006629, GO:0006897, GO:0030163]] | \n", + "0.29 | \n", + "
| 255 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "endocytosis-1 | \n", + "[[GO:0006897, GO:0006898, GO:0016197, GO:0015031, GO:0006886, GO:0007032, GO:0016192, endosomal sorting]] | \n", + "[[GO:0006897, GO:0007032, GO:0036010, GO:0006898, GO:0016192]] | \n", + "0.44 | \n", + "
| 256 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "glycolysis-gocam-0 | \n", + "[[GO:0006096, GO:0005975, GO:0006006, GO:0019318]] | \n", + "[[GO:0006006, GO:0006096]] | \n", + "0.50 | \n", + "
| 257 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "glycolysis-gocam-1 | \n", + "[[GO:0006096, GO:0006006, GO:0006007]] | \n", + "[[GO:0005975, GO:0006006, GO:0006096, GO:0006754]] | \n", + "0.40 | \n", + "
| 258 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "go-postsynapse-calcium-transmembrane-0 | \n", + "[[GO:0005509, GO:0005262, GO:0019722, GO:0006874, GO:0034765]] | \n", + "[[GO:0006816, GO:0015075, GO:0099601, GO:0007268, GO:0034765]] | \n", + "0.11 | \n", + "
| 259 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "go-postsynapse-calcium-transmembrane-1 | \n", + "[[GO:0005509, GO:0004970, GO:0051966, GO:0046928, GO:0005216, GO:0034765, GO:0004672, GO:0051924, GO:0051247]] | \n", + "[[GO:0005216, neurotransmitter signaling, GO:0050804, GO:0005509, GO:0008066]] | \n", + "0.17 | \n", + "
| 260 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "go-reg-autophagy-pkra-0 | \n", + "[[GO:0033554, GO:0010506, GO:0007165]] | \n", + "[[GO:0006950, GO:0006915, GO:0042981, GO:0043123, GO:0046330]] | \n", + "0.00 | \n", + "
| 261 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "go-reg-autophagy-pkra-1 | \n", + "[[GO:0097190, GO:0016485, GO:0031323]] | \n", + "[[autophagy regulation, GO:0033554, GO:0006915]] | \n", + "0.00 | \n", + "
| 262 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[[glycoside hydrolase activity, GO:0005975, GO:0006027, GO:0009311, GO:0005764, GO:0005783, catabolism of carbohydrate, MONDO:0019249]] | \n", + "[[GO:0005975, GO:0005764, GO:0016798, glycoside hydrolase activity, GO:0004556, GO:0008422, acid alpha-glucosidase activity, GO:0004565, GO:0015929, GO:0015923, n-acetylglucosaminidase activity, GO:0004308, GO:0015926, GO:0005980, GO:0006027, mucopolysaccharide catabolic process, GO:0016266, GO:0006491]] | \n", + "0.18 | \n", + "
| 263 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[[GO:0006096, metabolism of carbohydrates, GO:0019318, GO:0006013, GO:0009311, chitin catabolic/metabolic process, hyaluronan catabolic/metabolic process, glycosphingolipid metabolic/catabolic process, sialic acid catabolic/metabolic process]] | \n", + "[[GO:0005975, GO:0070085, GO:0000272, GO:0004553, GO:0015929, GO:0004556, GO:0004565]] | \n", + "0.00 | \n", + "
| 264 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "ig-receptor-binding-2022-0 | \n", + "[[GO:0002377, t cell receptor signaling, GO:0042113, t cell activation. \\n\\nhypotheses: this list of genes is heavily enriched in those involved in the function and development of b cells and t cells. specifically, they play a role in the production and function of immunoglobulins and t cell receptors, as well as the activation of these cell types. this suggests that these genes are integral to the proper functioning of the immune system]] | \n", + "[[GO:0002376, GO:0046649, GO:0002250, GO:0042113, GO:0003823, antibody-mediated immunity\\n\\nmechanism]] | \n", + "0.11 | \n", + "
| 265 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "ig-receptor-binding-2022-1 | \n", + "[[GO:0006955, GO:0046649, GO:0030098]] | \n", + "[[GO:0002377, GO:0042113, GO:0016064]] | \n", + "0.00 | \n", + "
| 266 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "meiosis I-0 | \n", + "[[meiotic recombination, crossover formation, GO:0007130, GO:0006281, GO:0035825]] | \n", + "[[GO:0006281, GO:0035825, GO:0140013, GO:0007059, GO:0007129, GO:0006974, m phase of meiosis, dna replication-independent nucleosome assembly, crossover junction formation, GO:0007281, GO:0036093, GO:0009994, GO:0007283, GO:0071173, GO:0006298, GO:0033554]] | \n", + "0.11 | \n", + "
| 267 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "meiosis I-1 | \n", + "[[GO:0007059, GO:0051321, GO:0006310, synapsis of chromosomes, GO:0051276, GO:0051177]] | \n", + "[[GO:0140013, GO:0006281, GO:0007059, MESH:D011995, GO:0035825, GO:0006302, GO:0007129, crossing-over, GO:0051276]] | \n", + "0.15 | \n", + "
| 268 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "molecular sequestering-0 | \n", + "[[GO:0002376, GO:0006950, GO:0006457, GO:0051641, GO:0006396, GO:0006829, GO:0010467, GO:0007165]] | \n", + "[[GO:0034599, GO:0001558, GO:0032088, GO:0043066, GO:0051726, GO:0010468, GO:0008285]] | \n", + "0.00 | \n", + "
| 269 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "molecular sequestering-1 | \n", + "[[GO:0006979, GO:0032088, GO:0055072, GO:0016567, GO:0043066]] | \n", + "[[GO:0006979, GO:0006974, GO:0080135, regulation of protein localization to organelles, GO:0043065, GO:0043066, GO:0008285, GO:0050821]] | \n", + "0.18 | \n", + "
| 270 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "mtorc1-0 | \n", + "[[GO:0006457, GO:0050776, GO:0009117, GO:0006629, gluconeogenesis and glycolysis, mrna processing and splicing]] | \n", + "[[glycolysis; tca cycle; cholesterol biosynthesis; pentose phosphate pathway\\n\\nmechanism and hypotheses:\\nthe enriched terms suggest that these genes are involved in various aspects of cellular metabolism. glycolysis is the central pathway for glucose metabolism, converting glucose into pyruvate. the tca cycle is responsible for generating energy from the breakdown of carbohydrates, MESH:D005227, and amino acids. the cholesterol biosynthesis pathway is responsible for producing cholesterol, which is involved in membrane structure, steroid hormone synthesis, and bile salt production. the pentose phosphate pathway is involved in the production of nadph, which is critical for many cellular processes, including antioxidant defense and biosynthesis.\\n\\noverall, these genes are likely involved in regulating various aspects of cellular metabolism, including energy production, biosynthesis of important molecules like cholesterol and nadph, mediating the cellular response to oxidative stress]] | \n", + "0.00 | \n", + "
| 271 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "mtorc1-1 | \n", + "[[GO:0006457, GO:0015031, GO:0042254]] | \n", + "[[GO:0006810, GO:0008152, GO:0006457]] | \n", + "0.20 | \n", + "
| 272 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "peroxisome-0 | \n", + "[[GO:0005778, peroxisome targeting, GO:0007031]] | \n", + "[[GO:0007031, peroxisome biogenesis, protein import into peroxisome, peroxisome membrane organization, peroxisomal matrix organization]] | \n", + "0.14 | \n", + "
| 273 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "peroxisome-1 | \n", + "[[peroxisome biogenesis, peroxisome membrane organization, GO:0016559]] | \n", + "[[GO:0007031, peroxisome biogenesis, GO:0016559]] | \n", + "0.50 | \n", + "
| 274 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "progeria-0 | \n", + "[[GO:0006281, GO:0051276, regulation of transcription]] | \n", + "[[GO:0006281, GO:0006997, GO:0010467, GO:0007568]] | \n", + "0.17 | \n", + "
| 275 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "progeria-1 | \n", + "[[GO:0006281, GO:0006325, GO:0090398]] | \n", + "[[GO:0006325, GO:0006281, GO:0000723, nuclear localization, nuclear lamina organization, genome stability regulation]] | \n", + "0.29 | \n", + "
| 276 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "regulation of presynaptic membrane potential-0 | \n", + "[[GO:0004970, GO:0099536, GO:0001505, GO:0007268, GO:0043269, GO:0005244, GO:0042391]] | \n", + "[[GO:0006811, GO:0048666, GO:0007268, GO:0042391, GO:0034765]] | \n", + "0.20 | \n", + "
| 277 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "regulation of presynaptic membrane potential-1 | \n", + "[[GO:0005216, GO:0007268, GO:0005261, GO:0007215, GO:0019228, GO:0006813, GO:0060080, MESH:D005680, sodium ion transport. \\n\\nhypotheses: \\n1. the enrichment of ion channel activity-related terms suggests that the genes play a crucial role in regulating ion transport during neuronal signaling, which in turn influences synaptic plasticity and memory formation.\\n2. the enrichment of synaptic transmission-related terms points towards the involvement of the genes in various aspects of synaptic signaling, including the glutamate and gaba receptor signaling pathways, inhibition of neuronal activity, and modulation of action potential generation. \\n3. overall, the enrichment of these terms hints at a potential interaction between the listed genes in regulating various aspects of neural signal processing, synaptic transmission, and plasticity]] | \n", + "[[GO:0005216, GO:0042803, GO:0008066, GO:0016917, GO:0005261]] | \n", + "0.17 | \n", + "
| 278 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "sensory ataxia-0 | \n", + "[[mitochondrial function, GO:0006457, GO:0030163, GO:0055085]] | \n", + "[[GO:0042552, GO:0007411, GO:0007399, GO:0008104, GO:0031175]] | \n", + "0.00 | \n", + "
| 279 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "sensory ataxia-1 | \n", + "[[\"nervous system development\", \"axon guidance\", \"myelination\", \"neuron projection\", \"synaptic transmission\"]] | \n", + "[[GO:0044237, neurological development, myelin sheath formation]] | \n", + "0.00 | \n", + "
| 280 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "term-GO:0007212-0 | \n", + "[[GO:0030594, GO:0007186, GO:0046928, GO:0007212, GO:0007188]] | \n", + "[[GO:0007186, GO:0007188, GO:0046928, GO:0032225, positive regulation of camp biosynthetic process, GO:0007194, GO:0007212, prostaglandin receptor signaling pathway]] | \n", + "0.44 | \n", + "
| 281 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "term-GO:0007212-1 | \n", + "[[g protein coupled receptor signaling pathway, g protein beta/gamma subunit complex binding]] | \n", + "[[GO:0007186, dopamine receptor activity, GO:0007188, GO:0004952, GO:0099528, d1 dopamine receptor signaling pathway]] | \n", + "0.00 | \n", + "
| 282 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "tf-downreg-colorectal-0 | \n", + "[[transcriptional regulation, GO:0006325]] | \n", + "[[transcription regulation, GO:0016569, GO:0032502, GO:0065004, GO:0006950]] | \n", + "0.00 | \n", + "
| 283 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "tf-downreg-colorectal-1 | \n", + "[[GO:0003677, regulation of transcription, GO:0003682, GO:0008134, GO:0003713, negative regulation of transcription]] | \n", + "[[GO:0003677, transcriptional regulation, GO:0010468, GO:0000988, GO:0003682, GO:0006357, GO:0006355, GO:0000977, GO:0043565, GO:0051090]] | \n", + "0.14 | \n", + "
| 284 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "EDS-0 | \n", + "[[GO:0030199, GO:0030198, GO:0006024, GO:0061448]] | \n", + "[[GO:0030199, GO:0061448, GO:0062023, GO:0030198, GO:0006024]] | \n", + "0.80 | \n", + "
| 285 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "EDS-1 | \n", + "[[GO:0030199, GO:0030198, GO:0030166, GO:0061448]] | \n", + "[[GO:0030198, GO:0030199, GO:0030166, GO:0006024, GO:0061448]] | \n", + "0.80 | \n", + "
| 286 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "FA-0 | \n", + "[[GO:0006281, GO:0000724, GO:0006513, fanconi anemia complementation group]] | \n", + "[[GO:0006281, GO:0006513]] | \n", + "0.50 | \n", + "
| 287 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "FA-1 | \n", + "[[GO:0006281, GO:0006513, GO:0000724, fanconi anemia complementation group, GO:0000785, GO:0005654, GO:0140513]] | \n", + "[[GO:0006281, GO:0006513]] | \n", + "0.29 | \n", + "
| 288 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ADIPOGENESIS-0 | \n", + "[[fad binding activity, GO:0016407, lipid binding activity, coenzyme binding, identical protein binding activity, citrate biosynthetic process]] | \n", + "[[mitochondrial function, GO:0006754, GO:0006629, GO:0005515, GO:0023052]] | \n", + "0.00 | \n", + "
| 289 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ADIPOGENESIS-1 | \n", + "[[mitochondrial respiration, mitochondrial function, GO:0008152, energy production, GO:0022900, GO:0006629, GO:0006631, GO:0006637]] | \n", + "[[GO:0005746, GO:0022900, GO:0006754, GO:0006631, GO:0015746, GO:0016746, dehydrogenase activity, GO:0016491, GO:0022857]] | \n", + "0.13 | \n", + "
| 290 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[[GO:0005125, GO:0004896, integrin binding activity, GO:0004672, GO:0000988, t-cell receptor binding activity, abc-type peptide antigen transporter activity.\\n\\nmechanism: these genes are involved in various aspects of immune response, including cytokine activity, cytokine receptor activity, and t-cell receptor binding activity. they also play a role in antigen processing and presentation through the abc-type peptide antigen transporter activity. the integrin binding activity reflects the involvement of integrins in leukocyte adhesion and migration. finally, the transcription factor activity reflects the importance of transcriptional regulation in immune responses]] | \n", + "[[GO:0005125, chemokine receptor binding activity, interleukin receptor binding activity, mhc class protein complex binding activity, identical protein binding activity\\n\\nmechanism: these genes are involved in the regulation of the immune response, including the production of cytokines and chemokines, binding to immune receptors, and mhc class protein complex binding. their common function is likely related to the regulation of the immune system and the activation of the immune response against foreign invaders]] | \n", + "0.09 | \n", + "
| 291 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[[GO:0005125, GO:0008009, mhc class ii protein complex binding activity, signaling receptor binding activity, protein kinase binding activity, integrin binding activity, identical protein binding activity, sh2 domain binding activity, GO:0004252, rna binding activity, GO:0046982, GO:0008083]] | \n", + "[[GO:0005125, chemokine receptor binding activity, GO:0004672, GO:0004896, identical protein binding activity, integrin binding activity, GO:0002376, GO:0005840, GO:0042803, GO:0042110, transcription activator activity, rna polymerase ii-specific. \\n\\nmechanism and hypotheses: these enriched terms suggest that the identified genes are involved in immune system processes such as cytokine signaling, chemokine receptor binding, and t cell activation. protein kinase activity may be involved in signaling pathways downstream of cytokine receptors or chemokine receptors. the presence of ribosome-related terms suggests these genes may play a role in protein synthesis in immune cells. the identified enriched terms point to a central role of the immune system in the functions of these genes, with potential impacts on inflammation, infection, and other immune-related diseases]] | \n", + "0.15 | \n", + "
| 292 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[[binding activity, GO:0008152, GO:0043167, nucleic acid binding. \\n\\nmechanism: the enriched terms suggest that the listed genes have a common function in binding and metabolic processes. it is possible that these genes are involved in regulating the flow and utilization of energy and molecules within cells]] | \n", + "[[GO:0006468, GO:0035556, GO:0010604]] | \n", + "0.00 | \n", + "
| 293 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[[GO:0004672, GO:0035556, GO:0000079, GO:0007166]] | \n", + "[[1. binding of metal ions \\n2. protein kinase activity \\n3. positive regulation of protein kinase activity \\n4. cytoskeletal protein binding activity \\n5. signal transduction \\n\\nmechanism: these enriched terms indicate that the genes have a role in signal transduction pathways and cytoskeletal organization. the genes are involved in the binding of metal ions and protein kinases, which are important components of these pathways. additionally, the positive regulation of protein kinase activity suggests that these genes have a role in the amplification of signal transduction through cascade-like pathways]] | \n", + "0.00 | \n", + "
| 294 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ANGIOGENESIS-0 | \n", + "[[extracellular matrix organization; cell adhesion; protein binding; signaling pathway; regulation of cell proliferation.\\n\\nmechanism: the enriched terms suggest that these genes are involved in extracellular matrix organization and cell signaling pathways that regulate cell proliferation and adhesion. many of the genes are structural constituents of the extracellular matrix and influence cell-matrix interactions. others are involved in cell signaling pathways, such as the notch and fibroblast growth factor pathways, that play critical roles in cell proliferation and differentiation. some of the genes have also been implicated in diseases involving abnormal extracellular matrix formation or cell signaling dysregulation, such as ehlers-danlos syndrome, MONDO:0004975, MONDO:0004992]] | \n", + "[[extracellular matrix organization; cell signaling; blood coagulation; lipid metabolism; immunity.\\n\\nmechanism and hypotheses: these genes appear to be involved in a variety of pathways related to extracellular matrix organization, cell signaling, and intercellular communication. specifically, several genes encode proteins that are structural components of the extracellular matrix or interact with extracellular matrix proteins, suggesting a role in tissue development, remodeling, or repair. many of these genes also participate in signaling pathways that control cell proliferation, differentiation, and migration. additionally, several genes are involved in blood coagulation and lipid metabolism, which may be related to their roles in cardiovascular disease. finally, some genes have roles in immunity and host defense against infectious pathogens, possibly contributing to susceptibility or resistance to infectious diseases. overall, these common functions may point to a greater role for extracellular matrix and signaling pathways in disease pathogenesis]] | \n", + "0.00 | \n", + "
| 295 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ANGIOGENESIS-1 | \n", + "[[UBERON:4000022, binding activity]] | \n", + "[[GO:0030198, cell signaling, protein binding activity, GO:1902533, GO:0062023]] | \n", + "0.00 | \n", + "
| 296 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-0 | \n", + "[[GO:0007010, GO:0007155, GO:0005102, kinase activity.\\n\\nmechanism: these genes are involved in the maintenance of cell structure and organization through regulation of the cytoskeleton. they also contribute to cell-cell interactions and signaling through receptor binding and kinase activity. a biological pathway that might be involved is the rho gtpase signaling pathway, which regulates actin cytoskeleton dynamics and cell adhesion]] | \n", + "[[actin filament binding activity, integrin binding activity, protein kinase binding activity, sh2 domain binding activity, cell adhesion molecule binding activity, identical protein binding activity, GO:0005096, atp binding activity, cadherin binding activity, collagen binding activity, GO:0051219, GO:0042803]] | \n", + "0.00 | \n", + "
| 297 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-1 | \n", + "[[cell adhesion: cdh3, cdh4, cdh6, cdh11, cdh15, cd276, cd209, icam5, icam2, icam1, itga3, itga9, itga10, itgb1, cldn4, cldn5, cldn6, cldn7, cldn8, cldn9, cldn11, cldn14, cldn18, cldn19\\n- protein kinase activity: cdk8, ptk2, syk, taok2, vav2, src\\n- actin filament binding: actn1, actn3, lima1, nexn, calb2, pfn1\\n- metalloendopeptidase activity: adamts5, adam23, mmp2, mmp9\\n- integrin binding: jup, vcam1, slit2]] | \n", + "[[integrin binding activity, cell adhesion molecule binding activity, sh3 domain binding activity, identical protein binding activity, actin filament binding activity, protein kinase binding activity]] | \n", + "0.00 | \n", + "
| 298 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_SURFACE-0 | \n", + "[[GO:0007165, cell surface receptor activity, protein binding activity]] | \n", + "[[GO:0005886, GO:0005615, signaling receptor binding activity, protein domain specific binding activity, protein kinase binding activity, GO:0006811, GO:0051247, GO:0010468, GO:0007155, GO:1902531]] | \n", + "0.00 | \n", + "
| 299 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_SURFACE-1 | \n", + "[[GO:0005886, GO:0009986, GO:0055085, GO:0038023, positive regulation of transcription, GO:0010468, GO:0006468, GO:0005615]] | \n", + "[[GO:0010468, signaling receptor binding activity, GO:0045944, GO:2001234, GO:0006811, GO:0060244, GO:0051965, carbohydrate binding activity, GO:1902531, GO:1904054]] | \n", + "0.06 | \n", + "
| 300 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_APOPTOSIS-0 | \n", + "[[GO:0006915, GO:0005125, transcription factor binding activity. \\n\\nmechanism/]] | \n", + "[[GO:0097190, GO:0006955, GO:0005125, identical protein binding activity, protease binding activity, enzyme binding activity, GO:0000988, dna binding activity]] | \n", + "0.10 | \n", + "
| 301 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_APOPTOSIS-1 | \n", + "[[GO:0006915, GO:0005125, GO:0010941, GO:2001233, GO:0001819, GO:0042981, GO:0043067, positive regulation of apoptotic process.\\n\\nmechanism: these genes are involved in apoptotic signaling and cytokine activity, which suggests that they play a role in regulating cell death and programmed cell death. the enriched terms suggest that these genes may be regulated by shared signaling pathways or transcriptional programs that control apoptosis and cytokine production. one potential underlying mechanism could involve the activation of pro-apoptotic proteins in response to cellular stress or damage, leading to the release of cytokines that further promote cell death. alternatively, these genes may be involved in controlling the balance between cell survival and death in response to external cues such as cytokine signaling or nutrient availability. further research is needed to fully elucidate the molecular mechanisms underlying these gene functions]] | \n", + "[[apoptotic process; cytokine activity; protein binding activity.\\n\\nmechanism: the genes in this list are involved in processes related to cell death, GO:0006955, and molecular interactions. the enriched terms suggest that these genes may be involved in pathways related to apoptosis, cytokine signaling, protein interactions. it is possible that these genes contribute to the regulation of cell death through cytokine-mediated signaling pathways protein-protein interactions]] | \n", + "0.00 | \n", + "
| 302 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[[GO:0006629, GO:0030301, GO:0006633]] | \n", + "[[cholesterol binding activity, GO:0016887, GO:0005319, GO:0008559, atp binding activity, GO:0007031, vitamin d receptor binding activity, GO:0042626]] | \n", + "0.00 | \n", + "
| 303 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[[GO:0030301, GO:0015908, GO:0007031, GO:0004467, GO:0008123, atp binding activity, ubiquitin-dependent protein binding activity. \\n\\nmechanism: these genes are likely involved in the regulation and transport of lipids, particularly cholesterol and long-chain fatty acids, in cells and tissues. peroxisomal proteins and functions may also play a role in this process, including in the regulation of lipid metabolism]] | \n", + "[[GO:0008610, GO:0006631, GO:0008203, GO:0007031, GO:0015908, peroxisome matrix targeting, abc-type transporter activity. \\n\\nmechanism]] | \n", + "0.17 | \n", + "
| 304 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[[GO:0042632, GO:0008610, GO:0010883, phospholipid binding activity, fatty acid binding activity, low-density lipoprotein particle binding activity, more]] | \n", + "[[GO:0006695, GO:0008610, GO:0019216, GO:0042632, GO:0090181]] | \n", + "0.20 | \n", + "
| 305 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[[GO:0006695, GO:0008299, GO:0055088, GO:0006646, GO:0000122, GO:0045944, GO:0070458, GO:0001676]] | \n", + "[[GO:0006695, GO:0008299, GO:0006633]] | \n", + "0.22 | \n", + "
| 306 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_COAGULATION-0 | \n", + "[[GO:0006508, complement pathways, GO:0007596, GO:0007155]] | \n", + "[[GO:0006956, GO:0050817, GO:0008237]] | \n", + "0.00 | \n", + "
| 307 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_COAGULATION-1 | \n", + "[[GO:0006508, GO:0007596, GO:0006956, negative regulation of proteolysis. \\n\\nmechanism: the enriched terms suggest that these genes are involved in the regulation of proteolytic activity in several biological processes, including blood coagulation and immune response]] | \n", + "[[metalloendopeptidase activity; serine-type endopeptidase activity; protease binding activity; identical protein binding activity; complement binding activity \\n\\nmechanism and hypotheses: these enriched terms suggest that the common mechanism or pathway involves the regulation of proteolysis and immune response, particularly the complement system. metalloendopeptidase and serine-type endopeptidase activity are involved in the proteolytic degradation of various extracellular matrix components including collagen, GO:0005577, and proteoglycan, as well as destruction of pathogenic microorganisms during immune response. protease binding activity, identical protein binding activity, and complement binding activity are involved in protein-protein interactions that regulate proteolysis and activation of complement components. therefore, the hypothesis is that the common mechanism of these genes is related to the regulation of proteolysis and complement system activity]] | \n", + "0.00 | \n", + "
| 308 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_COMPLEMENT-0 | \n", + "[[GO:0004867, protease binding activity, enzyme binding activity, calcium ion binding activity]] | \n", + "[[GO:0005515, GO:0046872, GO:0019899, GO:0042802, GO:0005524, GO:0003677, calcium ion binding. \\n\\nmechanism]] | \n", + "0.00 | \n", + "
| 309 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_COMPLEMENT-1 | \n", + "[[GO:0005515, GO:0019899, GO:0005488, GO:0004175, metal ion binding.\\n\\nmechanism: the enriched terms suggest that these genes play a role in protein-protein interactions and enzymatic reactions involving metal ions]] | \n", + "[[GO:0004222, GO:0004252, complement binding activity, heparin binding activity, GO:0008234, GO:0004869, GO:0005201, serine-type endopeptidase inhibitor activity involved in apoptotic process, GO:0004722, MESH:D011809]] | \n", + "0.00 | \n", + "
| 310 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_DNA_REPAIR-0 | \n", + "[[GO:0006281, GO:0097747, nucleotide metabolism. \\n\\nmechanism: these genes are predominantly involved in regulating dna replication, transcription, and repair. they may also play roles in the metabolism of nucleotides and nucleotide analogs that target dna synthesis. the enrichment of terms related to rna polymerase may reflect the closely intertwined nature of dna and rna synthesis]] | \n", + "[[dna binding activity, transcription initiation, rna binding activity, GO:0009117, rna splicing. \\n\\nmechanism: these genes are likely involved in regulating dna replication, transcription, and various steps in rna processing, including splicing and export from the nucleus. they could also be involved in nucleotide metabolism and/or maintaining genomic stability]] | \n", + "0.00 | \n", + "
| 311 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_DNA_REPAIR-1 | \n", + "[[GO:0006260, GO:0006281, rna transcription]] | \n", + "[[GO:0003677, GO:0003723, GO:0009117, GO:0006281, transcription initiation, protein-macromolecule adaptor activity.\\n\\nmechanism: these genes work together to maintain the integrity and expression of genetic information, with a focus on dna-related processes]] | \n", + "0.12 | \n", + "
| 312 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_E2F_TARGETS-0 | \n", + "[[GO:0006260, GO:0051726, GO:0006325]] | \n", + "[[GO:0006260, GO:0006281, GO:0051726, GO:0003682, GO:0005524, GO:0019899, GO:0042393, GO:0043130]] | \n", + "0.22 | \n", + "
| 313 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_E2F_TARGETS-1 | \n", + "[[dna binding activity, protein binding activity, enzyme binding activity, chromatin binding activity, atp binding activity, histone binding activity, rna binding activity, identical protein binding activity]] | \n", + "[[dna binding activity, chromatin binding activity, rna binding activity, enzyme binding activity, GO:0042803, single-stranded dna binding activity, identical protein binding activity, histone binding activity, atp binding activity, cyclin binding activity, nucleic acid binding activity]] | \n", + "0.58 | \n", + "
| 314 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[[GO:0005201, integrin binding activity, collagen binding activity, identical protein binding activity, fibrinogen binding activity, protease binding activity]] | \n", + "[[GO:0005201, collagen binding activity, heparin binding activity, GO:0005125, GO:0008083, signaling receptor binding activity, wnt-protein binding activity]] | \n", + "0.18 | \n", + "
| 315 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[[GO:0005201, collagen binding activity, integrin binding activity, heparin binding activity, GO:0008237, signaling receptor binding activity.\\n\\nmechanism: these genes are involved in the maintenance and formation of the extracellular matrix, which provides structural support to cells and tissues. they play a role in cell adhesion, signaling, and migration through interactions with the extracellular matrix. the enriched binding activities suggest that these genes are involved in extracellular matrix remodeling and regulation of growth factor signaling. metallopeptidase activity may be involved in the degradation of extracellular matrix components]] | \n", + "[[collagen binding activity, integrin binding activity, heparin binding activity, GO:0005201, GO:0008237, platelet-derived growth factor binding activity, GO:0008009, fibronectin binding activity, GO:0004867]] | \n", + "0.50 | \n", + "
| 316 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[[GO:0005509, GO:0000166, enzyme binding activity, MESH:D048788, gene transcription, GO:0006811]] | \n", + "[[GO:0004888, GO:0022857, GO:0001216]] | \n", + "0.00 | \n", + "
| 317 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[[GO:0005515, GO:0000988, transmembrane transporter activity.\\n\\nmechanism: the enriched terms suggest that the genes on the list are involved in various cellular processes that require protein-protein interaction, transcriptional regulation, and transmembrane transport of substances. a possible hypothesis is that these genes play a role in signal transduction and regulation of gene expression]] | \n", + "[[GO:0007165, transcriptional regulation, GO:0003824, GO:0038023, GO:0003676, GO:0007154, GO:0042445, protein-protein interaction\\n\\nhypotheses: the enriched terms suggest that the genes in this list are involved in various aspects of signaling and transcriptional regulation. they may function in pathways such as cell signaling, hormone metabolism, and protein-protein interaction. this list includes genes encoding enzymes with specific activities, as well as receptor and nucleic acid binding proteins that are crucial for signaling and transcriptional regulation]] | \n", + "0.00 | \n", + "
| 318 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[[GO:0022857, protein binding activity]] | \n", + "[[enzyme binding activity, identical protein binding activity, calcium ion binding activity, GO:0005215, phosphorylation-dependent protein binding activity, atpase binding activity, GO:0004930, GO:0004712, nucleotide binding activity, ubiquitin protein ligase binding activity, transcription factor binding activity, histone deacetylase binding activity, GO:0016787, GO:0016491]] | \n", + "0.00 | \n", + "
| 319 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[[(1) enzymatic activity; (2) binding activity; (3) transcription regulation. \\n\\nmechanism: these genes likely play roles in various biological pathways, such as metabolism, cell signaling, and gene expression regulation. given the enrichment in enzymatic activity, it is possible that some of these genes are involved in metabolic pathways, such as lipid metabolism. the enrichment in binding activity may reflect the importance of protein-protein interactions and signaling cascades in cellular processes. the enrichment in transcription regulation suggests that many of these genes may be key players in regulating gene expression and ultimately cell fate]] | \n", + "[[binding activity, GO:0005215, enzyme binding activity, identical protein binding activity, protein kinase binding activity, GO:0004930]] | \n", + "0.00 | \n", + "
| 320 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[[GO:0047617, GO:0006631, GO:0120227, GO:0008289, GO:0004467, GO:0006099, GO:0046356]] | \n", + "[[fatty acid-coa ligase activity, GO:0003995, long-chain fatty acid binding activity, GO:0003985, GO:0016615, GO:0000104, GO:0016616]] | \n", + "0.00 | \n", + "
| 321 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[[GO:0016491, binding activity, GO:0006631, GO:0006084, heme-binding activity]] | \n", + "[[GO:0003824, GO:0016491, GO:0006631, GO:0006629, metabolic pathways. \\n\\nmechanism: these genes may be involved in the regulation of lipid and fatty acid metabolism, potentially through oxidation-reduction processes and metabolic pathways]] | \n", + "0.25 | \n", + "
| 322 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-0 | \n", + "[[dna binding activity, chromatin binding activity, protein binding activity, enzyme binding activity, histone binding activity, GO:0003714]] | \n", + "[[dna binding activity, transcription regulation, GO:0004672, protein binding activity, GO:0016570]] | \n", + "0.22 | \n", + "
| 323 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-1 | \n", + "[[dna-binding transcription factor activity; protein kinase activity; microtubule binding activity. \\n\\nmechanism: these genes are likely involved in the regulation of gene expression, cell cycle progression, and cytoskeletal dynamics through the binding and modification of dna, MESH:D011506, and microtubules. specifically, they may be involved in processes such as transcriptional regulation, dna replication and repair, GO:0007059, GO:0051301]] | \n", + "[[dna-binding transcription factor, GO:0004672, protein binding activity, GO:0140014, GO:0006260, GO:0010467]] | \n", + "0.00 | \n", + "
| 324 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_GLYCOLYSIS-0 | \n", + "[[GO:0008378, GO:0015020, n-acetylglucosamine sulfotransferase activity, GO:0035250, glucosaminyl-proteoglycan 3-beta-glucosyltransferase activity, GO:0016758, GO:0045130, GO:0016779]] | \n", + "[[GO:0008194, GO:0008146, GO:0008378, GO:0015020, GO:0004553, heparan sulfate binding activity, several others]] | \n", + "0.15 | \n", + "
| 325 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_GLYCOLYSIS-1 | \n", + "[[GO:0005975, GO:0006024, GO:0006493]] | \n", + "[[enzyme binding activity, GO:0008194, atp binding activity, GO:0008378, GO:0004340, fructose binding activity, heme binding activity, GO:0016787, rna binding activity, identical protein binding activity, GO:0046983, nucleoside triphosphate activity]] | \n", + "0.00 | \n", + "
| 326 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[[GO:0006357, GO:0016525, GO:0007155, GO:0030036, GO:0010604, GO:0007411, GO:0030336]] | \n", + "[[GO:0032502, GO:0007165, MESH:D005786]] | \n", + "0.00 | \n", + "
| 327 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[[GO:0007165, GO:0007155, GO:0007399, transcription regulation]] | \n", + "[[GO:0007155, transcription regulation, GO:0007165, negative regulation, positive regulation]] | \n", + "0.50 | \n", + "
| 328 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_HEME_METABOLISM-0 | \n", + "[[GO:0020037, GO:0015075, protein binding activity, GO:0000988]] | \n", + "[[GO:0005215, binding activity, GO:0003824]] | \n", + "0.00 | \n", + "
| 329 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_HEME_METABOLISM-1 | \n", + "[[transmembrane transport; protein binding activity; metal ion binding activity; dna-binding transcription activator activity\\n\\nmechanism: these genes are involved in various transport and binding activities, especially transmembrane transport, indicating a possible importance in cellular trafficking and signaling pathways. additionally, they exhibit a significant enrichment in protein and metal ion binding activities, which may suggest a role in protein-protein interactions and redox reactions, respectively. finally, dna-binding transcription activator activity is found to be enriched, indicating that these genes may regulate gene expression]] | \n", + "[[enzyme binding activity, protein domain specific binding activity, GO:0046982, identical protein binding activity, GO:0042803]] | \n", + "0.00 | \n", + "
| 330 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_HYPOXIA-0 | \n", + "[[enzyme binding activity, GO:0005515, GO:0003700, carbohydrate binding activity, signaling receptor binding activity, identical protein binding activity, atp binding activity, nad binding activity, phosphoprotein binding activity, metal ion binding activity, GO:0003924, GO:0008083, GO:0008194, phospholipid binding activity, platelet-derived growth factor binding activity]] | \n", + "[[enzyme binding activity, protein kinase binding activity, identical protein binding activity, GO:0003700, GO:0004674, calcium ion binding activity, nucleic acid binding activity, atp binding activity, GO:0060422, gtp binding activity, GO:0004340, GO:0005353, GO:0008459, heparin binding activity, apolipoprotein binding activity]] | \n", + "0.15 | \n", + "
| 331 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_HYPOXIA-1 | \n", + "[[GO:0006006, GO:0016301, transcriptional regulation, GO:0023052]] | \n", + "[[GO:0042802, GO:0019899, GO:0005524, GO:0019901, GO:0005509, GO:0005102, GO:0015035, GO:0016538, GO:0008083, GO:0005353, GO:0004347, nadph binding activity, GO:0042803, MESH:D013213]] | \n", + "0.00 | \n", + "
| 332 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[[GO:0005125, interleukin receptor binding activity, cytokine binding activity, GO:0031295, GO:0051250, GO:0006952, GO:0006955, interleukin binding activity]] | \n", + "[[GO:0042802, GO:0003700, GO:0005125, GO:0005096, interleukin receptor binding activity, ubiquitin protein ligase activity.\\n\\nmechanism: these genes likely play a role in regulating various cell signaling pathways, including cytokine and growth factor signaling, as well as intracellular protein degradation via ubiquitin-proteasome system]] | \n", + "0.17 | \n", + "
| 333 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[[GO:0004896, interleukin binding activity, identical protein binding activity, gtp binding activity, GO:0001216, protein kinase binding activity, atp binding activity, GO:0016787, collagen binding activity, small gtpase binding activity, GO:0061630, GO:0004197, GO:0005215, rna binding activity, calcium ion binding activity, signaling receptor binding activity, GO:0005125, GO:0008083, enzyme binding activity, several others.\\n\\nmechanism: these genes are involved in immune response cytokine activity. many of them encode for cytokine receptors, transcription factors, enzymes involved in immune system pathways processes. the enrichment of terms related to protein binding, including dna binding identical protein binding, may suggest that many of these genes act as transcriptional regulators in immune cells, coordinating the expression of genes involved in immune function. the enrichment of transporter activity may indicate that some of these genes are involved in cell migration or trafficking of immune cells to sites of inflammation or infection. additionally, the enrichment of terms related to enzyme activity may suggest that some of]] | \n", + "[[GO:0004896, protein binding activity, GO:0003824, dna binding activity, rna binding activity, apoptosis. \\n\\nmechanism: these genes are involved in various cellular processes such as signaling and cytokine receptor activity, where they play a role in transmitting signals from the outside to the inside of the cell, as well as in regulating the immune system. they are also involved in enzyme activity, dna and rna binding activity, and apoptosis, playing a role in various pathways such as the regulation of gene expression and programmed cell death]] | \n", + "0.08 | \n", + "
| 334 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[[GO:0005125, GO:0004896, protein kinase binding activity, GO:0006954, GO:0006955, GO:0007165]] | \n", + "[[GO:0004896, GO:0004896, growth factor receptor binding activity]] | \n", + "0.12 | \n", + "
| 335 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[[GO:0004896, interleukin binding activity, GO:0008009, GO:0001819, GO:0050778, GO:0098542, GO:0010604]] | \n", + "[[GO:0005125, signaling receptor binding activity, GO:0001819, GO:0019221, GO:0009967, GO:0004896, GO:0050776]] | \n", + "0.17 | \n", + "
| 336 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[[GO:0005125, GO:0008009, identical protein binding activity, GO:0038023, GO:0006811]] | \n", + "[[GO:0005125, GO:0004896, GO:0004930, GO:0002376, GO:0006954, GO:0008009]] | \n", + "0.22 | \n", + "
| 337 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[[GO:0004930, GO:0004896, enzyme binding activity, identical protein binding activity, GO:0007165, calcium ion binding activity, protease binding activity, transporter activity.\\n\\nmechanism: these genes are involved in various mechanisms related to cell signaling and transport. one hypothesis is that these genes may collectively contribute to the regulation of calcium levels and calcium-dependent signaling pathways, as well as cytokine-mediated signaling pathways involved in immune response]] | \n", + "[[GO:0004896, GO:0004930, signaling receptor binding activity, identical protein binding activity, enzyme binding activity]] | \n", + "0.44 | \n", + "
| 338 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[[GO:0005125, GO:0098542, GO:0046597, rna binding activity, identical protein binding activity]] | \n", + "[[GO:0006955, GO:0019882, cytokines/chemokines, interferon-related genes, rna processing/editing]] | \n", + "0.00 | \n", + "
| 339 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[[GO:0098542, GO:0050709, GO:0046597, GO:0045071, GO:0030501, GO:0002688, regulation of transcription]] | \n", + "[[GO:0098542, GO:0045071, GO:0035458, GO:0071345, GO:0042590, GO:0006469, GO:0010604, GO:0046597, GO:0019221, GO:0045669, GO:0052548]] | \n", + "0.20 | \n", + "
| 340 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[[GO:0004896, GO:0000981, identical protein binding activity, enzyme binding activity, GO:0042110, cell adhesion molecule binding activity, positive regulation of activated cd8-positive t cell proliferation, GO:0038187, GO:0061630, GO:0000166, GO:0004930, protein kinase binding activity, calcium ion binding activity, complement binding activity, GO:0004867, GO:0008009, integrin binding activity.\\n\\nmechanism: these genes predominantly function in the immune system and are related to the activation and proliferation of t cells, cytokine signaling, pattern recognition, and complement cascades. the enriched terms suggest an association with signaling cascades, receptor binding, enzyme activity, and immune response to pathogens]] | \n", + "[[GO:0005125, GO:0008009, GO:0001216, enzyme binding activity, identical protein binding activity, protease binding activity, GO:0042803, rna binding activity, GO:0050852, GO:0061630]] | \n", + "0.17 | \n", + "
| 341 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[[GO:0019882, GO:0045087, cytokine signaling, GO:0045321, antiviral defense]] | \n", + "[[GO:0019882, cytokine signaling, antiviral defense]] | \n", + "0.60 | \n", + "
| 342 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[[calcium ion binding activity, atp binding activity, GO:0008511, GO:0004930, GO:0004888, GO:0016887, identical protein binding activity, protein kinase binding activity]] | \n", + "[[GO:0003824, protein binding activity, GO:0000988, identical protein binding activity, ion binding activity.\\n\\nmechanism]] | \n", + "0.08 | \n", + "
| 343 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[[protein binding activity, calcium ion binding activity, atp binding activity, identical protein binding activity, GO:0008507, GO:0005337, GO:0043273, GO:0003924, GO:0015432]] | \n", + "[[GO:0005488, GO:0003824, GO:0004930, GO:0000988, GO:0005509, GO:0005524, protein homodimerization activity.\\n\\nmechanism: the enriched terms suggest that these genes are involved in cellular regulation and signaling processes through binding and enzymatic activities, particularly involving calcium ions and atp. many genes also have transcription factor activity, indicating a role in gene expression regulation. g protein-coupled receptor activity is also overrepresented, suggesting a role in cellular signaling processes]] | \n", + "0.00 | \n", + "
| 344 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[[binding activity; enzyme activity; transcription activator activity. \\n\\nmechanism: these enriched terms suggest that the commonality among these genes is that they are involved in various types of binding and enzymatic activities, as well as regulating transcription. it is possible that these genes work together in regulatory pathways to bind to specific targets, catalyze reactions, modulate transcriptional activity in the cell]] | \n", + "[[GO:0005515, enzyme binding activity, transcriptional regulation, ion binding activity, dna binding activity, GO:0004930, GO:0005125, identical protein binding activity]] | \n", + "0.00 | \n", + "
| 345 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[[GO:0005178, GO:0005515, GO:0005524, GO:0071345, GO:0043167, ubiquitin protein ligase binding. \\n\\nmechanism: the shared function of binding among the enriched terms suggests that these genes may play a role in mediating protein regulation and signal transduction pathways through protein-protein or protein-ligand interactions. the involvement in cellular response to cytokine stimulus may suggest a potential role in modulating immune responses]] | \n", + "[[enzymatic activity, GO:0019901, binding activity\\n\\nmechanism: the enriched functions suggest that these genes may be involved in the regulation of cellular processes through protein-protein interactions, including enzymatic activities and binding activities. this could involve pathways such as signal transduction or gene expression regulation]] | \n", + "0.00 | \n", + "
| 346 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[[microtubule binding activity, GO:0005096, actin filament binding activity, microtubule plus-end binding activity, identical protein binding activity, protein kinase binding activity, kinetochore binding activity, cytoskeletal protein binding activity, gamma-tubulin binding activity]] | \n", + "[[microtubule binding activity, actin binding activity, GO:0005096]] | \n", + "0.20 | \n", + "
| 347 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[[microtubule binding activity, GO:0007052, GO:0000226]] | \n", + "[[GO:0008017, mitotic processes, GO:0000910, GO:0007018, spindle organization. \\n\\nmechanism: these genes play important roles in the regulation and organization of microtubules, which are key components of the cytoskeleton involved in cell division processes such as mitosis and cytokinesis. the enrichment of terms related to microtubule binding and regulation suggest that these genes may function together in a pathway that regulates the dynamics and organization of microtubules during these cellular processes. they may also be involved in microtubule-based movement, which is crucial for various cellular activities such as intracellular transport and cell migration]] | \n", + "0.00 | \n", + "
| 348 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-0 | \n", + "[[binding activity, enzymatic activity, GO:0006412, GO:0023052, GO:0008152]] | \n", + "[[GO:0005515, GO:0003723, enzymatic activity, structural constituent of cytoskeleton. \\n\\nmechanism: these genes likely play a role in cellular processes such as transcription, translation, protein folding, and cytoskeletal organization]] | \n", + "0.12 | \n", + "
| 349 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-1 | \n", + "[[GO:0005515, enzyme activity. \\n\\nmechanism: the enriched terms suggest that these genes play a role in protein-protein interactions and enzymatic reactions, potentially involved in metabolic pathways or signal transduction cascades]] | \n", + "[[GO:0006457, GO:0005783, ubiquitin-proteasome system, GO:0015031, GO:0030163]] | \n", + "0.00 | \n", + "
| 350 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-0 | \n", + "[[ribosome binding activity; rna binding activity; translation initiation factor activity; protein folding chaperone activity\\n\\nmechanism: these genes are involved in different aspects of protein synthesis, such as ribosome binding, GO:0006413, and rna binding. they also contribute to protein folding processes as chaperones. the enrichment of these terms suggests that these genes function together to ensure proper protein synthesis and folding, which are vital to numerous cellular processes]] | \n", + "[[GO:0003743, ribosome binding activity, rna binding activity, GO:0003735, protein folding chaperone activity, GO:0140713]] | \n", + "0.00 | \n", + "
| 351 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-1 | \n", + "[[GO:0006396, GO:0003676, GO:0006457, ribosomal structural activity. \\n\\nmechanism: these genes likely function together in the post-transcriptional regulation of gene expression, from rna splicing to translation initiation and ribosome assembly]] | \n", + "[[GO:0000394, GO:0006413, GO:0003723, GO:0003676, GO:0006457, ribosome structure\\n\\nmechanism: these genes are involved in rna processing, including mrna splicing and translation initiation, as well as binding to rna and nucleic acids. some genes also play roles in protein folding and ribosome structure. the underlying biological mechanism or pathway is likely related to rna processing and regulation of gene expression]] | \n", + "0.25 | \n", + "
| 352 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-0 | \n", + "[[GO:0006364, rna binding activity, GO:0046982, mitochondrial function, GO:0051726]] | \n", + "[[GO:0006364, GO:0042273, snorna binding activity, GO:0005730, rna binding activity]] | \n", + "0.25 | \n", + "
| 353 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-1 | \n", + "[[GO:0006364, snorna binding activity, GO:0042273, rna binding activity, GO:0005730]] | \n", + "[[GO:0006364, ribosomal biogenesis, rna binding activity, GO:0005730]] | \n", + "0.50 | \n", + "
| 354 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MYOGENESIS-0 | \n", + "[[cytoskeletal protein binding activity, actin binding activity, atp binding activity, calcium ion binding activity, identical protein binding activity, enzyme binding activity, GO:0042803]] | \n", + "[[actin binding activity, calcium ion binding activity, atp binding activity, identical protein binding activity, cytoskeletal protein binding activity, enzyme binding activity, UBERON:0005090]] | \n", + "0.75 | \n", + "
| 355 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MYOGENESIS-1 | \n", + "[[actin binding activity, cytoskeletal protein binding activity, calcium ion binding activity, myosin binding activity, atp binding activity, kinase binding activity, muscle structure development. \\n\\nmechanism: these genes are involved in muscle structure and function as they encode proteins that bind to actin, myosin, and other cytoskeletal proteins to form the muscle fibers. they also bind to calcium ions and atp, which are necessary for muscle contraction, and contribute to the development of muscle structure]] | \n", + "[[GO:0006936, GO:0030036, GO:0006600, GO:0032956, regulation of muscle contraction.\\n\\nmechanism: these genes are involved in the regulation of muscle contraction and actin cytoskeleton organization, likely through their roles in calcium ion binding, myosin light chain kinase activity, and actin filament binding. several of the genes are also involved in creatine metabolism, which is important for energy generation in muscle tissues]] | \n", + "0.00 | \n", + "
| 356 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-0 | \n", + "[[GO:0007219, GO:0016567]] | \n", + "[[GO:0007219, GO:0016567, GO:0006357, GO:0051247, GO:0016055, scf-dependent proteasomal ubiquitin-dependent protein catabolic process, cyclin-dependent protein kinase holoenzyme complex]] | \n", + "0.33 | \n", + "
| 357 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-1 | \n", + "[[\"notch signaling pathway,\" \"protein ubiquitination,\" \"negative regulation of cell differentiation,\" \"regulation of dna-templated transcription.\"]] | \n", + "[[GO:0007219, GO:0016567]] | \n", + "0.00 | \n", + "
| 358 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[[GO:0022900, GO:0006119, mitochondrial metabolism, GO:0006637, ketone body metabolism.\\n\\nmechanism and]] | \n", + "[[GO:0009055, ubiquitin protein ligase binding activity, MESH:D014451, rna binding activity, GO:0042803, metal ion binding activity.\\n\\nmechanism and]] | \n", + "0.00 | \n", + "
| 359 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[[GO:0005746, GO:0006118, GO:0006754, MESH:D009245, MESH:D003576, GO:0016467, flavin adenine dinucleotide]] | \n", + "[[mitochondria\\n- atp synthesis\\n- respiratory chain complex\\n- electron transfer\\n- oxidoreductase activity\\n- iron-sulfur cluster binding\\n\\nmechanism: these genes are involved in the regulation of metabolic processes and energy production in the mitochondria. they play important roles in cellular respiration, which involves the conversion of nutrients into energy necessary for cellular activities. the enriched terms suggest that these genes are closely related to the function of the mitochondrial respiratory chain complex and atp synthase, both of which are necessary for energy production in the form of atp. additionally, several of these genes are involved in electron transfer and oxidoreductase activity, which are also important in metabolic processes that lead to energy production. finally, there is a common theme of iron-sulfur cluster binding, which suggests a common mechanism in the regulation of metabolic processes and energy production]] | \n", + "0.00 | \n", + "
| 360 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_P53_PATHWAY-0 | \n", + "[[GO:0042981, protein binding activity, GO:0003700]] | \n", + "[[GO:0003677, GO:0005515, GO:0003824, GO:0000988, growth factor activity. \\n\\nmechanism: these genes likely play roles in regulating transcription, protein-protein interactions, metabolism, and growth factor signaling pathways]] | \n", + "0.00 | \n", + "
| 361 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_P53_PATHWAY-1 | \n", + "[[GO:0000988, rna binding activity, enzyme binding activity, identical protein binding activity, dna binding activity, histone binding activity]] | \n", + "[[GO:0005515, dna binding activity, GO:0016301]] | \n", + "0.12 | \n", + "
| 362 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[[GO:0006006, GO:0030073, GO:0006357]] | \n", + "[[GO:0042593, GO:0050796, GO:0046326, GO:0006006]] | \n", + "0.17 | \n", + "
| 363 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[[GO:0006006, GO:0030073, glucose homeostasis.\\n\\nmechanism]] | \n", + "[[GO:0030073, GO:0006006, transcriptional regulation, transcription factor binding activity, rna polymerase ii-specific dna binding activity, GO:0000122, positive regulation of transcription by rna polymerase ii. \\n\\nmechanism and]] | \n", + "0.25 | \n", + "
| 364 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PEROXISOME-0 | \n", + "[[GO:0006629, GO:0006631, GO:0006810, GO:0003824, GO:0005501, steroid binding.\\n\\nmechanism and]] | \n", + "[[GO:0001676, GO:0043574, GO:0008203, GO:0006633, lipid binding activity, atp binding activity, GO:0016491]] | \n", + "0.00 | \n", + "
| 365 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PEROXISOME-1 | \n", + "[[GO:0004467, GO:0016401, GO:0047676, GO:0031957, peroxisome targeting sequence binding activity, GO:0006633]] | \n", + "[[GO:0006629, mitochondrial function, GO:0006281]] | \n", + "0.00 | \n", + "
| 366 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[[GO:0004672, cytoskeleton structure, GO:0006629, protein binding activity]] | \n", + "[[GO:0004672, g protein-coupled receptor binding activity, transcription factor binding activity, enzyme binding activity, GO:0007166, GO:0035556, GO:0032007, GO:0010971, negative regulation of vasc, negative regulation of nitrogen com, actin filament binding activity, cytoskeletal protein binding activity]] | \n", + "0.07 | \n", + "
| 367 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[[GO:0006468, intracellular signaling, GO:0016301, GO:0016791, enzyme binding activity. \\n\\nmechanism: the enriched terms suggest that many of the genes are involved in regulatory processes related to protein modification through phosphorylation and dephosphorylation. this could implicate several signaling pathways, such as mapk, pi3k/akt, and nf-kappab pathways]] | \n", + "[[GO:0006468, GO:0035556, GO:0016301, enzyme binding activity, GO:0004672, identical protein binding activity, scaffold protein binding activity]] | \n", + "0.20 | \n", + "
| 368 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-0 | \n", + "[[GO:0007030, GO:0006888, retrograde transport, vesicle recycling, GO:0090110, GO:0006891, GO:0008333, GO:0006893, GO:0048488, GO:0016192, vesicle recycling]] | \n", + "[[GO:0007030, GO:0048193, GO:0090110, GO:0006888, retrograde transport, vesicle recycling, GO:0034260, negative regulation of autophagosome formation and maturation, GO:1905604, GO:1905280, GO:0002091, GO:0009967]] | \n", + "0.24 | \n", + "
| 369 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-1 | \n", + "[[GO:0048193, GO:0032456, GO:0035493, GO:0006891, GO:0070836]] | \n", + "[[GO:0006888, GO:0048193, GO:0006891, GO:0034067, snare complex assembly.\\n\\nmechanism and]] | \n", + "0.25 | \n", + "
| 370 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[[GO:0098869, GO:0006750, GO:0042744, oxidation-reduction process, GO:0006979]] | \n", + "[[cellular redox homeostasis, GO:0006979, protein disulfide reduction, GO:0006749, GO:0003954, GO:0004601, GO:0006826, GO:0016209, MESH:D015227]] | \n", + "0.08 | \n", + "
| 371 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[[GO:0045454, GO:0006979, GO:0016209, GO:0004602, GO:0004784, GO:0004601, GO:0003954, GO:0032981]] | \n", + "[[GO:0045454, GO:0006979]] | \n", + "0.25 | \n", + "
| 372 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-0 | \n", + "[[GO:0005515, GO:0005524, GO:0042802, GO:0016301, GO:0000166]] | \n", + "[[GO:0005515, GO:0016301, GO:0051726, GO:0010467]] | \n", + "0.29 | \n", + "
| 373 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-1 | \n", + "[[identical protein binding activity, protein folding chaperone binding activity, GO:0004672, rna binding activity, chromatin binding activity, atp binding activity, nucleotide binding activity, GO:0004722, GO:0061630, calcium ion binding activity, rna polymerase iii binding activity, cytokine binding activity, GO:0004930, integrin binding activity, many others]] | \n", + "[[GO:0005515, GO:0008047, atp binding activity]] | \n", + "0.06 | \n", + "
| 374 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[[GO:0007178, GO:0010862, GO:0010991, GO:0045668, GO:0030512, GO:0010604, GO:0009967]] | \n", + "[[GO:0060395, GO:0006357, GO:0010604, GO:0090101, GO:0045668, establishment of sert, positive regulation of vascular associated smooth muscle cell proliferat, several others]] | \n", + "0.15 | \n", + "
| 375 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[[signal transduction; regulation of gene expression; transcription regulation; protein phosphorylation; smad protein signal transduction.\\n\\nmechanism: these genes are involved in various aspects of signal transduction, including regulation of gene expression, transcription regulation, MESH:D016212, where they regulate transcription of target genes. genes in this list may activate or inhibit smad signaling and affect downstream transcriptional regulation. additionally, many of these genes play roles in other signaling pathways and regulatory processes, such as the wnt signaling pathway and negative regulation of protein degradation]] | \n", + "[[GO:0005024, GO:0046332, GO:0009967, GO:0006357, GO:0000122, GO:0007166, GO:0010604, nucleic acid binding activity]] | \n", + "0.00 | \n", + "
| 376 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[[GO:0005125, GO:0003700, enzyme binding activity, GO:0006955]] | \n", + "[[GO:0003700, rna polymerase ii-specific; cytokine activity; protein binding activity.\\n\\nmechanism: these genes are involved in the regulation of transcription and cytokine activity, likely playing a role in immune responses and cellular differentiation. they are involved in binding to dna and rna polymerases to regulate the expression of genes, as well as in the production and regulation of cytokines and growth factors that play a role in cell signaling and differentiation]] | \n", + "0.14 | \n", + "
| 377 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[[cytokine activity; dna-binding transcription factor activity; enzyme binding activity; phosphatidylinositol-3,4-bisphosphate binding activity; g protein-coupled receptor activity.\\n\\nmechanism: the enriched terms suggest that the genes on the list are involved in signaling pathways that regulate gene expression and cellular responses through cytokine receptors, GO:0035556, and various enzymatic activities. these pathways play essential roles in several biological processes, including immune responses, cell differentiation and development, cell survival death]] | \n", + "[[GO:0005125, GO:0008009, GO:0001216, GO:0006955, interleukin-12 alpha subunit binding activity, GO:0004707, protein kinase binding activity, GO:0001817, GO:0002682, smad binding activity, transcription factor binding activity]] | \n", + "0.00 | \n", + "
| 378 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[[protein folding and processing, GO:0015031, GO:0003723, GO:0043022, GO:0003743]] | \n", + "[[protein folding and chaperone activity, rna binding and transcriptional regulation, rna processing and degradation]] | \n", + "0.00 | \n", + "
| 379 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[[rna binding activity, protein folding chaperone binding activity, ribosome binding activity, histone binding activity, dna-binding transcription factor binding activity, ubiquitin protein ligase binding activity]] | \n", + "[[GO:0003723, GO:0051087, GO:0090304, endoplasmic reticulum stress response pathway]] | \n", + "0.00 | \n", + "
| 380 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-0 | \n", + "[[extracellular matrix organization; growth factor signaling; regulation of transcription, dna-templated; positive regulation of protein kinase activity; organic acid metabolic process.\\n\\nmechanism: these genes are involved in extracellular matrix structural constituent, growth factor signaling, GO:0000988, GO:0005515, and nucleotide binding. this suggests that they may be involved in the regulation of gene transcription, cellular growth and differentiation, and the organization of extracellular matrices. a hypothesis for the underlying biological mechanism or pathway is that these genes may be involved in the regulation of extracellular matrix formation and growth factor signaling pathways, which then contribute to cellular differentiation and growth. additionally, the binding of proteins with transcription factor activity and nucleotide binding activity suggests that these genes are involved in the regulation of gene transcription, which may have downstream effects on cellular function and behavior]] | \n", + "[[GO:0005201, identical protein binding activity, enzyme binding activity, smad binding activity]] | \n", + "0.00 | \n", + "
| 381 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-1 | \n", + "[[GO:0005201, GO:0005178, identical protein binding activity, protease binding activity, calcium binding, platelet-derived growth factor binding activity]] | \n", + "[[GO:0005201, GO:0005515, GO:0016563, GO:0005102]] | \n", + "0.11 | \n", + "
| 382 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-0 | \n", + "[[enzyme binding activity, protein kinase binding activity, GO:0042803, rna binding activity, atp binding activity, identical protein binding activity, ubiquitin protein ligase binding activity, GO:0001228, ion binding activity, g protein-coupled receptor binding activity, dna polymerase binding activity, peptide hormone receptor binding activity. \\n\\nmechanism: these genes are involved in a variety of molecular activities, including enzyme activity, protein binding, and transcription factor activity. one potential underlying biological mechanism is the regulation and interaction of proteins in various cellular processes]] | \n", + "[[enzyme binding activity, GO:0003700, protein kinase binding activity, identical protein binding activity, rna binding activity, atp binding activity, ubiquitin protein ligase binding activity]] | \n", + "0.46 | \n", + "
| 383 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-1 | \n", + "[[atp binding activity, GO:0001216, identical protein binding activity, rna binding activity, protein kinase binding activity, cysteine-type endopeptidase activity involvement in apoptotic signaling, GO:0004602, histone binding activity, GO:0030594, glucagon receptor binding activity, GO:0004499, peptide hormone receptor binding activity, gtp binding activity, more]] | \n", + "[[enzyme binding activity, GO:0006508, protein phosphatase binding activity, GO:0004725]] | \n", + "0.00 | \n", + "
| 384 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[[GO:0090090, regulation of transcription, GO:0000981, histone deacetylase binding activity, ubiquitin protein ligase binding activity, notch binding activity, protein kinase binding activity, GO:0003713, identical protein binding activity]] | \n", + "[[GO:0060070, transcription regulation, MESH:D012319, transcription activator, beta-catenin complex, GO:0007219]] | \n", + "0.00 | \n", + "
| 385 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[[GO:0060070, GO:0031398, GO:0090090, GO:0031397, GO:0030162]] | \n", + "[[GO:0060070, GO:0010468]] | \n", + "0.17 | \n", + "
| 386 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "T cell proliferation-0 | \n", + "[[GO:0050776, intracellular signaling, GO:0008037, GO:0009617, GO:0008284, GO:0005125, protein kinase binding activity, identical protein binding activity]] | \n", + "[[GO:0050852, GO:0005125, interleukin-2 receptor binding activity, negative regulation of peptid, intracellular signal transduction\\n\\nmechanism: the genes analyzed in this study are primarily involved in signaling and receptor binding activities. this suggests that these genes may play an important role in the communication between cells and regulation of immune response. \\n\\n t cell receptor signaling pathway, cytokine activity, interleukin-2 receptor binding activity, negative regulation of peptid..., and intracellular signal transduction]] | \n", + "0.08 | \n", + "
| 387 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "T cell proliferation-1 | \n", + "[[GO:0042110, GO:0001816, GO:0010468, GO:0050671, GO:0001819, GO:0001933, GO:0045840, protein kinase binding activity, GO:0004697, GO:0004911, GO:0004896, GO:0097190, GO:0007005, GO:0043065, GO:0042100, GO:0004931]] | \n", + "[[GO:0050863, GO:0001819, GO:0006468, GO:0043066, GO:0002687, GO:0030890, GO:0006879, GO:0010468]] | \n", + "0.09 | \n", + "
| 388 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "Yamanaka-TFs-0 | \n", + "[[transcription regulation, GO:0010468, GO:0045944, GO:0003700, cellular differentiation]] | \n", + "[[transcriptional regulation, GO:0010467, GO:0003700, GO:0009889, GO:0019219]] | \n", + "0.11 | \n", + "
| 389 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "Yamanaka-TFs-1 | \n", + "[[GO:0010468, transcriptional regulation, GO:0003700, GO:0001714, GO:0045944]] | \n", + "[[GO:0010467, transcription regulation, dna binding activity, rna polymerase ii-specific, GO:0010468, transcription cis-regulatory region binding activity]] | \n", + "0.10 | \n", + "
| 390 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "amigo-example-0 | \n", + "[[GO:0030198, GO:0007165, GO:0007596]] | \n", + "[[GO:0007160, GO:0030198, GO:0030199, GO:0008034]] | \n", + "0.17 | \n", + "
| 391 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "amigo-example-1 | \n", + "[[GO:0005178, GO:0005201, GO:0008083, platelet-derived growth factor binding activity, GO:0030199]] | \n", + "[[GO:0007160, GO:0030199, GO:0030198, GO:1902533, GO:0010604, GO:0030334]] | \n", + "0.10 | \n", + "
| 392 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_0-0 | \n", + "[[GO:0005515, GO:0005216, transcriptional regulation, ubiquitin-protein ligase activity]] | \n", + "[[GO:0003700, identical protein binding activity, protein kinase binding activity, actin binding activity, sequence-specific double-stranded dna binding activity, metal ion binding activity, calcium ion binding activity, chromatin binding activity, rna binding activity]] | \n", + "0.00 | \n", + "
| 393 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_0-1 | \n", + "[[metal ion binding activity, calcium ion binding activity, GO:0000981, g protein-coupled receptor binding activity, enzyme binding activity, sequence-specific double-stranded dna binding activity, cytoskeletal protein binding activity, GO:0061630]] | \n", + "[[binding activity, GO:0003700, GO:0046872, GO:0019904, GO:0061630]] | \n", + "0.08 | \n", + "
| 394 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_1002-0 | \n", + "[[GO:0006936, GO:0030239, GO:0043502, GO:0051015, GO:0005523]] | \n", + "[[GO:0006936, GO:0043502, GO:0016567]] | \n", + "0.33 | \n", + "
| 395 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_1002-1 | \n", + "[[GO:0003009, GO:0060048, GO:0010628, actin filament binding activity, GO:0008307]] | \n", + "[[GO:0006936, GO:0003009, GO:0016567, ion channel activity.\\n\\nmechanism: these genes likely play a role in muscle contraction and structure, possibly through the regulation of ion channels and protein ubiquitination]] | \n", + "0.12 | \n", + "
| 396 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "endocytosis-0 | \n", + "[[GO:0006897, GO:0015031, GO:0006898]] | \n", + "[[GO:0006897, GO:0007165, cellular adhesion, GO:0006869, GO:0030163, GO:0007009]] | \n", + "0.12 | \n", + "
| 397 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "endocytosis-1 | \n", + "[[GO:0006897, lysosomal function, GO:0038023, GO:0006955, GO:0008152]] | \n", + "[[GO:0006897, membrane traffic, GO:0015031]] | \n", + "0.14 | \n", + "
| 398 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "glycolysis-gocam-0 | \n", + "[[GO:0006006, GO:0005975, GO:0019725, GO:0008104, GO:0070062, GO:0005634]] | \n", + "[[GO:0006096, GO:0005975, GO:0006000, metabolic homeostasis]] | \n", + "0.11 | \n", + "
| 399 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "glycolysis-gocam-1 | \n", + "[[GO:0006096, GO:0005975, GO:0006000, cell development.\\n\\nhypotheses: the enriched terms suggest that these genes are involved in the glycolysis pathway, contributing to carbohydrate metabolic processes and the production of energy for cellular development. specifically, fructose metabolic processes are enriched, indicating that the genes may play a role in the conversion of fructose to glucose during glycolysis]] | \n", + "[[GO:0006096, GO:0005975, GO:0006002, GO:0005945]] | \n", + "0.33 | \n", + "
| 400 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "go-postsynapse-calcium-transmembrane-0 | \n", + "[[GO:0006816, GO:0007268, GO:0005245, GO:0098978, GO:0004972]] | \n", + "[[GO:0006816, GO:0005245, GO:0008066, GO:0005892]] | \n", + "0.29 | \n", + "
| 401 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "go-postsynapse-calcium-transmembrane-1 | \n", + "[[GO:0005509, GO:0006836, GO:0001505, GO:0016079, GO:0035235, GO:0007186, GO:0071318]] | \n", + "[[GO:0019722, voltage-gated calcium channel, GO:0051480, GO:0008066, GO:0017146, GO:0007268, GO:0051899, g-protein coupled receptor signaling pathway]] | \n", + "0.00 | \n", + "
| 402 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "go-reg-autophagy-pkra-0 | \n", + "[[GO:0006468, GO:0010604, GO:0038202, GO:0032006, GO:0016241, positive regulation of cyclin-dependent protein serine/threonine kinase activity.\\n\\nmechanism and]] | \n", + "[[GO:0006468, GO:0035556, GO:0031929, GO:0097190, kinase activity regulation, GO:0010604]] | \n", + "0.20 | \n", + "
| 403 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "go-reg-autophagy-pkra-1 | \n", + "[[intracellular signaling, pathway regulation, GO:0006915, GO:0004672, GO:0006468, GO:0010604, GO:0045859]] | \n", + "[[GO:0035556, protein kinase activity regulation, GO:0010604, GO:0038202, GO:0032008, GO:0045859, apoptosis signaling pathway, chromatin binding activity]] | \n", + "0.15 | \n", + "
| 404 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[[GO:0046479, GO:0006516, GO:0006032, GO:0030214]] | \n", + "[[GO:0016052, GO:0006516, GO:0006032, GO:0030214]] | \n", + "0.60 | \n", + "
| 405 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[[GO:0005975, MESH:D054794, glycan catabolism, GO:0006516, GO:0019377, GO:0006032, GO:0006004]] | \n", + "[[GO:0016052, GO:0030214, GO:0006516, GO:0019377, GO:0006032, GO:0006491, GO:0006517, mannose trimming involved in glycoprotein erad pathway.\\n\\nmechanism: one potential underlying biological mechanism is the regulation of cell surface and extracellular matrix composition, as well as the breakdown and recycling of molecules within these structures. glycosidases play a key role in breaking down complex carbohydrates into smaller subunits, which can then be reassembled into new molecules. the ability to break down specific types of carbohydrates, such as hyaluronic acid and chitin, may also be important for cellular processes such as cell migration and host defense]] | \n", + "0.25 | \n", + "
| 406 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "ig-receptor-binding-2022-0 | \n", + "[[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253]] | \n", + "[[immunoglobulin receptor binding activity, antigen binding activity]] | \n", + "0.67 | \n", + "
| 407 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "ig-receptor-binding-2022-1 | \n", + "[[GO:0002253, GO:0098542, GO:0019731, GO:0006959, GO:0002377, GO:0051130, GO:0045657]] | \n", + "[[GO:0006955, GO:0006952, antigen binding activity]] | \n", + "0.00 | \n", + "
| 408 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "meiosis I-0 | \n", + "[[GO:0061982, GO:0007131, GO:0007129, GO:0000712, GO:0000724]] | \n", + "[[homologous chromosome pairing, GO:0042138, GO:0000706, GO:0007131, GO:0000724, GO:0000712, GO:0000795]] | \n", + "0.33 | \n", + "
| 409 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "meiosis I-1 | \n", + "[[meiotic recombination, GO:0035825, GO:0006302]] | \n", + "[[meiotic recombination, GO:0006302, GO:0035825, chromosomal segregation, GO:0007130]] | \n", + "0.60 | \n", + "
| 410 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "molecular sequestering-0 | \n", + "[[molecular sequestering, protein binding activity, transport of metal ions, GO:0048523, response to infection and stress, GO:0010468, GO:0019722, regulation of transcription]] | \n", + "[[GO:0140313, GO:0140311, identical protein binding activity, GO:0060090, ubiquitin protein ligase binding activity, GO:0016567]] | \n", + "0.00 | \n", + "
| 411 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "molecular sequestering-1 | \n", + "[[GO:0140311, GO:0010468, GO:0031398, GO:0051238]] | \n", + "[[GO:0010468, GO:0042742, GO:0045185, GO:0002376, GO:0009267, GO:0032387, GO:0035556]] | \n", + "0.10 | \n", + "
| 412 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "mtorc1-0 | \n", + "[[binding activity, enzymatic activity, GO:0006412, GO:0023052, GO:0008152]] | \n", + "[[GO:0005515, GO:0003723, enzymatic activity, structural constituent of cytoskeleton. \\n\\nmechanism: these genes likely play a role in cellular processes such as transcription, translation, protein folding, and cytoskeletal organization]] | \n", + "0.12 | \n", + "
| 413 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "mtorc1-1 | \n", + "[[GO:0005515, GO:0042802, GO:0019899, GO:0043167, GO:0005524, GO:0031625, GO:0003723, GO:0003677, GO:0097159, GO:0017076, GO:0051015, GO:0042802, GO:0016491, phosphoprotein binding activity, GO:0005215, GO:0006793, GO:0044237, GO:0006457, GO:0003677, GO:0008380]] | \n", + "[[GO:0005515, GO:0003824, GO:0005215]] | \n", + "0.10 | \n", + "
| 414 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "peroxisome-0 | \n", + "[[GO:0017038, peroxisomal biogenesis, GO:0140036, atp binding and hydrolysis activity, lipid binding activity]] | \n", + "[[peroxisome biogenesis, peroxisome matrix targeting, GO:0017038]] | \n", + "0.14 | \n", + "
| 415 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "peroxisome-1 | \n", + "[[GO:0007031, GO:0016558, GO:0005778, peroxisomal biogenesis disorder, GO:0008611, lipid binding activity, atp binding activity, GO:0016887, ubiquitin-dependent protein binding activity, enzyme binding activity]] | \n", + "[[peroxisome biogenesis, GO:0017038, GO:0005778, ubiquitin-dependent protein binding activity, atp binding activity, GO:0016887]] | \n", + "0.33 | \n", + "
| 416 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "progeria-0 | \n", + "[[GO:0006259, GO:0006325, GO:0033554, GO:0006281, GO:0007568]] | \n", + "[[GO:0006259, GO:0006325, GO:0033554]] | \n", + "0.60 | \n", + "
| 417 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "progeria-1 | \n", + "[[GO:0006281, GO:0006950, GO:0090398, GO:0000723, chromatin condensation]] | \n", + "[[GO:0006281, GO:0000723, GO:0007568]] | \n", + "0.33 | \n", + "
| 418 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "regulation of presynaptic membrane potential-0 | \n", + "[[GO:0015276, GO:0099505, GO:0060078, GO:0071805, GO:0035725, GO:0035235]] | \n", + "[[GO:0007214, GO:0022849, GO:0005242, GO:0035235, GO:0015276, GO:0071805, GO:0005244]] | \n", + "0.30 | \n", + "
| 419 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "regulation of presynaptic membrane potential-1 | \n", + "[[GO:0007214, GO:0007215, GO:0006811, GO:0006836, GO:0007268]] | \n", + "[[GO:0006811, GO:0007268, membrane potential regulation, GO:0008066, GO:0007214]] | \n", + "0.43 | \n", + "
| 420 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "sensory ataxia-0 | \n", + "[[GO:0042552, GO:0007422, MONDO:0005071, GO:0022011, MONDO:0005244]] | \n", + "[[MONDO:0015626, GO:0042552, GO:0007422, GO:0006457, GO:0007600, nucleic acid metabolism, mitochondrial function]] | \n", + "0.20 | \n", + "
| 421 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "sensory ataxia-1 | \n", + "[[GO:0007399, GO:0042552, mitochondrial metabolism, GO:0030163, protein regulation, GO:0071260]] | \n", + "[[GO:0007399, MONDO:0015626, GO:0042552, UBERON:0000010, mitochondrial dysfunction, protein ubiquitination.\\n\\nmechanism]] | \n", + "0.20 | \n", + "
| 422 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "term-GO:0007212-0 | \n", + "[[GO:0007186, GO:0007212]] | \n", + "[[GO:0007212, GO:0007190, calcium ion regulation, g protein-coupled receptor pathway]] | \n", + "0.20 | \n", + "
| 423 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "term-GO:0007212-1 | \n", + "[[GO:0007212, GO:0007186, GO:0051480, GO:0004016, GO:0006469, GO:0050821, GO:0060828, GO:0007220, GO:0034205, GO:0006508, GO:0046325, GO:1904227, GO:0051247, GO:0015171, GO:0015108]] | \n", + "[[GO:0007186, GO:0004952, GO:0004016, GO:0051480, negative regulation of glycogen synthase activity, GO:0004672, GO:0019538, GO:0006468]] | \n", + "0.15 | \n", + "
| 424 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "tf-downreg-colorectal-0 | \n", + "[[dna-binding transcription factor, rna polymerase ii-specific transcription regulation, GO:0000122, GO:0045944, GO:0006355]] | \n", + "[[GO:0001216, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, GO:0045944, GO:0000122, GO:0006355, transcription factor binding activity, nucleic acid binding activity, chromatin binding activity, GO:0003713]] | \n", + "0.27 | \n", + "
| 425 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "tf-downreg-colorectal-1 | \n", + "[[GO:0000988, GO:0006355, GO:0045893, GO:0045892, dna-binding, GO:0003702]] | \n", + "[[GO:0003700, GO:0006355, GO:0010468, GO:0006337]] | \n", + "0.11 | \n", + "
| 426 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "EDS-0 | \n", + "[[connective tissue formation and repair, protein binding and folding, GO:0006955, GO:0042060, GO:0006024]] | \n", + "[[GO:0032964, collagen fiber formation, extracellular matrix maturation, transcriptional regulation, procollagen protein, MESH:D006025, metalloproteinase, proteolytic processing, peptidyl prolyl cis-trans isomerase, MESH:M0465019, tumor-rejection antigen, sulfotransferase, transmembrane protein, beta-1,3 galactosyltransferase]] | \n", + "0.00 | \n", + "
| 427 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "EDS-1 | \n", + "[[collagen maturation, GO:0006024, transcriptional regulation, GO:0006829]] | \n", + "[[GO:0006486, extracellular matrix remodeling, collagen production, GO:0061448, immunity response, GO:0006508, tumor rejection, MESH:M0465019, MESH:D008565, transcriptional repressor, peptidyl-prolyl isomerase, complement system, GO:0004226, peptidase s1]] | \n", + "0.00 | \n", + "
| 428 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "FA-0 | \n", + "[[GO:0006281, GO:0035825, GO:0016310, nucleoprotein complex assembly, formation of nuclear foci, double-strand dna repair, holliday junction resolution, function in tumor suppression, reca/rad51-related protein family, dna lesions, structural specific endonucleases, rad51 family, cellular responses to replication fork failure, brc motif]] | \n", + "[[GO:0006281, genome maintenance, MESH:D004249, nucleoprotein complex, GO:0035825, double-strand dna repair, holliday junction resolution, monoubiquinated, MESH:D051135, nuclear foci, structure-specific endonucleases, MESH:D051135, recq deah helicase, tumor suppression, ssdna-binding proteins]] | \n", + "0.16 | \n", + "
| 429 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "FA-1 | \n", + "[[GO:0006281, GO:0035825, monoubiquitination, holliday junction resolution, rad51 binding]] | \n", + "[[GO:0006281, nucleoprotein complex, GO:0035825, dna lesion, MESH:M0443450, fanconi anemia complementation group (fanc), GO:0006302]] | \n", + "0.20 | \n", + "
| 430 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ADIPOGENESIS-0 | \n", + "[[GO:0006629, GO:0006633, GO:0022900, GO:0005739, MESH:D000975, GO:0045333, MESH:D010084, acyltransferase, carboxylase, acyl-coenzyme a synthetase, ubiquitin protease, MESH:C021451, MESH:D010743, oxidoreductase, plasma lipase, hydratase]] | \n", + "[[GO:0010467, GO:0140657, GO:0006468, ubiquitin-mediated degradation, GO:0051726, GO:0005525, GO:0006839, GO:0006118, GO:0006119, MESH:D004789, enzyme inhibition, GO:0016491, GO:0016482, GO:0005515, GO:0006629, GO:0036211, ubiquitinylation]] | \n", + "0.03 | \n", + "
| 431 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ADIPOGENESIS-1 | \n", + "[[GO:0005515, transcription regulation, atpase, MESH:D020558, transcript processing, protein transduction, MESH:D014451, GO:0044237, energy production, GO:0006508]] | \n", + "[[atp production, GO:0005746, GO:0006118, GO:0030497, rna/dna binding, GO:0015031, MESH:D054875, GO:0016310, GO:0008017, GO:0006869]] | \n", + "0.00 | \n", + "
| 432 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[[immune/cytokine responses, GO:0006412, GO:0006351, cell surface signaling, receptor activation, MESH:D054875, MONDO:0002123, GO:0005524]] | \n", + "[[cell signalling, cytokine production/regulation, chemokine production/regulation, antimicrobial defence, plasma protein regulation, immune regulation, inflammatory regulation, transcriptional regulation, GO:0004672, GO:0008233, glycoprotein activity, receptor protein activity]] | \n", + "0.00 | \n", + "
| 433 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[[GO:0006412, cellular regulation, GO:0008152, cell signaling, GO:0006351, immunoregulation, stability, GO:0005515, GO:0016310, GO:0010467, g-protein coupled receptor, transmembrane protein, t-cell development]] | \n", + "[[integrin, cytokine, g-protein coupled receptor, MESH:D007372, MESH:D018124, MESH:D008562, MESH:D011494, chemokine, transmembrane receptor, GO:0007165, transcriptional regulation, GO:0006412, GO:0006955]] | \n", + "0.08 | \n", + "
| 434 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[[MESH:D011494, GO:0000981, GO:0005530, adhesion molecule, GO:0016538, MESH:D016601, protein tyrosine phosphatase, g protein, serine/threonine protein kinase, MESH:D008565, MESH:D006657, ubiquitin ligase, MESH:C052123, microtubule-associated protein, atp-binding cassette, alpha/beta-hydrolase, integrin alpha-chain, signal transducion, protein inhibitor of activated stat]] | \n", + "[[GO:0005524, GO:0006351, GO:0016310, MESH:D011494, protein tyrosine phosphatase, GO:0065007, GO:0005515, hydrolase, ribosomal s6 kinase, GO:0016192, regulatory subunit, acetyltransferase, modulation, GO:0005509, GO:0005783, GO:0000981, GO:0003723, n-myc downregulated, polypeptide, GO:0016125, MESH:D006657, protein inhibitor, MESH:D051116, structural fibre, disulfide oxidoreductase, adenine dinucleotide, non-sterol metabolism, calcium-induced, GO:0042593]] | \n", + "0.09 | \n", + "
| 435 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[[GO:0008283, GO:0006351, GO:0007165, structural components, metabolism of proteins, GO:0006629, GO:0005975, GO:0007155, binding activity, GO:0010467, GO:0003677, MESH:D011494, oxidoreductase, anchoring kinase to microtubules, GO:0005102, molecule transport, MESH:D010455]] | \n", + "[[transcriptional regulation, GO:0004672, GO:0005515, GO:0003723, GO:0007165, proteolytic enzyme activity, GO:0003677]] | \n", + "0.09 | \n", + "
| 436 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ANGIOGENESIS-0 | \n", + "[[this is a list of genes involved in a variety of pathways and processes related to cell adhesion, GO:0040007, GO:0008152, and other physiologic functions. the terms “cell adhesion”, “cell signaling”, “extracellular matrix”, “transcriptional regulation”, and “cell cycle progression and differentiation” are all enriched among this group of genes. a hypothesis of the underlying biological mechanism at work is that these genes work together to promote cell growth and regulation, that many of these genes interact to achieve greater cellular complexity]] | \n", + "[[GO:0042157, GO:0050817, GO:0007599, MESH:D016207, MESH:D018925, receptors, transporters, secreted extracellular matrix proteins, GO:0004868, MESH:D011509, GO:0007155, GO:0016477, GO:0023052, GO:0008283, GO:0006915, transcriptional regulation, tissue development and regeneration, GO:0006955]] | \n", + "0.00 | \n", + "
| 437 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ANGIOGENESIS-1 | \n", + "[[GO:0007155, extracellular matrix remodeling, GO:0007165, protease inhibition, transcriptional regulation]] | \n", + "[[cell-cell interactions, cell-matrix interactions, extracellular matrix production, processing of proteoglycans and glycoproteins]] | \n", + "0.00 | \n", + "
| 438 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-0 | \n", + "[[GO:0005207, GO:0007155, calcium-dependent proteins, MESH:D008565, intronless proteins, intracellular scaffolding proteins, fibrillin proteins, signaling receptors, MESH:D051193, MESH:D003598, tubulin proteins, type ii membrane proteins, MESH:D006023]] | \n", + "[[integrin, GO:0008014, GO:0005530, MESH:C119025, map kinase, protein tyrosine kinase, guanine nucleotide binding protein, MESH:D020558, act]] | \n", + "0.00 | \n", + "
| 439 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-1 | \n", + "[[GO:0007155, GO:0007165, actin binding and assembly, membrane localization, ecm protein binding and assembly]] | \n", + "[[GO:0007155, GO:0023052, scaffolding, cytoskeleton maintenance, GO:0031012, MESH:D016023, MESH:D057167, MESH:C119025, MESH:D011494, GO:0008014]] | \n", + "0.07 | \n", + "
| 440 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_SURFACE-0 | \n", + "[[GO:0007160, GO:0007165, MESH:D008565, transcriptional coactivation, signal recognition, GO:0055085, GO:0006898]] | \n", + "[[GO:0007155, GO:0006457, GO:0007154, GO:0006898, gpi-anchored cell surface proteins, cation transport atpase, transcriptional coactivation, interleukin signaling, hormone-dependence, MESH:D019812, heparin-binding, GO:0007160]] | \n", + "0.19 | \n", + "
| 441 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_SURFACE-1 | \n", + "[[GO:0007160, cell-matrix interactions, carbohydrate binding activity, GO:0007155, GO:0038023, GO:0007165, GO:0008284, GO:0048681, GO:0030506, protein tyrosine kinase, sh2 domain binding activity, sh3 domain binding activity]] | \n", + "[[cell signal transduction, GO:0007160, GO:0006457, GO:0030308, ligand binding, cell-surface glycoprotein, cation transmembrane transporter, growth arrest, MESH:D051246, transmembrane protein, regulatory subunit, membrane-bound glycoprotein, ammonium transmembrane transporter, cell surface receptor, insulin-regulated facilitative glucose transporter, cell surface adhesion molecule, GO:0140326, glycosylphosphatidylinositol-anchored protein]] | \n", + "0.03 | \n", + "
| 442 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_APOPTOSIS-0 | \n", + "[[GO:0006915, cytoplasmic signaling, transcriptional regulation, GO:0005515, cellular organization]] | \n", + "[[GO:0006915, transcriptional regulation, GO:0003677, tnf receptor superfamily, bcl-2 protein family]] | \n", + "0.25 | \n", + "
| 443 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_APOPTOSIS-1 | \n", + "[[cell death processes, GO:0023052, cytoplasmic proteins, MESH:M0015044, MESH:D015533, MESH:D004798, toxin removal, GO:0005102]] | \n", + "[[the genes summarized are involved in a wide range of processes, including apoptosis, tumor suppression, inflammation, thioredoxin binding, cytoplasmic protein and membrane glycoprotein regulation, dna topoisomerase and transcriptional activation. the commonalities that emerge from the enrichment test point to a specific biological pathway known as cell death regulation and signal transduction. this involves the interconnected network of genes that regulate apoptosis and maintain genetic stability, as well as others involved in the modulation of immune response pathways. enriched terms include apoptosis, cytoplasmic protein regulation, transcriptional regulation, tumor suppression, GO:0006954, MESH:D004264, thioredoxin binding, membrane glycoprotein regulation, transcriptional coactivation, death agonist, GO:0048018, serine/threonine phosphatase, voltage-dependent anion channel, MESH:D006136, class-1 polypeptide chain release factor, proapoptotic, nf-kappa-b.\\n\\nsummary: genes related to cell death regulation signal transduction pathways.\\nmechanism: interconnected network of genes that regulate apoptosis maintain genetic stability, as well as those involved in the modulation]] | \n", + "0.00 | \n", + "
| 444 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[[atp-binding, GO:0006810, GO:0004768, MESH:D010084, enzyme catalysis, GO:0000981]] | \n", + "[[GO:0006629, atp binding cassette, MESH:M0011631, GO:0005490, peroxin, gamma-glutamylcysteine synthetase, GO:0050632, MESH:D002785, flavoenzymes, GO:0042446, GO:0016209]] | \n", + "0.00 | \n", + "
| 445 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[[GO:0015031, GO:0006412, GO:0006629, MESH:D010084, hormone regulation, transcription regulation, GO:0006805, calcium binding, GO:0005524, MESH:D005982, GO:0008203, MESH:M0011631, sulfate conjugation, 2-hydroxyacid oxidase, MESH:D000214, MESH:D000215, coenzyme a ligase, natriuretic peptide, peroxisome biogenesis, tgf-beta ligand, adrenal steroid synthesis, nuclear receptor, copper zinc binding, GO:0050632, MESH:D012319, gamma-glut]] | \n", + "[[GO:0006629, GO:0006810, oxidation, bile acids synthesis, GO:0006790, GO:0005777, oxidative stress response]] | \n", + "0.03 | \n", + "
| 446 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[[MESH:D008565, MONDO:0018815, acetoacetyl-coa thiolase, cytosolic enzyme, actin isoforms, activation transcription factor (creb), annexin family, fructose-biphosphate aldolase, immunoglobulin superfamily, g-protein coupled receptor (gpcr), homotetramer, hydratase/isomerase superfamily, MESH:C022503, mal proteolipid, MESH:M0476528, sre-binding proteins (srebp), peroxisomal enzyme, transmembrane 4 superfamily, transmembrane protein, multispan transmembrane protein, tetr]] | \n", + "[[GO:0048870, energy generation, GO:0008652, GO:0009063, GO:0009101, GO:0016126, GO:0016127, GO:0006629, GO:0006869, transcriptional regulation]] | \n", + "0.00 | \n", + "
| 447 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[[GO:0006629, GO:0005543, GO:0004768, atp-binding cassette, GO:0016126, cytochrome p450 family proteins]] | \n", + "[[GO:0006695, GO:0006629, GO:0006636, cell growth/regulation, GO:0051726, GO:0005515, mhc class ii presentation, cellular antioxidant activity, GO:0000988]] | \n", + "0.07 | \n", + "
| 448 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_COAGULATION-0 | \n", + "[[complement system, GO:0007596, peptide hydrolysis, GO:0016485, inflammation regulation]] | \n", + "[[analysis of this set of human genes revealed high enrichment for terms related to proteases and protease inhibitors, GO:0005209, MESH:D006023, and serine proteinases. of particular note is the abundance of genes related to the regulation of the complement system and to the coagulation cascade, GO:0004235, there appears to be a strong emphasis on proteins that are involved in the maintenance of cellular integrity and in the regulation of inflammatory and immune responses. in particular, it appears that the presence of proteases, MESH:D011480, GO:0005209, MESH:D006023, and serine proteinases is significantly enriched. this suggests that these proteins are involved in the regulation of a variety of processes, including the complement system and the coagulation cascade. furthermore, the presence of various mmps suggests a regulatory role in the breakdown of proteins in the extracellular matrix, which is important for tissue remodeling and wound healing]] | \n", + "0.00 | \n", + "
| 449 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_COAGULATION-1 | \n", + "[[matrix metalloproteinase, cysteine-rich protein, serine protease inhibitor, transforming growth factor-beta, MESH:D054834, guanine nucleotide-binding proteins, peptidase s1 family, integrin beta chain, MESH:D001779, dipeptidyl peptidase, vitamin k-dependent glycoprotein, vitamin k-dependent coagulation factor, regulator of complement activation, protein tyrosine kinase, MESH:D006904, iron-sulfur cluster scaffold, disulfide bridge, kunitz-type serine protease, MESH:D042962, MESH:D037601, g-protein coupled receptor, cytosolic peptidase, GO:0030165, basic leucine zipper, a disintegrin and metalloprote]] | \n", + "[[cysteine-aspartic acid protease, MESH:D020782, peptidase, guanine nucleotide-binding proteins, GO:0030165, metalloproteinase, MESH:D042962, regulator of complement activation, regulator of g protein signal transduction, rnase a superfamily, MESH:D011505, subtilisin-like proprotein convertase, MESH:D011973, vitamin k-dependent plasma glycoprotein, vitamin k-dependent coagulation factor, GO:0005161, lysosomal cysteine proteinase, MESH:D015842, transforming growth factor-beta, MESH:D006904, kunitz-type serine protease, integ]] | \n", + "0.21 | \n", + "
| 450 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_COMPLEMENT-0 | \n", + "[[cell signaling, cell structure/stability, GO:0008152, vitamin k/clotting, GO:0005856, GO:0005886, GO:0006954]] | \n", + "[[MESH:D010770, GO:0000502, GO:0004868, cysteine-aspartic acid protease (caspase), GO:0006915, inflammation signalling, MESH:D005165, factor]] | \n", + "0.00 | \n", + "
| 451 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_COMPLEMENT-1 | \n", + "[[protein production, cell surface glycoprotein regulation, GO:0006956, GO:0007165, heat shock protein, MESH:D003564, metalloproteinase, guanine nucleotide-binding protein, lysosomal cysteine protease, zinc finger protein, cysteine-aspartic acid protease, MESH:D001053, metallothionein.\\nmechanism: the genes may be involved in various signalling pathways to facilitate the regulation of cell surface glycoprotein as well as the production of proteins. cytidine deaminase, metalloproteinase, guanine nucleotide-binding protein and cysteine-aspartic acid protease are likely enzymes that the list of genes may be involved in. heat shock proteins and zinc finger proteins, in addition to apolipoproteins and metallothionein, may be involved in the regulation and transportation of cell proteins]] | \n", + "[[cell signaling, GO:0007155, GO:0008233, transcriptional regulation, GO:0008152, cytoskeletal functions]] | \n", + "0.00 | \n", + "
| 452 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_DNA_REPAIR-0 | \n", + "[[summary: this enrichment test provides evidence of a common biological mechanism underlying many genes in human genetics: dna repair, replication, and transcription.\\n\\nmechanism: the mechanism underlying this term enrichment is the need for accurate dna repair, replication, and transcription, which all require the co-ordinated efforts of many protein families, such as those encoded by the wd-repeat, MESH:D000262, argonaute, MESH:D000263, purine/pyrimidine phosphoribosyltransferase, b-cell receptor associated proteins, MESH:C056608, clp1, GO:0016538, MESH:C010098, dna helicase, MESH:M0251357, general transcription factor (gtf) ii, MESH:D005979, histone-fold proteins, mhc, MESH:C110617, GO:0005662, saccharomyces cerevisiae rad52, schizosaccharomyces pombe rae1, splicing factor (sf3a), GO:0003734, MESH:D011988, transcription factor b (tfb4), trans]] | \n", + "[[GO:0003677, transcription control, post-splicing, MESH:D012319, GO:0006281, GO:0071897]] | \n", + "0.00 | \n", + "
| 453 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_DNA_REPAIR-1 | \n", + "[[GO:0003677, transcription regulation, GO:0006281, GO:0000394, GO:0006397, GO:0003723, GO:0003682, GO:0019899, GO:0003684, general transcription factor, transcription/repair factors, MESH:M0006668, hypothalamic hormone receptor binding, GO:0004016, nuclear cap-binding protein, GO:0016567, transcription initiation, dna polymerase, GO:0006605]] | \n", + "[[GO:0019899, GO:0003723, GO:0003677, GO:0005515, chromosomal binding, dna polymerase, MESH:D012321, phosphorolysis, GO:0010629, GO:0016567]] | \n", + "0.21 | \n", + "
| 454 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_E2F_TARGETS-0 | \n", + "[[GO:0006260, GO:0006281, GO:0006351, GO:0003682, GO:0016569, GO:0051726, ran binding, GO:0000808, atpase, GO:0016538, cyclin-dependent kinase, polycomb, dead box protein, gtpase activating protein, GO:0042393, GO:0003723, nucleolar protein, ubiquitously expressed protein, smc subfamily protein, pp2c family, elongation of primed dna template synthesis, dna interstrand cross-linking, import of proteins into nucleus, MESH:D004264, tumor suppressor protein, MESH:D051981, ubr box protein, p80 autoantigen]] | \n", + "[[dna replication/repair, chromatin regulation, GO:0006396, ser/thr protein kinase, MESH:D063146, nuclear transport and export, GO:0016567, gtpase activation, GO:0006413, GO:0003723, GO:0003677, GO:0042393, ubiquitin protein ligase, cyclin-dependent kinase, MESH:D000251, MESH:D003842]] | \n", + "0.07 | \n", + "
| 455 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_E2F_TARGETS-1 | \n", + "[[GO:0003676, GO:0006260, GO:0036211, GO:0006259, GO:0000785, GO:0051726, GO:0016570, protein assembly and disassembly]] | \n", + "[[GO:0006260, nuclear import/export, GO:0003723, chromatin regulation/modification, GO:0030163, GO:1901987, GO:0006281]] | \n", + "0.07 | \n", + "
| 456 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[[cell signaling, extracellular matrix formation, GO:0007155, connective tissue formation, GO:0001525, metabolic regulation, MESH:D016207, tissue repair]] | \n", + "[[GO:0003779, actin regulation, GO:0007155, cell signaling, GO:0005518, cytokine regulation and signaling, GO:0005207, growth factor family members, peptidase genes]] | \n", + "0.13 | \n", + "
| 457 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[[MESH:D016326, GO:0005202, MESH:D007797, MESH:D005353, MESH:D014841, integrin, MESH:D016189, fibulin proteins]] | \n", + "[[GO:0007155, GO:0005518, GO:0003779, MESH:D024022, MESH:D016326, cytoskeletal components, cell signalling]] | \n", + "0.07 | \n", + "
| 458 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[[GO:0042277, membrane structure modification, GO:0003677, GO:0006631, GO:0051427, signalling transcription, gtpase activation, adenylate cyclase modulation, GO:0016301, GO:0006897, glycoprotein production, GO:0019838, GO:0016570, GO:0006644, zinc-binding]] | \n", + "[[GO:0007165, GO:0010467, GO:0006810, MESH:D008565, GO:0043687, GO:0005515, ligand binding, acyltransferase]] | \n", + "0.00 | \n", + "
| 459 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[[dna-binding, GO:0005515, GO:0043687, GO:0007165, metabolic activity]] | \n", + "[[cytoskeletal organization, dna-binding transcription regulation, GO:0055085, membrane-associated signaling, receptor activation and signaling, cytokine and growth factor signaling]] | \n", + "0.00 | \n", + "
| 460 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[[MESH:D011494, GO:0000981, GO:0005509, MESH:D054794, hormone receptors, GO:0007155, GO:0006457, GO:0010467]] | \n", + "[[g-protein signaling, ion channel transport, membrane receptor signalling, cytoskeletal protein scaffolding, enzyme regulation, glycoprotein modulation.\\nmechanism: the genes identified as being related to these topics are involved in the regulation of cell signalling pathways and the transport of ions across cellular membranes. in addition, the genes are involved in biochemical processes such as enzyme regulation and glycoprotein modulation, which may be important in modulating the amount or type of molecules entering the cell and in organizing the cytoskeleton]] | \n", + "0.00 | \n", + "
| 461 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[[membrane processes, transmembrane processes, GO:0006811, GO:0007155, GO:0016049, GO:0008152, MESH:D011506, GO:0023052, processing, MESH:D048788, reparative pathways, immune pathways, disease pathways]] | \n", + "[[GO:0007165, gene transcription, ion transport and binding, protein-protein interaction, GO:0043687, GO:0007155, MESH:M0518050, GO:0016310, MESH:D011494, membrane recognition, GO:0003676, MESH:D018118, enzymatic reactions, lipid transport, glucose transport, cytokine receptor, molybdenum cofactor biosynthesis]] | \n", + "0.04 | \n", + "
| 462 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[[GO:0006732, GO:0006754, GO:0006096, oxidative decarboxylation, GO:0006631, nad/nadh-dependent oxidation, pyridine nucleotide oxidation, amino acid oxidation, glycerol-3-phosphate dehydrogenase activity, GO:0022900, MESH:D042942, nadp-dependent oxidation, l-amino acid oxidation, endogenous and xenobiotic n-methylation, conversion of pyruvate to acetyl coa, 2-oxoglutarate catabolism, galectin family activity]] | \n", + "[[GO:0008152, GO:0009117, GO:0006631, GO:0006096, oxidation-reduction processes, GO:0006595, GO:0003824, amino acid metabolism, protein homodimerization, protein biotransformation, protein-macromolecule adaptor, protein-tat binding]] | \n", + "0.07 | \n", + "
| 463 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[[GO:0008152, fatty acid transport and processing, oxidoreductase, GO:0009653, GO:0030154, GO:0030674]] | \n", + "[[GO:0006099, GO:0006118, GO:0005504, MESH:D042964, pyruvate dehydrogenase, nad-dependent glycerol-3-phosphate dehydrogenase, nad-dependent dehydrogenase, MESH:D013385, MESH:D000154, lyase, flavin adenine dinucleotide-dependent oxidoreductase, gtp-specific beta subunit, MESH:D006631, nad-retinol dehydrogenase, hydratase/isomerase, MESH:D006631, carnitine o]] | \n", + "0.00 | \n", + "
| 464 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-0 | \n", + "[[GO:0006325, GO:0051726, GO:0016570, MESH:D011494, atp-binding, rna-binding]] | \n", + "[[transcriptional regulation, epigenetic regulation, GO:0051169, GO:0043687, dna replication and repair, chromatin structure, GO:0140014, GO:0036211, GO:0006397]] | \n", + "0.00 | \n", + "
| 465 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-1 | \n", + "[[GO:0051301, GO:0003677, GO:0003723, transcriptional regulation, chromatin restructuring, GO:0004672, GO:0051169, cytoplasmic transport, nucleic acid metabolism, GO:0016570, GO:0016310, GO:0032259, MESH:D000107, MESH:D054875]] | \n", + "[[GO:0006913, GO:0016573, chromatin-associated processes, GO:0051726, transcriptional regulation, signal- and energy- dependent processes, nuclear phosphoproteins, GO:0006334, dna unwinding enzymes, protein heterodimers, GO:0000910, GO:0000398, MESH:D004264, GO:0035064, rna binding proteins, microtubule polymersization, nuclear localization, ubiquitin modification, mitosis regulation, centromere-interacting proteins.\\nmechanism: the genes in this list participate in a wide variety of mechanisms in the context of cellular development, including nucleocytoplasmic transport, histone acetylation, chromatin-associated processes, cell cycle regulation, and transcriptional regulation. these mechanisms are often interdependent and]] | \n", + "0.03 | \n", + "
| 466 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_GLYCOLYSIS-0 | \n", + "[[GO:0016310, GO:0009100, GO:0007155, transcription regulation, GO:0009117, energy production]] | \n", + "[[MESH:D006023, transmembrane protein, cell-surface protein, enzymes plus coenzymes, GO:0000981, hormones, cytokines, and growth factors, ligand-receptor interaction, regulatory proteins, cargo-binding proteins, cell adhesion and morphogenesis, MESH:D000604, metabolism and transport within the cell, metabolism of macromolecules, cellular energy metabolism, cellular homeostasis and signaling, cell signaling and transcription, protein modification and degradation, GO:0007049, dna replication and repair, GO:0008219, enzyme-substrate interaction\\n\\nmechanism:\\nthis list of genes is primarily involved in cellular metabolism, ligand-receptor interactions, and cell signaling and transcription. there are a variety of molecules that are acted upon, such as glycoproteins, transmembrane proteins, hormones, enzymes, and transcription factors. in terms of metabolic functions, the gene list includes proteins for metabolic control, cargo-binding proteins, and enzymes involved in macromolecule metabolism and transport within the cell. additionally, many of these genes are involved in the regulation of cell cycle and homeostasis, as]] | \n", + "0.00 | \n", + "
| 467 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_GLYCOLYSIS-1 | \n", + "[[GO:0008152, GO:0005975, GO:0048468, GO:0009100, GO:0006629, GO:0015031, nucleic acid metabolism, GO:0009117, GO:0070085, ferric ion binding, GO:0016491, GO:0003677, GO:0000988, GO:0031545, GO:0004736]] | \n", + "[[enzyme function, GO:0005488, GO:0006810, GO:0008152, MESH:D007477, sugars, GO:0006351, cytoskeleton structure, GO:0007155]] | \n", + "0.04 | \n", + "
| 468 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[[GO:0007155, GO:0007165, GO:0000981, MESH:D018121, MESH:D039921, rho-gtpase-activating protein, transmembrane protein, GO:1902911, transduction pathway, growth factor, g protein-coupled receptor, cadherin superfamily, basic helix-loop-helix, phosphoprotein, zinc finger protein, cytoplasmic domain, dna-binding, GO:0005886, neurotransmitter, MESH:D057057, coiled-coil, pdz binding motif, cholesterol moiety, fibronectin-like repeat, MESH:D000070557, GO:0016604, MESH:D006655, collapsin response mediator, tripartite motif, hedgehog signaling.\\nmechanism: the genes seem to be primarily involved in regulating signal transduction pathways that control cell migration, proliferation and differentiation, by modulating transcription, cell adhesion and receptor activities. the proteins encoded by these genes interact]] | \n", + "[[GO:0006897, GO:0019838, receptor-mediated pathways;neuron survival;neuron differentiation;neuronal development;cell adhesion, transcription factor regulation, GO:0007165, extracellular protein interaction]] | \n", + "0.03 | \n", + "
| 469 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[[GO:0007155, GO:0007165, neuron signalling, regulatory activity, GO:0009987, GO:0040007, differentiation, motility, GO:0032502]] | \n", + "[[structure-specific proteins, GO:0006898, g-protein coupled receptors, GO:0007155, gene transcription, post-translational regulation]] | \n", + "0.07 | \n", + "
| 470 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_HEME_METABOLISM-0 | \n", + "[[GO:0005515, GO:0000910, transcription regulation, metabolic & enzymatic function, cell cortex formation, GO:0006810, GO:0016310, MESH:D000107, protein formation & modification]] | \n", + "[[GO:0005515, GO:0006351, catalyzing reactions, gtpase activating protein activation, GO:0016575, carbohydrate & lipid metabolism, receptor binding & signaling, GO:0005574]] | \n", + "0.06 | \n", + "
| 471 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_HEME_METABOLISM-1 | \n", + "[[GO:0006351, GO:0003723, post-transcriptional regulation, GO:0006096, GO:0006090, GO:0006749, GO:0006508, transcriptional regulation, MESH:D054875, GO:0003677, MESH:D006655, GO:0006915, cytoskeletal protein, atp-binding, GO:0048870, ubiquitin specific protease, MESH:D015220, voltage-gated chloride channel, GO:0004384, GO:0023052, GO:0051726, cation transporters]] | \n", + "[[GO:0003677, GO:0016573, GO:0005515, transcription regulation, leucine residue modification, GO:0003729, zinc metalloenzymes, atp-binding, protein serine/threonin, endoribonuclease, GO:0031545, 6-phosphogluconate dehydrase, GO:0003723, dynein heavy chain, MESH:C052997, chloride intracellular channel, GO:0003779, MESH:D051528, hexameric atpase, GO:0006814, rho gtpase, inositol polyphosphate, MESH:D011766, selenium-binding protein, clathrin assembly, c-myc, dual specificity protein kinase, MESH:D006021, gtpase-activating-protein, GO:0006914, ring between two helices]] | \n", + "0.06 | \n", + "
| 472 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_HYPOXIA-0 | \n", + "[[GO:0006096, GO:0016310, GO:0004672, GO:0006508, GO:0085029, transcription regulation, GO:0051726, GO:0097009, GO:0006954, cell-cell communication, oxidative stress response]] | \n", + "[[cell signaling, metabolic regulation, GO:0043687]] | \n", + "0.00 | \n", + "
| 473 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_HYPOXIA-1 | \n", + "[[GO:0006915, GO:0016310, MESH:D011494, GO:0005515, GO:0006351, GO:0031005, glycolytic enzyme, carboyhydrate binding, cell binding, GO:0042157, GO:0007165, UBERON:2000098, GO:0040007]] | \n", + "[[cellular transport, GO:0008152, scaffolding, transcriptional regulation, GO:1901987, transcription activity, GO:0016310, cysteine-aspartic acid, GO:0016020, cell surface heparan sulfate, glycosyl hydrolase family, MESH:D000263, MESH:D000262, glyceraldehyde-3-phosphate, cytokine, glycosyltransferase, MESH:D000070778, sulfatase, sulfotransferase, serine/threonine kinase, MESH:D016232, MESH:D008668, MESH:D011973, basic helix-loop-helix]] | \n", + "0.03 | \n", + "
| 474 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[[GO:0051726, receptor signaling, MESH:D008565, GO:0000981]] | \n", + "[[GO:0005515, GO:0005102, transcription regulation, enzyme regulation, GO:0001816, GO:0007155, structure, membrane-associated]] | \n", + "0.00 | \n", + "
| 475 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[[GO:0007165, protein homodimerization, GO:0005525, GO:0003676, GO:0055085, GO:0004672, GO:0007049, GO:0006955, GO:0006915]] | \n", + "[[an underlying biological mechanism of intracellular signaling and cell adhesion proteins working together to regulate gene expression and control cell functions was identified. enriched terms related to this mechanism include gtpases, MESH:D008565, intracellular signaling, calcium-dependent proteins, rna and dna binding, GO:0007155, GO:0000981, enzyme regulation, GO:0005515]] | \n", + "0.00 | \n", + "
| 476 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[[MESH:D016207, GO:0016049, GO:0048468, transmembrane proteins, MESH:D011494, GO:0000981, cell cycle progression]] | \n", + "[[MESH:D018121, MESH:D018925, tgf-beta superfamily, transcriptional regulation, MESH:D017027, MESH:D011494]] | \n", + "0.08 | \n", + "
| 477 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[[the list of gene summaries reveals a group of genes involved in cell trafficking, GO:0007165, GO:0007155, ligand binding, and regulation of the immune response. enriched terms include cytokine, chemokine, MESH:D007378, receptor, GO:0007155, ligand binding, GO:0007165, and regulation of the immune response.\\n\\nmechanism: the mechanism involving these genes involve ligand binding to cytokine, chemokine, or other receptors, resulting in the activation of intracellular pathways leading to signal transduction, GO:0007155, regulation of the immune response]] | \n", + "[[the genes identified are part of the cytokine signaling system and its related pathways involved in immune response and regulation. more specifically, they belong to the type i cytokine receptor family, the phospholipase a2 family, the tumor necrosis factor receptor superfamily, the gp130 family of cytokine receptors, the toll-like receptor family, the interferon regulatory factor family, the bcl2 protein family, the reg gene family, the type ii membrane protein of the tnf family, the ring finger e3 ubiquitin ligase family, the protein tyrosine phosphatase family, the tgf-beta superfamily proteins, the hemopoietin receptor superfamily, the chemokine family, the integrin alpha chain family of proteins and the adapter protein family. there is a common function of these genes in the signaling of cell growth, UBERON:2000098, GO:0006915, migration, and differentiation, as well as the regulation of gene transcription, apoptosis and immune response. \\n\\nmechanism:\\nthe genes identified are part of a gene network that functions together to allow for cell signaling, GO:0040007, and differentiation, as well as inflammatory and immune responses. the various cytokine receptors, protein ty]] | \n", + "0.00 | \n", + "
| 478 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[[GO:0005102, cytokine signalling, GO:0016049, cellular function regulation, immune signalling, inflammation regulation, GO:0051726, apoptosis coordination]] | \n", + "[[MESH:D008565, g protein-coupled receptors, MESH:D018121, interferon-induced proteins, MESH:M0013343, MESH:D051116, MESH:D018925, MESH:D016023, MESH:D020782, MESH:D061566, tol-like receptors]] | \n", + "0.00 | \n", + "
| 479 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[[interactions, GO:0023052, MESH:D008055, GO:0000981, MESH:D016207, MESH:D006728, MESH:D021381, receptors, GO:0007165]] | \n", + "[[GO:0005102, GO:0023052, GO:0055085, calcium binding, GO:0055085]] | \n", + "0.08 | \n", + "
| 480 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[[protein-binding, subunit-binding, rna-binding, transcriptional regulation, GO:0007165, GO:0006955, ligand binding, GO:0032991, GO:0036211]] | \n", + "[[ligand binding, GO:0005102, GO:0003824, GO:0003677, GO:0003723, protein activation, GO:0030163, MESH:D054875]] | \n", + "0.06 | \n", + "
| 481 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[[transcriptional regulation, GO:0008181, MESH:D010447, cytoplasmic proteins, antiviral, MESH:M0369740, GO:0009165, chemokine receptor, dna-binding, rna-binding, lipid-binding, protein adp-ribosylation, GO:0016567, GO:0048255, GO:0016556, GO:0006479, gtp-metabolizing, GO:0008283, GO:0006955, GO:0006952]] | \n", + "[[these genes are connected by their participation in immune regulation and defense, either directly regulating the innate and acquired immune response, or acting as downstream inhibitors and activators of such responses. specific enriched terms include interferon regulation, transcriptional regulation, tumor suppression, MESH:D054875, chemokine receptor signaling, GO:0003723, GO:0009165, GO:0051607, GO:0048255, GO:0005525, GO:0008289, viral invasion, GO:0045087, GO:0030701, GO:0008134, and antigen presentation.\\n\\nmechanism: the commonalities between these genes suggest that they act at various levels of a complex innate and acquired immune response, controlling transcriptional regulation, protein modification and silencing, viral response, and antigen presentation. there are multiple pathways overlapping or influencing each gene's particular role in the overall immune defense, merging into a greater shared mechanism of host immunity]] | \n", + "0.07 | \n", + "
| 482 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[[immune regulation, GO:0003677, GO:0003723, GO:0016567, anti-viral response, cytokine signaling, GO:0006954]] | \n", + "[[the genes in the list encode proteins involved in a variety of processes including immunity, GO:0006954, GO:0006351, GO:0007165, and protein folding and assembly. these processes are typically carried out by two main classes of molecules; ubiquitin ligases and cytokines. the genes in this list are enriched for terms including \"signal transduction\", \"ubiquitin ligases\", \"immune modulation\", \"cytokine activity\", \"transcription regulation\", \"proteasome activity\", \"rna binding\", and \"metallothionein\".\\n\\nmechanism:\\nthe genes in this list encode proteins involved in a variety of processes, with an emphasis on immunity and inflammation. these processes are typically mediated by ubiquitin ligases, MESH:D016207, and other signal transduction proteins. ubiquitin ligases mark target proteins for ubiquitination and other modifications, while cytokines affect the activity of multiple cells. signal transduction proteins transmit signals across cell membranes, affecting the activity of cells. metallothioneins play a role in detoxification and protein folding and assembly, while proteasomes carry out protein degradation within the cell. transcripts are regulated by transcription factors, many genes contain rna binding domains]] | \n", + "0.04 | \n", + "
| 483 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[[GO:0006954, immune cell signaling and development, immune regulation, GO:0044237, regulation of innate and adaptive immunity, metabolic and transcriptional regulation, GO:0003677, GO:0003723]] | \n", + "[[transcriptional regulation, GO:0003824, binding ability, protein structure, cell signalling, MESH:D016207, growth factor signalling, MESH:D007109, GO:0000981, MESH:D054875, MESH:D006136, tripartite motif, GO:0070085, atpase, intracellular sensor, MESH:D015088, GO:0003723, calcium-binding, GO:0004930, MESH:M0476528, cysteine-aspartic acid protease, regulator of complement activation, protein tyrosine phosphatase, ubiquitin-specific protease, antiviral activity, inter]] | \n", + "0.03 | \n", + "
| 484 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[[protein-binding, transcriptional regulation, GO:0007155, cell membrane channel activity, protein metabolism/modification, receptor signalling]] | \n", + "[[ion channels & transporters, receptor proteins, MESH:D002135, MESH:D004798, cell signaling, hormone regulation, GO:0008152]] | \n", + "0.00 | \n", + "
| 485 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[[MESH:D011506, GO:0016049, cellular development, MESH:D009068, GO:0001508, calcium binding, GO:0005496, GO:0008152, GO:0006351, GO:0005488, MESH:C062738, GO:0005562, g proteins, dna-binding]] | \n", + "[[catalyzing reactions, GO:0055085, GO:0023052, dna-binding, GO:0006351, extracellular signaling, calcium-ion binding, immune system signaling, cell growth/maintenance, GO:0007154, hormone regulation, GO:0032502, GO:0008152]] | \n", + "0.12 | \n", + "
| 486 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[[GO:0007155, regulation of growth factors, cytokine regulation, calcium activation, transcriptional regulation]] | \n", + "[[MESH:D008565, MESH:D010447, receptor proteins, MESH:D004268, MESH:D010770, GO:0000981, GO:0008217, MESH:M0022898, GO:0007165, transcriptional regulation, GO:0006811, GO:0006936, immunologic regulation, GO:0001816, GO:1901987, GO:0006915, GO:0007155, MESH:D063646]] | \n", + "0.10 | \n", + "
| 487 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[[GO:0003677, MESH:D015533, cytokine regulation, GO:0008083, GO:0005515, GO:0007165, transmembrane protein activity, GO:0004930, GO:0003723, GO:0003924, GO:0005509, GO:0016571, glutamine-fructose-6-phosphate transaminase activity, cell growth control, GO:0019725, GO:0016491]] | \n", + "[[receptor functions]] | \n", + "0.00 | \n", + "
| 488 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[[cytoskeletal organization, GO:0003677, microtubule organization, gtpase regulation, centrosome interaction, chromatin structure, protein homodimerization]] | \n", + "[[cytoskeleton regulation, cellular communication, gtpase regulation, actin-binding, dna-dependent protein binding, microtubule-associated protein, filamentous cytoskeletal protein, 14-3-3 family protein, MESH:D020662]] | \n", + "0.07 | \n", + "
| 489 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[[MESH:D020558, nucleotide exchange regulation, cellular signaling, GO:0006338, cytoskeleton structure, GO:0006260, GO:0007155, GO:0003779, actin regulation]] | \n", + "[[gtpase activation, GO:0005525, structural maintenance, GO:0003677, GO:0005856, GO:0006915, GO:0007049]] | \n", + "0.00 | \n", + "
| 490 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-0 | \n", + "[[GO:0006412, GO:0015031, protein signaling, GO:0008152, GO:0010467]] | \n", + "[[GO:0006412, GO:0008152, GO:0006457, MESH:D054875, GO:0006351, GO:0003677, damage control, GO:0032502, cellular pathway regulation, GO:0006915, GO:0007049, GO:0030163]] | \n", + "0.13 | \n", + "
| 491 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-1 | \n", + "[[GO:0005515, MESH:D054875, GO:0006351, GO:0003824, GO:0006457, chaperoning, GO:0051726, GO:0006629, GO:0046323, cytoskeleton formation]] | \n", + "[[atp production, amino acid homeostasis and metabolism, stress response, transcription and mrna regulation, chaperones and proteasome degradation pathways, GO:0006629]] | \n", + "0.07 | \n", + "
| 492 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-0 | \n", + "[[GO:0006351, GO:0006412, GO:0003729, MESH:D054657, MESH:D000072260, GO:0043687, cytoplasmic proteins, MESH:M0015044, GO:0003677, GO:0032508, GO:0005652, GO:0005681]] | \n", + "[[GO:0006351, GO:0006412, GO:0006413, GO:0003723, MESH:D054875, GO:0005840, GO:0006412, GO:0032508, MESH:D039102, GO:0003734, GO:0045292, heat shock proteins, MESH:D006655, MESH:D011073, MESH:D000604, GO:0043687]] | \n", + "0.17 | \n", + "
| 493 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-1 | \n", + "[[GO:0009299, GO:0042254, GO:0006412, MESH:D049148, GO:0003723, GO:0043687, GO:0045292, polymerase, GO:0006913, MESH:D054875, GO:0006457, 14-3-3 family proteins]] | \n", + "[[poly(a)-binding, GO:0003723, GO:0032508, GO:0006913, GO:0032183, GO:0000394, GO:0003676, GO:0006473, GO:0006413, GO:0036211, GO:0006457, MESH:D014176, GO:0006412, MESH:D018832, peptidyl-prolyl cis-trans isomerization, antioxidant function, heat shock protein, ubiquitin protein ligase, 14-3-3 family, dna-unwinding enzymes, dna polymerase, voltage-dependent anion]] | \n", + "0.13 | \n", + "
| 494 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-0 | \n", + "[[GO:0003723, ribosomal biogenesis, GO:0008283, GO:0006335, GO:0007165, cell cycle progression, GO:0003682]] | \n", + "[[GO:0005515, transcriptional regulation, cell cycle progression, protein chaperoning, GO:0008283, nuclear localization, rna binding activity, pre-rrna processing, GO:0042254]] | \n", + "0.14 | \n", + "
| 495 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-1 | \n", + "[[GO:0006351, rna binding activity, GO:0006457, cell cycle progression, GO:0006281, protein homodimerization, GO:0006468, GO:0065003, protein kinase/phosphatase activity, mitochondrial mrna processing. mechanism: this list of genes encodes proteins which work together to regulate key cellular activities such as dna replication, transcription, cell cycle progression, and rna processing. these proteins can either complex together or work in tandem to form kinase/phosphatase complexes, which control phosphorylation of key substrates and regulate protein folding to ensure proper protein function. these proteins also interact with dna to regulate genomic activities such as dna replication, transcription, and repair processes]] | \n", + "[[rna binding activity, GO:0006364, protein homodimerization, GO:0008283, GO:0007165, GO:0042254, GO:0006457, GO:0034246]] | \n", + "0.20 | \n", + "
| 496 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MYOGENESIS-0 | \n", + "[[motor protein activity, GO:0019722, GO:0006936, transcriptional regulation, intracellular fatty acid-binding, ligand binding, MESH:D007473, GO:0005884, MESH:D008565, regulation of transcription, phosphorylation of proteins]] | \n", + "[[GO:0006936, calcium channel regulation, ion channel regulation, protein ubiquitination/degradation, actin-based motor proteins, GO:0007165, MESH:D004734]] | \n", + "0.06 | \n", + "
| 497 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MYOGENESIS-1 | \n", + "[[MESH:M0496924, protein regulation, ion channeling, cellular transport, GO:0006629, GO:0010468, neurotransmitter signaling, small molecules, large molecules]] | \n", + "[[summary: the list of genes provided contains components of muscle formation, GO:0023052, and growth.\\nmechanism: the genes encode the components of signaling pathways and physical structures involved in the formation of muscle, including proteins that serve as receptors, binders, MESH:D004798, and structural components like spectrins, GO:0005202, laminin.\\nenriche terms: muscular development; musculosketetal function; signal transduction; protein phosphorylation degradation; cytoplasmic proteins; structural proteins; cytochrome oxidase]] | \n", + "0.00 | \n", + "
| 498 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-0 | \n", + "[[cell fate decisions, GO:0007219, GO:0007165, wnt signalling pathway, cell-cell interaction, GO:0016567, GO:0006355, protein ligase activity, GO:0006468]] | \n", + "[[GO:0007219, GO:0016055, GO:0016567, transcriptional repressor, MESH:D015533, cell fate decisions, MESH:D044767, MESH:D011494]] | \n", + "0.21 | \n", + "
| 499 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-1 | \n", + "[[notch signaling, GO:0016567, cell-cycle regulation, protein breakdown and turnover, intracellular signalling pathways, cell fate]] | \n", + "[[GO:0007219, GO:0016567, GO:0001709, transcriptional regulation, GO:0031146, gamma secretase complex, MESH:D011493, wnt family, basic helix-loop-helix family of transcription factors]] | \n", + "0.07 | \n", + "
| 500 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[[GO:0005739, MESH:D004798, MESH:D010088, MESH:D010088, GO:0006754]] | \n", + "[[GO:0006006, GO:0006631, amino acid metabolism, GO:0005746, MESH:D007506, nadh-ubiquinone oxidoreductase, MESH:D009245, pyruvate dehydrogenase, GO:0022900, oxidative decarboxylation, nad+/nadh oxidoreductase, GO:0016467, MESH:D003576, MESH:D063988, matrix processing, shuttling mechanism.\\n\\nmechanism: the gene products involved in this metabolic pathways work to convert small molecules such as glucose and fatty acids into energy-containing molecules, such as atp and nadh, through a combination of redox reactions, electron transfer processes, and other catalytic systems. these processes involve the participation of numerous proteins, including membrane-associated proteins, enzymes, and enzyme complexes. these proteins form a complex network of interactions that enable the conversion of energy from one form to another, ultimately leading to atp production]] | \n", + "0.00 | \n", + "
| 501 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[[oxidative decarboxylation, MESH:D010088, MESH:D010084, GO:0006754, mitochondrial respiration, GO:0008152, MESH:D003580, MESH:D000214, pyruvate dehydrogenase, MESH:D005420, hydratase/isomerase, leucine-rich protein, 3-hydroxyacyl-coa]] | \n", + "[[terminal enzyme, GO:0006754, GO:0005746, nad/nadh-dependent, cytochrome c oxidase (cox), GO:0006118]] | \n", + "0.06 | \n", + "
| 502 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_P53_PATHWAY-0 | \n", + "[[GO:0007049, GO:0006351, GO:0023052, GO:0006412, GO:0065007, GO:0042592]] | \n", + "[[GO:0005515, GO:0003677, transcriptional regulation, GO:0051726, cell signaling]] | \n", + "0.00 | \n", + "
| 503 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_P53_PATHWAY-1 | \n", + "[[GO:0051726, GO:0016049, GO:0006915, GO:0007165, GO:0006281, transcriptional regulation, chromatin structure, tumor suppression, enzymatic activity, GO:0000988, GO:0004725, GO:0003925]] | \n", + "[[MESH:D011494, GO:0000981, GO:0007049, GO:0006281, GO:0003677, GO:0006412, tnf receptor superfamily, zinc finger, calcium-activated, cyclin dependent, iron-sulfur, GO:0015629, GO:0007165]] | \n", + "0.09 | \n", + "
| 504 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[[analysis of the human genes abcc8, akt3, chga, dcx, dpp4, elp4, foxa2, foxo1, g6pc2, gcg, gck, hnf1a, iapp, UBERON:0002876, insm1, isl1, lmo2, mafb, neurod1, neurog3, nkx2-2, nkx6-1, pak3, pax4, pax6, pcsk1, pcsk2, pdx1, pklr, scgn, sec11a, slc2a2, spcs1, srp14, srp9, srprb, UBERON:0035931, stxbp1, syt13, vdr was performed to determine commonalities in gene function. term enrichment indicated a commonalty in genes that are involved in the regulation of glucose and insulin metabolism, GO:0008283, differentiation and apoptosis, as well as glycogen synthesis and glucose uptake. additionally, many of the genes are involved in the development of neural tissues and the regulation of gene transcription. the underlying biological mechanism could involve alterations in the phosphorylation of proteins and signaling pathways,]] | \n", + "[[GO:0000981, homeobox domain, signal peptide cleavage, MESH:D011494, atp-binding, chromogranin/secretogranin, GO:0005180, protease, MESH:D011770, MESH:D005952, MESH:D000243, MESH:D006593, nuclear receptor, dna-binding, g-protein linked receptor, cysteine-rich protein, gtp-bound proteins, GO:0048500, bhlh transcription factor, doublecortin, calcium-binding protein\\n\\nsummary: genes identified in this list facilitate a variety of essential biological processes, particularly in terms of cell signaling and transcription regulation. among these processes are signal peptide cleavage, atp-binding, peptide hormone secretion and regulation, protease activity, glucose metabolism, adenosine deaminase, gtp-bound protein binding, and transcription factor actions. \\n\\nmechanism: these genes are involved in transcriptional regulation and signaling processes through binding of dna and g-protein linked receptors, homeobox domains, cysteine-rich proteins]] | \n", + "0.00 | \n", + "
| 505 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[[this analysis identifies the common functions of 18 human genes: dpp4, scgn, pklr, pax4, neurod1, srprb, srp14, isl1, insm1, pak3, pax6, elp4, dcx, iapp, lmo2, neurog3, gck, stxbp1, nkx2-2, pdx1, UBERON:0035931, pcsk1, nkx6-1, UBERON:0002876, pcsk2, spcs1, g6pc2, foxo1, sec11a, vdr, foxa2, slc2a2, mafb. they are related to metabolic regulation (glucose, GO:0016088, MESH:D004837, citrate), developmental regulation (neural tissues, UBERON:0001264, UBERON:0002107, lymph nodes), signal transduction (g proteins, ace, atp binding proteins) and hormone regulation related (somatostatin, GO:0016088, vitamin d3). these factors likely work in concert to control and maintain metabolic parameters throughout the body. mechanism: these genes act through various methods including transcriptional regulation, protein interactions, protein cleavage, signaling casc]] | \n", + "[[transcriptional regulation, MESH:M0496924, endocrine system regulation, GO:0006006, cell signalling, MESH:D020558, GO:0000981, GO:0005180, MONDO:0018815, MESH:D043484]] | \n", + "0.00 | \n", + "
| 506 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PEROXISOME-0 | \n", + "[[MONDO:0018815, an antioxidant enzyme, a hormone binding protein, a nuclear receptor transcription factor, a fatty acid desaturase, a carnitine acyltransferase, an isocalate dehydrogenase, a peroxisomal membrane protein, MESH:D005182, antioxidant enzyme, hormone binding protein, nuclear receptor transcription factor, GO:0004768, carnitine acyltransferase, isocalate dehydrogenase, peroxisomal membrane protein, and fad-dependent oxidoreductase.\\n\\nmechanism: many of the genes are involved in regulating the production and movement of lipids and fatty acids, as well as the synthesis of hormones, MESH:D000305, and signalling receptors. the underlying biological mechanism is that these genes act as regulators of metabolic pathways, ensuring that their respective pathways are functioning correctly and that metabolites are transported correctly]] | \n", + "[[GO:0140359, oxidoreductase, dehydrogenase/reductase, hydratase/isomerase, enzymes responsible for fatty acid beta-oxidation, enzymes catalyzing the]] | \n", + "0.00 | \n", + "
| 507 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PEROXISOME-1 | \n", + "[[GO:0006629, GO:0006635, GO:0006281, transcription and replication, MESH:D018384, GO:0006536, GO:0005502, GO:0008202]] | \n", + "[[MESH:D018384, MONDO:0018815, atpases associated with diverse cellular activities, vitamin a family, GO:0004879, nad-dependent oxidoreductases, GO:0005783, MESH:D015238, cyclin-dependent protein kinase, hydratase/isomerase superfamily, GO:0005515, GO:0003677, GO:0050632, carnitine acyltransferase, MESH:D011960]] | \n", + "0.05 | \n", + "
| 508 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[[GO:0016310, GO:0006412, mrna expression, GO:0005515, cell signalling, MESH:D054875, protein phosphatase]] | \n", + "[[MESH:D011494, GO:0016791, GO:0005525, protein-protein interaction, GO:0030552, GO:0000981, peptidyl-prolyl cis/trans isomerase, cytoskeletal function, protein tyrosine phosphatase, protein phosphatase, GO:0140597, MESH:D020662, receptor interacting protein, transmembrane glycoprotein, MESH:D018123, MESH:D054387, inositol trisphosphate receptor, plexin domain, phosphoinositide 3-kinase, ubiquitin activation/conjugation, GO:0003925]] | \n", + "0.04 | \n", + "
| 509 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[[GO:0007165, MESH:D011494, GO:0004707, MONDO:0008383, gpcr, GO:0016791, MESH:D020662, endoplasmic reticulum chaperone protein]] | \n", + "[[MESH:D011494, guanine nucleotide-binding protein, receptor-interacting protein, chaperone protein, protein tyrosine kinase, MESH:D020558, MESH:D000262, protein phosphatase, cytoplasmic face, GO:0006468, GO:0007165, GO:0036211]] | \n", + "0.11 | \n", + "
| 510 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-0 | \n", + "[[GO:0005480, GO:0006897, GO:0006887, intracellular trafficking, MESH:D001678, MESH:D008565, GO:0005906, MESH:D020558, GO:0005794, GO:0005484]] | \n", + "[[MESH:D008565, MESH:D020558, coatomer complex, GO:0016192, MESH:D001678, GO:0035091, GO:0065007, MESH:D002966, GO:0005906, GO:0005794, GO:0030136, MONDO:0018815, GO:0042393, GO:0005802, MESH:M0013340, GO:0006811, GO:0005159, GO:0005783, MESH:D057056, GO:0005483, GO:0005764, GO:0005794, multifunctional proteins]] | \n", + "0.18 | \n", + "
| 511 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-1 | \n", + "[[GO:0003924, snare binding activity, GO:0005484, phosphoinositide-binding, coatomer protein complex, MESH:D052067, protein kinase binding activity, adaptor complexes, atpases associated with diverse cellular activities, snare recognition molecules, gold domain, GO:0030136, transmembrane 4 superfamily, GO:0070273, sec7 domain, membrane mannose-specific lectin, signal-transducing adaptor molecule, identical protein binding activity]] | \n", + "[[this list of genes codes for proteins of various functions, primarily related to organelle trafficking, membrane associations, and receptor binding activities. these proteins are involved in the regulation of intracellular vesicles, endoplasmic reticulum and golgi organization, protein sorting and secretion, cell surface receptor binding, cell-signaling and immunity, protein phosphorylation and kinase binding, and lipid protein modifications. the enriched terms found in the functions of these genes include vesicular transport, MESH:M0354322, organelle trafficking, GO:0007030, GO:0005102, GO:0006457, GO:0006468, snare recognition molecules, clathrin coated vesicles, endoplasmic reticulum-golgi transport, MESH:D025262, GO:0005906, and dystrophin-glycoprotein complex. \\n\\nmechanism: the enriched terms in the gene functions indicate that these proteins are involved in various pathways and process of intracellular cargo trafficking, where proteins, membranes and signaling molecules are sorted, distributed and regulated. the processes are involved with vesicular transport, protein co-translocation, GO:0030258, and protein phosphorylation, which coordinate the mobilization and distribution of proteins, MESH:D008055]] | \n", + "0.02 | \n", + "
| 512 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[[MONDO:0018815, copper chaperone, MESH:D002374, GO:0004861, hypoxia inducible factor (hif), nucleotide excision repair pathway, GO:0004672, GO:0009487, MESH:D005979, MESH:D009195, MESH:D010758, phosphofructokinase, MESH:D054464, GO:0050115, arginine/serine-rich splicing factor, iron/manganese superoxide dismutase, GO:0016491, germinal centre kinase iii (gck iii) subfamily, thioredoxin (trx) system]] | \n", + "[[this list of genes were found to be involved in oxidoreductase activity, intracellular binding and catalytic activity, cellular response regulation, dna and transcription regulation, membrane function, mitochondrial function and antioxidant activity. the enriched terms include oxidoreductase activity, intracellular binding, GO:0003824, cell growth regulation, transcription regulation, membrane function, mitochondrial function, GO:0016209, GO:0020037, GO:0005507, GO:0003677, GO:0043565, tyrosine-specific protein kinase activity, f-actin binding. the underlying biological mechanism is probable related to redox homeostasis, the oxygen metabolism pathway, the cell cycle dna repair pathways, the regulation of transcription membrane function]] | \n", + "0.00 | \n", + "
| 513 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[[GO:0016049, GO:0007049, GO:0006351, redox regulation, MESH:D018384, MESH:D005721, hydroxylase, protease, free-radical scavenging, protein phosphatase]] | \n", + "[[redox processes, MESH:D018384, GO:0006281, GO:0008152, cell growth regulation, inflammation control, cellular defense, MESH:D006419, MESH:D005980, superoxide dism]] | \n", + "0.05 | \n", + "
| 514 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-0 | \n", + "[[protein binding activity, GO:0003714, dna binding activity, rna binding activity, zinc ion binding activity, GO:0004596, serine/threonine-protein kinase activity, GO:0004016, snare binding activity, clathrin binding activity, myosin light chain binding activity, double-stranded dna binding activity, phosphatidic acid phosphohydrolase activity, ubiquitin-protein ligase activity, rna polymerase binding activity, GO:1990817, GO:1990817, GO:0060090, phosphatase binding activity, atp-ases associated activity, GO:0044183, GO:0016165, adp-ribosylation factor-like activity]] | \n", + "[[cell cycle regulatory proteins and kinases, dna binding proteins and chaperones, nucleotide and polypeptide binding proteins, GO:0016791, proteins involved in transcription, gene transcription, GO:0051276, apoptosis regulation, GO:0006281, protein folding and transport, cell signaling and growth regulation, MESH:D004734, cytoskeletal organization, vesicular trafficking\\n\\nmechanism: the underlying biological mechanism is likely involved in multiple steps in cell division and the regulation of gene expression, and in the maintenance of cell homeostasis]] | \n", + "0.00 | \n", + "
| 515 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-1 | \n", + "[[GO:0006457, transcriptional regulation, GO:0007165, GO:0051726, chromatin structure and nuclear envelop function, cell adhesion and motility, GO:0008152, GO:0016567, detection and binding, enzymatic activity, GO:0042311]] | \n", + "[[this list of genes is associated with a range of diverse functions, including intracellular and intercellular trafficking, adhesion, enzyme regulation, transcriptional regulation, ion channel and receptor regulation, and processes related to stress, GO:0007568, and metabolism. common enriched terms include protein kinase and phosphatase, GO:0140359, g-protein coupled receptors, receptors, transcriptional regulation, GO:0016569, GO:0051726, heat shock, GO:0005515, ubiquitin-protein ligase and ubiquitin protease, zinc metalloproteases, and peptide n-acetyltransferase. the underlying biological mechanism or pathway associated with these genes may involve signal transduction as mediated by enzyme activity, MESH:D007473, receptors, and other proteins, as well as cell-to-cell adhesion and trafficking processes involved in membrane dynamics.\\n\\nsummary: list of genes associated with diverse functions including intracellular and intercellluar trafficking, adhesion, regulation of enzymes, GO:0006351, ion channels and receptors, and processes related to stress, GO:0007568, and metabolism.\\nmechanism: signal transduction as mediated by enzyme activity, MESH:D007473, receptors, and other proteins, as well as cell-to]] | \n", + "0.05 | \n", + "
| 516 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[[transmembrane proteins, receptor signaling pathways, transcription regulation, cell signaling, GO:0007155, GO:0016049, tgf-beta superfamily, MESH:D010749, ubiquitin ligases, tight junction adaptors]] | \n", + "[[the human gene summaries represent a variety of cell signaling, cell growth and differentiation, transcription regulation, adhesion and migration, and apoptosis-related functions. several genes in the list (acvr1, GO:0005680, arid4b, bmpr1a, bmpr2, cdh1, ifngr2, junb, lefty2, map3k7, ncor2, ppm1a, pp1ca, rahb, smad1, smad3, smad6, smurf1, smurf2, tgfb1, tgfbr1, MESH:D016212, cdk9, cdkn1c, ctnnb1, eng, fnta, MESH:D045683, hipk2, id1-3, klf10, ltbp2, pmepa1, ppp1r15a, serpine1, ski, skil, slc20a]] | \n", + "0.02 | \n", + "
| 517 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[[transmembrane serine/threonine kinases, transcriptional repressors, transforming growth factor (tgf)-beta superfamily, rho family of small gtpases, smad family, c2h2-type zinc finger domains, MESH:M0460357, caax geranylgeranyltransferase, smad interacting motif (sim), homeodomain-interacting protein kinase, MESH:D004122, transforming growth factor-beta (tgfb) signal transduction, MESH:D018398, MESH:D054645, protein folding and trafficking]] | \n", + "[[GO:0007165, transcription regulation, cell-to-cell communication, MESH:D018398, serine/threonine protein kinase, disulfide-linked homotrimeric proteins, protein phosphatase, transmembrane proteins, smurf protein, cystein-rich motif, GO:0006457]] | \n", + "0.04 | \n", + "
| 518 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[[GO:0006351, cytokine, inflammatory, UBERON:2000098, GO:0006915, cell signalling, receptor regulation, GO:0003924, GO:0003723]] | \n", + "[[transcriptional regulation, GO:0005125, GO:0008283, GO:0006629]] | \n", + "0.00 | \n", + "
| 519 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[[MESH:D016207, MESH:D018925, MESH:D010770, GO:0000981, MESH:D016212, nf-kappa-b, myc/max/mad, jagged 1, stat-regulated pathways, MESH:D008074, MESH:M0496065]] | \n", + "[[GO:0006954, GO:0007165, transcriptional regulation, GO:1901987, cytokine, MESH:D011506, receptor, GO:0000981, enzyme, growth factor, MESH:D019204, chemokine, MESH:D008074, pentraxin protein, GO:0016791, MESH:D010770, stress response]] | \n", + "0.12 | \n", + "
| 520 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[[rna-binding, protein-binding, GO:0019538, GO:0009058, GO:0044183, GO:0000981, GO:0006457]] | \n", + "[[GO:0003723, transcription regulation, GO:0006457, protein targeting and covalent modifications, endoplasmic reticulum function, GO:0006413]] | \n", + "0.08 | \n", + "
| 521 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[[GO:0003723, GO:0005783, transcriptional regulation, GO:0006457, GO:0140597, mrna decapping, MESH:M0465019, GO:0030163, MESH:D021381]] | \n", + "[[GO:0006412, endoplasmic reticulum stress response, GO:0003723, protein expression, conformation folding]] | \n", + "0.08 | \n", + "
| 522 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-0 | \n", + "[[cellular response regulation, GO:0007165, transcriptional regulations, MESH:D011956, GO:0016310, calcium binding, MESH:D011494, transmembrane proteins, protein tyrosine kinases, MESH:D017027, MESH:M0015044, protein inhibitor of activated stats, integrin beta, annexin family, adp-binding cassette family, MESH:D020690, arfaptin family, wd repeat proteins, maguk family, camp-dependent pathways, MESH:D000071377, MESH:D008869, pak family, MESH:D015220, mitogen-responsive phosphoproteins, nuclear histone/protein, celf/brunol family, four-and-a-half-lim-only proteins]] | \n", + "[[GO:0007155, GO:0005207, nuclear phosphoprotein, phosphoprotein, cytoplasmic receptor, MESH:D020558, GO:0016791, receptor tyrosine kinase, GO:0006351, camp, ion transport atpase, transmembrane protein]] | \n", + "0.00 | \n", + "
| 523 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-1 | \n", + "[[GO:0007165, MESH:D016326, cellular adhesion, GO:0000981, MESH:D011494, MESH:D020558, camp, calcium-dependent phospholipid binding protein, MESH:D011505, MESH:D017868, scaffolding protein, MESH:D020690, MESH:D010711, protein tyrosine phosphatase, rho-like gtpase, calcium-activated bk channel, cyclin-dependent kinase, n6-methyladenosine-containig protein, helix-loop-helix proteins, MESH:D016601, atpase, guanine nucleotide-binding protein, cytoplasmic surface protein, serine protease inhibitor, protein inhibitor of activated stat, GO:0004384, mitogen-responsive]] | \n", + "[[GO:0000981, receptor, GO:0005488, growth factor, phosphoprotein, MESH:D010770, cytoplasmic surface, nuclear histone/protein methyltransferase, MESH:D020558, wd repeat protein, protein tyrosine phosphatase, serine/threonine kinase, caveolae plasma membrane, g-protein coupled receptor, MESH:D000071377, ab hydrolase superfamily, microtubule-associated protein, protein-tyros]] | \n", + "0.07 | \n", + "
| 524 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-0 | \n", + "[[cell regulation, GO:0055085, metabolic catabolism, transcription support, GO:0006468, non-classical heavy chain, GO:0020037, GO:0007165, cytoskeleton formation, GO:0030163, cell signaling, GO:0006412, GO:0010467]] | \n", + "[[GO:0005515, MESH:D002384, transcriptional regulation, cell signaling, metabolic reactions]] | \n", + "0.06 | \n", + "
| 525 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-1 | \n", + "[[GO:0005515, GO:0005525, GO:0005215, reactive catalysis, cell signaling, membrane-associated functions]] | \n", + "[[regulatory proteins, GO:0000981, membrane and transport proteins, structural proteins, MESH:D004798, biosynthesis of heme, cellular signaling, transcription control, GO:0008152, GO:0006955]] | \n", + "0.00 | \n", + "
| 526 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[[wnt signalling pathway, transmembrane glycoprotein, MESH:D006655, GO:0000981, GO:0007219, GO:0005515, GO:0007165, GO:0006511, transcriptional regulation, dna replication and repair]] | \n", + "[[cell-cell interactions, MESH:D047108, transcriptional regulation, GO:0006281, wnt signaling, notch signaling, hedgehog signaling, MESH:D044783]] | \n", + "0.06 | \n", + "
| 527 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[[wnt signaling, notch signaling, hedgehog signaling, transcriptional regulation, cell cycle progression, developmental events, dna replication and repair, transcriptional silencing, GO:0043161]] | \n", + "[[transcriptional regulation, GO:0001709, signaling pathway activation, MESH:D060449, notch pathway, hedgehog pathway, protein interactions, cell growth regulation, GO:0004672, GO:0030163, cell-cell interaction, cell-matrix interaction, protein ligase binding activity, GO:0004842, membrane-bound protease activity, transcriptional repressor, GO:0006338, notch receptor cleavage, intracellular domain formation, ectodomain shedding, MESH:D015533, nuclear receptor co-repressor]] | \n", + "0.03 | \n", + "
| 528 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "T cell proliferation-0 | \n", + "[[GO:0004888, calmodulin binding activity, GO:0061630, GO:0033192, GO:0004721, GO:0004725, GO:0004672, MESH:D015533, guanine nucleotide exchange activity, ligand binding activity]] | \n", + "[[the provided list of genes and associated descriptions demonstrates variation in generic cellular processes like protein degradation, protein and nucleic acid binding and kinase activity, as well as specific pathways involving cytokine and chemokine signaling, transcriptional regulation and regulation of immune cell activity. across these processes, the significant terms enriched across the genes include: protein tyrosine kinase activity; protein/nucleic acid/oligomeric binding activities; protein ubiquitination; transcriptional and immune cell activation and proliferation; intracellular receptor signaling and nf-kappab pathways; and cell cycle regulation.\\n\\nmechanism:\\nthe identified genes likely affect several common pathways, including signaling pathways that mediate cell division, motility, adhesion, chemokine- and cytokine-mediated responses, and immune cell function. in particular, the proteins encoded by these genes likely play roles in the regulation of post-translational modifications, such as protein ubiquitination, and the regulation of gene transcription, likely in response to extracellular cues. additionally, the identified proteins may mediate the recruitment of the cbm signalosome, leading to the activation of nf-kappab pathways. finally, cell cycle-related processes]] | \n", + "0.00 | \n", + "
| 529 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "T cell proliferation-1 | \n", + "[[transcriptional regulation, cellular signaling pathways and processes, GO:0016049, differentiation, GO:0006950, GO:0006955, protein folding and trafficking, MESH:D051192, transmembrane proteins, receptor tyrosine kinases, ubiquitin e3 ligases, MESH:D020134, cgmp-binding phosphodiesterase]] | \n", + "[[GO:0007165, GO:0008037, GO:0004721, GO:0061630, lipid enzyme, MESH:D011505, cgmp kinases, GO:0000981, protein scaffold, cytokine, adaptor protein, GO:0051301, adhesion, differentiation, GO:0006950, negatively regulated, MESH:D021381, cell fate and patterning, MESH:D002470, ligand-gated ion channel, GO:0051092, GO:0006569, er stress-induced protection, transmembrane glycoprotein, MESH:D050503, wnt gene family, GO:0016020]] | \n", + "0.05 | \n", + "
| 530 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "Yamanaka-TFs-0 | \n", + "[[this set of genes is involved in embryonic development, stem cell pluripotency, stem-cell maintenance, and dna damage response. commonly enriched terms include cell cycle regulation, transcription regulation, GO:0006915, cellular transformation, and dna damage repair. mechanism:these genes control critical functions of cell cycle progression, gene transcription, and dna repair, providing the necessary foundation for the development of the organism. these pathways provide the structural and biochemical features of embryonic development, maintenance of stem cells and pluripotency, response to cellular damage]] | \n", + "[[genes in this list are transcription factors involved in the development of various organ systems, such as the skin and cns, as well as responding to dna damage, GO:0006915, and cellular transformation. the enriched terms are transcription factor activity; gene expression regulation; cell cycle regulation; dna damage response; pluripotency; and embryo development.\\n\\nmechanism: the transcription factors in this list interact with dna, regulate gene expression, and influence cell cycle progression, GO:0006915, and cellular transformation. combined, these genes are thought to play a role in creating and maintaining cellular and tissue identity, as well as responding to environmental changes. this could be part of a larger mechanism that governs organism development and homeostasis]] | \n", + "0.04 | \n", + "
| 531 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "Yamanaka-TFs-1 | \n", + "[[GO:0000981, MESH:D047108, stem cell maintenance, MESH:D063646, GO:0030154]] | \n", + "[[GO:0000981, zinc finger proteins, GO:0007049, MESH:D004249, MESH:D016147, MESH:D047108, stem cell maintenance, translocation, homeodomain]] | \n", + "0.27 | \n", + "
| 532 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "amigo-example-0 | \n", + "[[GO:0007155, MESH:D016326, MESH:M0023728, cellular communication, GO:0042592, GO:0042060, GO:0006915, motility, GO:0001525]] | \n", + "[[GO:0007155, GO:0016477, cell signalling, GO:0008152, GO:0006915, GO:0009653, GO:0007599, MESH:D007109, extracellular matrix maintenance]] | \n", + "0.12 | \n", + "
| 533 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "amigo-example-1 | \n", + "[[GO:0007219, osteoclast attachment/mineralized bone matrix, jagged 1/notch 1 signaling, GO:0007155, GO:0006915]] | \n", + "[[GO:0048729, matrix metalloproteinase inhibitor, regulated cell adhesion, cytoplasmic protein tyrosine kinase, GO:0005161, cytokine-induced gene expression, GO:0005583, cell signaling pathway, MESH:D015533, antimicrobial activity, GO:0031012, GO:0016477, GO:0008283]] | \n", + "0.00 | \n", + "
| 534 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_0-0 | \n", + "[[GO:0055085, growth factor regulation, calcium regulation, transcription regulation, MESH:D007473, calcium-dependent processes, protein binding activity, chromatin binding activity, gtpase activating protein binding activity, histone binding activity, dna-binding activity, sequence-specific double-stranded dna binding activity, GO:0000988]] | \n", + "[[GO:0007165, transcription regulation, ion regulation, GO:0005515, cytoskeletal adaptor, MESH:D006023]] | \n", + "0.06 | \n", + "
| 535 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_0-1 | \n", + "[[this list of genes is involved predominantly in processes related to binding activities, dna-binding transcription factor activities, chromatin binding activities, and protein domain-specific binding. the underlying biological mechanism involves pathways that regulate cell morphology and cytoskeletal adaptor proteins. the enriched terms include: binding activity, GO:0003700, chromatin binding activity, protein domain-specific binding activity, cell morphology, MESH:D051179]] | \n", + "[[GO:0000988, metal ion binding activity, dna binding activity, chromatin binding activity, rna binding activity, protein domain-specific binding activity, histone binding activity, methylated histone binding activity]] | \n", + "0.17 | \n", + "
| 536 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_1002-0 | \n", + "[[GO:0007165, protein-protein interactions, MESH:D004734, GO:0051015, troponin binding, GO:0005523, GO:0051219, GO:0032515, GO:0043531, atp binding. mechanism: these genes are involved in pathways of signal transduction, protein-protein interactions, and energy metabolism, which lead to muscle contraction and tissue development. activation of these pathways leads to calcium release, which in turn activates contractile proteins such as troponin, tropomyosin, and actin. these proteins act together to promote muscle contraction and cytoskeletal structure]] | \n", + "[[GO:0051015, GO:0048870, GO:0004722, myosin-binding proteins, MESH:D002154, GO:0045010, GO:0005523, calcium sensitivity, MESH:D044767, GO:0003735, GO:0004930, GO:0042923, GO:0050262, GO:0061769, GO:0019674, GO:0007015, GO:0006936, GO:0055008, GO:0030838]] | \n", + "0.07 | \n", + "
| 537 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_1002-1 | \n", + "[[MESH:D024510, actin and tropomyosin binding, calcium- and energy-regulation, ion channeling, negative regulation of cytokine signaling pathways, GO:0033173]] | \n", + "[[actin filament binding activity, muscle alpha-actinin binding activity, actin monomer binding activity, tropomyosin binding activity, GO:0006936, GO:0045214, GO:0071691, GO:0045010, GO:0030838, muscle excitation-contraction coupling, calcium release complex, muscle associated proteins, GO:0030036, GO:0007507]] | \n", + "0.00 | \n", + "
| 538 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "endocytosis-0 | \n", + "[[GO:0006897, GO:0015031, GO:0051639, endoplasmic reticulum and recycling endosome membrane organization, GO:0044351, GO:0016043, intracellular signaling, GO:0051260]] | \n", + "[[GO:0030030, MESH:D021381, MESH:D011494, GO:0048870, membrane reorganization, GO:0006897, cytoskeletal reorganization, mitogen-activated protein kinase, lysosomal degradation, GO:0051168]] | \n", + "0.06 | \n", + "
| 539 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "endocytosis-1 | \n", + "[[GO:0015031, GO:0006897, GO:0006898, GO:0051260, GO:0007155, GO:0048870, amino acid residues, MESH:D054875, GO:0015908, cytoskeletal reorganization, GO:0016192, signaling complex regulation, GO:0140014, GO:0006919]] | \n", + "[[GO:0006897, lysosomal degradation, GO:0015031, GO:0006898, membrane processes, gtpase regulation, MESH:D044767, death domain-fold]] | \n", + "0.16 | \n", + "
| 540 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "glycolysis-gocam-0 | \n", + "[[GO:0006096, GO:0016310, MESH:D006593, glucose phosphate isomerase, phosphofructokinase, MESH:D005634, fructose-1,6-bisphosphate, MESH:D014305, glyceraldehyde-3-phosphate dehydrogenase, MESH:D010736, MESH:D011770, MESH:D010751]] | \n", + "[[GO:0006006, GO:0006096, GO:0016310, GO:0006000, GO:0006094, GO:0004332, glycogen storage, GO:0016853, GO:0004743, GO:0004396]] | \n", + "0.10 | \n", + "
| 541 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "glycolysis-gocam-1 | \n", + "[[muscle maturation, MESH:D024510, GO:0001525, GO:0006096, MONDO:0003664, MONDO:0002412, plasmin regulation]] | \n", + "[[GO:0006096, GO:0008152, regulation of energy conversion, MESH:D024510, tumor progression, GO:0006094, GO:0001525, neurotrophic factor, MESH:M0025255]] | \n", + "0.23 | \n", + "
| 542 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "go-postsynapse-calcium-transmembrane-0 | \n", + "[[GO:0006816, calcium ion regulation, postsynaptic ion channel, GO:0005892, glutamate receptor channel, g protein-coupled receptor, plasma membrane protein, ligand-gated ion channel]] | \n", + "[[calcium homeostasis, calcium-channel activity, MESH:D007473, g-protein coupled receptor, ligand-gated ion channel]] | \n", + "0.08 | \n", + "
| 543 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "go-postsynapse-calcium-transmembrane-1 | \n", + "[[calcium ion regulation, GO:0006816, n-methyl-d-aspartate receptor family, MESH:C413185, MESH:D011954, p-type primary ion transport atpases]] | \n", + "[[calcium homeostasis, calcium influx, GO:0007268, neuronal development, MESH:D058446, purinergic receptor, GO:0004972, MESH:C413185, g-protein coupled receptor]] | \n", + "0.07 | \n", + "
| 544 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "go-reg-autophagy-pkra-0 | \n", + "[[GO:0043539, protein serine/threonine kinase binding activity, GO:0004860, GO:0005085, GO:0032008, GO:0010605, GO:0032956, GO:0032006, GO:0016241, regulation of nf-kappab activation, GO:0001558, regulation of cell survival, GO:0038187, GO:0006281, GO:0045087]] | \n", + "[[GO:0016049, GO:0006915, GO:0007165, serine/threonine kinase activator activity, GO:0035004, GO:0005085]] | \n", + "0.05 | \n", + "
| 545 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "go-reg-autophagy-pkra-1 | \n", + "[[this term enrichment test looked at a list of human genes together with their functions. it found that the genes have functions related to cell cycle regulation, GO:0007165, GO:0043170, protein kinase binding and regulating chromatin remodeling and transcription. the enriched terms include cell cycle regulation, GO:0007165, GO:0043170, GO:0019901, GO:0016310, chromatin remodeling and transcriptional regulation.\\n\\nmechanism: the genes in this list are involved in processes such as cell cycle regulation, GO:0007165, GO:0043170, GO:0019901, phosphorylation and chromatin remodeling and transcription, which are interconnected. these processes all depend on the activity of various protein kinases and their activation by various components, including snca, MESH:D053148, trib3, ccny, pik3ca, akt1, nod2, kat5, rptor, smcr8, mlst8, tab2, hspb1, irgm, GO:0033868, cdk5r1 and other proteins. they interact and cooperate with each other to form pathways and complexes responsible for cell cycle regulation and activation or inhibition of specific genes. ph]] | \n", + "[[GO:0006281, apoptosis regulation, GO:0007165, GO:0016049, nutrient and insulin levels, macromolecule metabolic process regulation, GO:1901987, GO:0006338]] | \n", + "0.03 | \n", + "
| 546 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[[GO:0016798, GO:0005980, GO:0006516, GO:0051787, GO:0036503, glycosaminoglycan hydrolysis, heparan sulfate hydrolysis, cell surface hyaluronidase.\\nhpyothesis: the genes listed serve key roles in the degradation of polysaccharides and glycoproteins, the recognition of misfolded proteins and their subsequent degradation by endoplasmic reticulum-associated degradation, the hydrolysis of glycosaminoglycans, and the hydrolysis of heparan sulfate for the maintenance of cell proteins and structure]] | \n", + "[[glycosyl hydrolase, glycosyl bond hydrolysis, oligosaccharide processing, MESH:D006023, MESH:D011134, n-linked oligosaccharide, o-linked n-acetylglucosamine, β-1,4-glucosidase, β-glucosidase, β-hexosaminidase]] | \n", + "0.00 | \n", + "
| 547 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[[glycohydrolase enzymes, glycosaminoglycans (gag]] | \n", + "[[glycosyl hydrolase, glycohydrolytic enzyme, MESH:D006821, MESH:D005644, lysosomal hydrolase, n-linked oligosaccharide processing, MESH:D001616, MESH:D001619, MESH:D001617, MESH:D009113, alpha-1,4-glucosidase, MESH:D043323, MESH:D000520, MESH:D055572, mannosidase, MESH:M0012138, alpha-l-iduronic acid, alpha]] | \n", + "0.00 | \n", + "
| 548 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "ig-receptor-binding-2022-0 | \n", + "[[antigen binding activity, immunoglobulin receptor binding activity, GO:0002377, GO:0002250, protein homodimerization]] | \n", + "[[antigen binding activity, immunoglobulin receptor binding activity, activated/inactivated immune response, GO:0042803, peptidoglycan binding activity]] | \n", + "0.25 | \n", + "
| 549 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "ig-receptor-binding-2022-1 | \n", + "[[immunoglobulin receptor binding activity, GO:0002253, antigen binding activity, GO:0042803, immunoglobulin lambda-like polypeptides, preb cell receptor, src family of protein tyrosine kinases, c-type lectin/c-type lectin-like domain]] | \n", + "[[antigen binding activity, immunoglobulin receptor binding activity, GO:0002253, GO:0042803, peptidoglycan binding activity, phosphatidylcholine binding activity, transduction of signals, allelic exclusion, myristylation, palmitylation, protein tyrosine kinases, sh2 and sh3 domains, MESH:D008285, MESH:D010455, antigen presenting cells, preb cells, src family of protein tyrosine kinases (ptks), c-type lectin domain]] | \n", + "0.18 | \n", + "
| 550 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "meiosis I-0 | \n", + "[[GO:0004519, bcl-2 homology domain 3 binding, GO:0003682, GO:0003677, GO:0003678, GO:0003697, 3'-5' exode]] | \n", + "[[the gene summaries indicate that most of the genes are involved in processes related to dna binding, GO:0006281, GO:0006310, and meiotic processes. the enriched terms include \"dna binding\", \"dna repair\", \"dna recombination\", \"meiosis\", \"double-stranded dna binding\", \"single-stranded dna binding\", GO:0003682, GO:0004519, dead-like helicase activity, and bcl-2 homology domain activity.\\n\\nmechanism: the mechanism underlying the enrichment of these gene functions appears to be related to the repair and maintenance of chromosomal integrity as well as the regulation of cell division, differentiation, and development. through their combined activities, the genes appear to be involved in the maintenance of genome stability and the efficient transmission of genetic information from one generation to the next]] | \n", + "0.10 | \n", + "
| 551 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "meiosis I-1 | \n", + "[[meiotic recombination, GO:0006281, GO:0007059, double-strand dna break repair, homologous chromosome pairing, dna binding activity, GO:0051289]] | \n", + "[[GO:0006281, meiotic recombination, GO:0006302, GO:0035825, chromosome synapsis, GO:0007059, MESH:D023902, holliday junction resolution, dna strand-exchange, reciprocal recombination, GO:0007130, GO:2000816, positive regulation of response to dna damage, GO:0006611, GO:0031297, GO:0000712, GO:0060629, GO:0003677, GO:0003697, single-str]] | \n", + "0.12 | \n", + "
| 552 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "molecular sequestering-0 | \n", + "[[this list of genes encodes proteins involved in a range of cellular processes such as cell cycle progression, GO:0006897, iron storage and regulation, cellular response to stress and inflammation, GO:0006915, transcriptional regulation, GO:0046907, GO:0016567, and toxic metal and cytosolic signaling. enriched terms include protein binding, lipid and hormone transport, GO:0003779, GO:0003724, GO:0006511, cell cycle progression, and negative regulation of nitrogen compound metabolic process. mechanism: these genes are involved in a wide range of processes related to regulating cell growth, GO:0032502, and homeostasis. they play a role in pathways such as the cell cycle, GO:0006915, inflammatory metabolic processes]] | \n", + "[[GO:0005515, GO:0046907, GO:0043161, GO:0051726, regulation of cell growth and survival, cholesterol and lipids metabolism, nf-κb inhibiting proteins, GO:0009792, GO:0007283, GO:0045087, cytokines and growth factors, antioxidant enzymes, GO:0030097]] | \n", + "0.03 | \n", + "
| 553 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "molecular sequestering-1 | \n", + "[[GO:0005515, MESH:D015533, GO:0008152, MESH:D007109, GO:0006915, GO:0007049, GO:0016310]] | \n", + "[[GO:0006897, iron storage, GO:0008610, GO:0006915, GO:0008283, GO:0030154, defense from bacterial infection, transcription regulation, translation regulation]] | \n", + "0.07 | \n", + "
| 554 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "mtorc1-0 | \n", + "[[GO:0006412, GO:0015031, protein signaling, GO:0008152, GO:0010467]] | \n", + "[[GO:0006412, GO:0008152, GO:0006457, MESH:D054875, GO:0006351, GO:0003677, damage control, GO:0032502, cellular pathway regulation, GO:0006915, GO:0007049, GO:0030163]] | \n", + "0.13 | \n", + "
| 555 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "mtorc1-1 | \n", + "[[metabolic reactions, GO:0051726, energy production, MESH:D011494, GO:0016791, MESH:D003577, MESH:D000604, peptidase c1 family, GO:0031545, ion transporter, ubiquitin-like proteases, ubiquitin ligases, serine/threonine protein kinases, glyceraldehyde-3-phosphate dehydrogenase, nadp-dependent dehydrogenases, rna binding protein, GO:0016467, pyruvate dehydrogenase, MESH:D012321, GO:0016538, MESH:D005634, heat shock protein, hetero trimeric co-factors, MESH:D050603, MESH:D000263, MESH:D013762, MONDO:0008090]] | \n", + "[[GO:0008152, GO:0023036, GO:0007165, transcriptional regulation, epigenetic regulation, GO:0044183, proteolytic activity, GO:0051726]] | \n", + "0.03 | \n", + "
| 556 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "peroxisome-0 | \n", + "[[this set of genes are enriched for terms related to peroxisomal biogenesis and peroxisomal protein import. the aaa atpase family, peroxisomal membrane proteins, c-terminal pts1-type tripeptide peroxisomal targeting signals, and peroxisomal targeting signal 2 are all over-represented in the gene list.\\n\\nmechanism: the mechanism behind these genes is the import of proteins into peroxisomes, resulting in peroxisomal biogenesis. the aaa atpases, peroxisomal membrane proteins, c-terminal pts1-type tripeptide peroxisomal targeting signals, peroxisomal targeting signal 2 are all involved in either targeting or catalyzing this protein import]] | \n", + "[[peroxisome biogenesis, peroxisomal protein import, tripeptide peroxis]] | \n", + "0.00 | \n", + "
| 557 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "peroxisome-1 | \n", + "[[this set of genes is related to the function of peroxisome biogenesis and associated disorders. the enriched terms are peroxisome biogenesis, GO:0017038, peroxisomal matrix proteins, atpase family, and pti2 receptor/pex7.\\n\\nmechanism: peroxisomes are important organelles for a variety of metabolic functions, and the synthesis and organization of these organelles is mediated by the pex genes. pex6 and pex2 are involved in protein import, where the pex2 protein forms a membrane-restricted complex, and pex6 is predominantly cytoplasmic and plays a direct role in peroxisomal protein import and receptor activity. pex3 and pex7 are required for peroxisomal biogenesis, and pex7 is the cytosolic receptor for the set of peroxisomal matrix enzymes targeted to the organelle by the peroxisome targeting signal 2. lastly, pex1 forms a heteromeric complex and plays a role in the import of proteins into peroxisomes and peroxisome biogenesis]] | \n", + "[[aaa atpase family, MONDO:0019234, peroxisomal protein import, peroxisomal matrix protein import, heteromeric complex, peroxisome targeting signal 2]] | \n", + "0.00 | \n", + "
| 558 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "progeria-0 | \n", + "[[GO:0000785, nuclear membr]] | \n", + "[[the genes in this list are associated with post-translational proteolytic cleavage, intermolecular integration, dna repair and dna helicase activity, and nuclear stability and chromatin structure. the underlying mechanism is likely related to protein modification and regulation of cellular components involved in dna metabolism and gene expression. the enriched terms include protein modification, proteolytic cleavage, GO:0003678, intermolecular integration, GO:0006281, chromatin structure, nuclear stability]] | \n", + "0.00 | \n", + "
| 559 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "progeria-1 | \n", + "[[these genes are all related to essential functions that facilitate the proper structure and organization of the nucleus and genome, primarily through the formation and maintenance of nuclear lamin, dna helicases and chromatin structures. there is evidence that all of these genes are involved in the proper functioning of cell division, GO:0006281, and transcription, as well as the maintenance of genome stability. the most enriched terms related to the functions of these genes are nuclear lamina, dna helicase, chromatin structure, GO:0006281, GO:0006351, genome stability, GO:0051301, nuclear membrane proteins, and nuclear localization signal. \\n\\nmechanism: the genes may be involved in pathways that coordinate the formation and maintenance of nuclear lamin, dna helicase, and chromatin structures, which are necessary for cell division and transcription, as well as the maintenance of genome stability. these pathways may involve the direct interactions between the gene products, as well as the recruitment of nuclear membrane proteins and signals involved in maintaining nuclear organization]] | \n", + "[[this set of genes is involved in the maintenance of genome stability and chromosome integrity, likely in terms of forming the nuclear lamina and promoting nuclear reassembly. the enriched terms are genome stability, chromosome integrity, GO:0005652, nuclear reassembly.\\n\\nmechanism: the set of genes are likely working together to form and maintain a matrix of proteins which form the nuclear lamina next to the inner nuclear membrane, thus providing stability to the genome and the chromosomes by helping to organize the dna within the nucleus. this is achieved through binding with both dna and inner nuclear membrane proteins and recruiting chromatin to the nuclear periphery to achieve nuclear reassembly]] | \n", + "0.00 | \n", + "
| 560 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "regulation of presynaptic membrane potential-0 | \n", + "[[neuronal signaling, neuron communication, MESH:D007473, excitatory dependent channels, inhibitory neurotransmitter, ligand-gated ion channel, g protein-coupled membrane receptor]] | \n", + "[[MESH:D007473, voltage-gated ion channel, MESH:D015221, ligand-gated ion channel, MESH:D018079, MESH:D017470, MESH:D015222]] | \n", + "0.17 | \n", + "
| 561 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "regulation of presynaptic membrane potential-1 | \n", + "[[MESH:D017981, MESH:D058446, GO:0009451, voltage-gated ion channels, channel subunits, channel polymorphisms, g-protein-coupled transmembrane receptors, MESH:D017470, MESH:D018079, MESH:D015221]] | \n", + "[[GO:0007268, MESH:D009482, inhibitory, excitatory, MESH:D017981, MESH:D015221, MESH:D018079, MESH:D017470, MESH:D007649, GO:0009451, voltage-gated, MESH:D007473, MESH:D058446, MESH:D019204]] | \n", + "0.33 | \n", + "
| 562 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "sensory ataxia-0 | \n", + "[[transcriptional regulation, mitochondrial rna synthesis, neurodevelopment, GO:0030218, GO:0036211, nucleolar function, neuronal network formation, sensory receptor function]] | \n", + "[[GO:0000981, GO:0009056, moonlighting proteins, GO:0002377, adapter molecules, heme transporter, myelin upkeep, GO:0005643, mitochondrial dna polymerase, ubiquitin ligase, aminoacyl-trna synthetase.\\n\\nmechanism: these genes work together in a joint mechanism to regulate biological processes like cell replication, neuronal development, protein folding, and enzymatic activity. in particular, their collective involvement in the coordination of transcriptional activity, ion transport, and dna-binding suggests a complex integrated process by which these genes serve to facilitate normal cell functions]] | \n", + "0.00 | \n", + "
| 563 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "sensory ataxia-1 | \n", + "[[GO:0000981, dna helicase, hexameric dna helicase, neurotrophic factor, pdz domain, ma cation channels, MESH:D005956, protein synthetase, mitochondrial dna polymerase, heme transporter, GO:0005643, MESH:D044767, transmembrane glycoprotein]] | \n", + "[[GO:0000981, dna helicase, nerve myelin maintenance, mechanically-activated cations channels, nerve motor neuron survival, MESH:D054875]] | \n", + "0.12 | \n", + "
| 564 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "term-GO:0007212-0 | \n", + "[[g-protein coupled receptor signaling, g-protein subunit signaling, GO:0004016, phospholipase c-beta activity, GO:0005102, GO:0007165, second messenger synthesis, transmembrane signaling]] | \n", + "[[the summaries of the provided gene functions describe proteins linked to the activity and regulation of g-protein coupled receptor signaling pathways, including dopamine, MESH:D016232, and serotonin receptors, as well as proteins involved in calcium ion regulation, GO:0003677, and apoptosis. statistically over-represented terms include: g-protein coupled signaling; calcium ion regulation; transmembrane signaling; dna binding; and apoptotic process. \\n\\nmechanism:\\nthe common function of these genes is likely to be linked to the regulation of g-protein coupled signaling pathways, which regulate a variety of cellular processes, including cellular signaling and growth, neuronal development, apoptosis. calcium ion regulation transmembrane signaling are also likely to be important for the functioning of these genes. dna binding proteins proteins that enable clathrin light chain binding activity may be involved in the transcriptional regulation of these signals]] | \n", + "0.00 | \n", + "
| 565 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "term-GO:0007212-1 | \n", + "[[the list of human genes supplied involves several different cell signaling pathways, including the dopamine receptor (drd1, drd2, drd3 and drd5) pathway, g-protein coupled receptor (gpcr) signalling pathway (gnas, gnai3, gnaq, gna11, gna14, gna15, gnb1, gnb5, gnao1, gng2, sl]] | \n", + "[[this gene set was comprised of dopamine and g-protein coupled receptors that participate in cellular signaling pathways and influence cellular functions such as metabolism and behavior. the genes are involved in a wide range of pathways such as signal transduction, transcriptional regulation, memory and behavior, GO:0007612, neural development and synaptic plasticity. the enriched terms in this list include: signal transduction, g protein-coupled receptor, camp, MESH:D000262, MESH:D054799, MESH:D017868, calcium ions, transcriptional regulation, GO:0000981, MESH:D011954, wnt and pi3k signaling pathways, neuronal growth and development, GO:0010467, and synaptic receptors.\\n\\nmechanism: this gene set is involved in many pathways such as signal transduction, transcriptional regulation, and synaptic organization. signal transduction occurs through g-protein coupled receptors and camp, which in turn regulate downstream effectors including adenylyl cyclase, MESH:D017868, and calcium ions. furthermore, transcriptional regulation occurs through various receptor signaling pathways, such as those related to the wnt and pi3k pathways, while dopamine receptors regulate neuronal growth and development, GO:0010467, and behavior. finally, synaptic receptors enable]] | \n", + "0.00 | \n", + "
| 566 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "tf-downreg-colorectal-0 | \n", + "[[transcriptional regulation, GO:0006338, GO:0003677, GO:0000981, coactivator, heterodimer, response element]] | \n", + "[[dna-binding, chromatin-binding, transcriptional regulation, e-box dna consensus sequence binding, dna damage response regulation, dna damage response maintenance, phosphoprotein shutting, MESH:D016335, interaction with cellular retinol-binding protein, hormone-dependent transcription, receptor-dependent transcription, nuclear hormone receptor-dependent transcription, transcriptional coactivator complex recruitment, GO:0000785]] | \n", + "0.05 | \n", + "
| 567 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "tf-downreg-colorectal-1 | \n", + "[[transcription factor regulation, GO:0016569, dna-binding activity, zinc-finger binding, GO:0032183, retinoid x receptor responsive element binding]] | \n", + "[[transcriptional regulation, dna-binding, chromatin binding activity, histone binding activity, GO:0000988]] | \n", + "0.00 | \n", + "
| 568 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "EDS-0 | \n", + "[[GO:0031012, ecm components, matrix components, ecm regulators]] | \n", + "[[GO:0001501, GO:0032964, cell-matrix interactions, extracellular matrix remodeling, cell signaling]] | \n", + "0.00 | \n", + "
| 569 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "EDS-1 | \n", + "[[extracellular matrix protein network, collagen fibril formation, GO:0030199, ecm protein network assembly, UBERON:2007004]] | \n", + "[[collagen production, GO:0061448, matrix remodeling, zinc finger protein regulation]] | \n", + "0.00 | \n", + "
| 570 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "FA-0 | \n", + "[[MONDO:0100339, \"double strand break repair\", \"fanconi anemia protein complex\", \"ubiquitin ligase complex formation\"]] | \n", + "[[GO:0006281, homologous recomination, MESH:M0006667, GO:0004518]] | \n", + "0.00 | \n", + "
| 571 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "FA-1 | \n", + "[[GO:0006974, dna damage recognition, GO:0006281, GO:0035825, double-stranded break repair, double-stranded break recognition]] | \n", + "[[MONDO:0100339, dna/rna damage response, dna/rna metabolism, GO:0051726, genome stability, MONDO:0019391]] | \n", + "0.00 | \n", + "
| 572 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ADIPOGENESIS-0 | \n", + "[[MESH:D004734, GO:0006631, GO:0045444, GO:0006695, GO:0006699]] | \n", + "[[metabolic regulation, GO:0050658, GO:0006412, cell membrane transport, transcription regulation, GO:0006915, GO:0006457, GO:0019432, GO:0003676, GO:0006633, GO:0006096, GO:0045454]] | \n", + "0.00 | \n", + "
| 573 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ADIPOGENESIS-1 | \n", + "[[MESH:D004734, cell death regulation, cell proliferation signaling, dna replication/remodeling, GO:0006396, GO:0006629]] | \n", + "[[GO:0008152, MESH:D004734, GO:0007165, GO:0006119, transcriptional regulation, GO:0006468, GO:0051726, GO:0006629, GO:0006457, protein assembly, mitochondrial function, GO:0006915, GO:0006839, GO:0055085, GO:0007010, GO:0006094, GO:0006096, GO:0042632]] | \n", + "0.09 | \n", + "
| 574 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[[cell surface molecules, MESH:D016207, MESH:M0000731, receptor signalling, transcriptional regulation, GO:0006915]] | \n", + "[[immune signalling, GO:0051726, cellular differentiation, transcriptional regulation]] | \n", + "0.11 | \n", + "
| 575 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[[GO:0019882, GO:0007165, b and t cell metabolism, GO:0001816, GO:0006935]] | \n", + "[[genes in this list are representative of various pathways involved in cell movement, GO:0019882, GO:0006954, immune regulation, and cell signaling events including jak-stat and mapk- pi3k pathways. enriched terms include “immune system processes”; “immune recognition pathways”; “cytokine-mediated signaling pathways”; “inflammatory response”; “cellular immune activation”; “intestinal immune network for iga production”; “cytokine secretion”; “tcr signaling pathway”; “cd4 t cell activation”; “t lymphocyte differentiation”; “innate immune response”; and “cytokine-cytokine receptor interaction”.\\n\\nmechanism: the genes are involved in pathways that affect cell movement, GO:0019882, GO:0006954, immune regulation, and cell signaling. these pathways control the activation, response, differentiation, and survival of t cells by regulating cytokine expression, activation of specific receptors, production of antibodies, regulation of transcription factors and their binding to promoters, other immune system processes]] | \n", + "0.05 | \n", + "
| 576 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[[genes in this list are involved in developmental processes, metabolism, and the inflammatory response. the terms enriched in these genes include: cell cycle regulation, GO:0008152, GO:0006260, GO:0015031, receptor signaling, GO:0006954, GO:0006915, GO:0006351, GO:0006457, GO:0016477, developmental processes.\\n\\nmechanism: these genes appear to work together to regulate a variety of cellular processes, such as cellular metabolism, transcription, growth, and differentiation, as well as communication between cells and the environment. these genes likely act in concert to coordinate the intricate interplay between these processes and respond to changes in the environment. furthermore, they likely play a role in the body’s inflammatory response when faced with a variety of external stimuli]] | \n", + "[[genes in this list are mainly involved in regulation of skeletal tissue formation and development, signal cascade activation, protein folding, cellular metabolism and movement, cell cycle regulation, and transcriptional regulation. the underlying biological mechanism may be related to the complex network of interactions among these genes in controlling the basic functions of a cell. the enriched terms are: bone morphogenesis, GO:0001501, signal cascade activation, GO:0006457, GO:0044237, cellular movement, GO:0051726, transcriptional regulation, chromatin and dna modification]] | \n", + "0.05 | \n", + "
| 577 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[[GO:0065007, GO:0023052, GO:0019538, GO:0051726, transcription regulation, MESH:D021381, GO:0007165, membrane trafficking, protein kinase regulation, GO:0044237, GO:0006259, GO:0006468, GO:0030163, mitochondrial function, GO:0006629, cytoskeleton regulation, GO:0007155, GO:0009117]] | \n", + "[[gene transcription and regulation, protein translation and metabolism, cytoskeletal organization, GO:0006629]] | \n", + "0.05 | \n", + "
| 578 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ANGIOGENESIS-0 | \n", + "[[extracellular matrix formation and maintenance, fibrous tissue development, vascular development, cell-cell communication and migration, extracellular secreted signaling, collagen and laminin-fibrillin proteins]] | \n", + "[[GO:0030198, vascularization, endothelial cell aggregation, GO:0007155, cell surface interactions]] | \n", + "0.00 | \n", + "
| 579 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ANGIOGENESIS-1 | \n", + "[[GO:0032502, GO:0009653, GO:0009888, GO:0030198, GO:0006954, MESH:D066253, cell-cell communication]] | \n", + "[[cytokine receptor signaling, growth factor signal transduction, transmembrane and extracellular matrix proteins, development of muscle, bone, and neuronal networks]] | \n", + "0.00 | \n", + "
| 580 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-0 | \n", + "[[this term enrichment test suggests that the genes provided are involved in cell adhesion, GO:0006955, and tissue morphogenesis. specifically, the adhesion-associated genes enriched in this dataset include icam1, icam2, icam4, icam5, nectin1, nectin2, nectin3, nectin4, nrxn2, ptprc, sdc3, thy1, vcam1, and vwf. the immune response-associated genes enriched in this dataset include cd34, cd86, cd209, ctnna1, icam2, icam4, icam5, map4k2, msn, pard6g, and tnfrsf11b. lastly, the tissue morphogenesis-associated genes enriched in this dataset include acta1, actb, actc1, actg1, actn1, actn2, actn4, adam15, adra1b, akt2, alox15b, amigo2, baiap2, cadm2, cadm3, MESH:M0359286, col9a1, MONDO:0011642, ctnnd1, MESH:C040896]] | \n", + "[[GO:0060348, joint development, MESH:D024510, GO:0061448, GO:0007155, adhesion receptor complex formation, GO:0007165, receptor-mediated signaling cascades]] | \n", + "0.00 | \n", + "
| 581 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-1 | \n", + "[[GO:0009653, GO:0016049, MESH:D047108, cellular signaling, GO:0031012, cytoskeletal organization, basal membrane assembly, GO:0098609, GO:0006915, GO:0016477, GO:0001816, growth factor production, tyrosine kinase activity, g-protein coupled receptor signaling pathway, nuclear receptor signaling pathway, GO:0016055, phosphatidylinositol 3-kinase signaling pathway, protein kinase b signaling pathway, map kinase signaling pathway, cell adhesion molecule signaling pathway, focal adhesion signaling pathway]] | \n", + "[[GO:0007155, GO:0016477, migration and interaction, cytoskeletal organization, actin cytoskeletal regulation, GO:0007165, regulation of actin cytoskeletal organization]] | \n", + "0.08 | \n", + "
| 582 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_SURFACE-0 | \n", + "[[GO:0016477, membrane receptor signaling, GO:0009100, protein tyrosine kinases, GO:0007155, cytoskeletal dynamics, receptor-mediated lectin binding, GO:0006629, GO:0007015]] | \n", + "[[cell regulation, GO:0007165, GO:0007155, GO:0006457, GO:0030198]] | \n", + "0.08 | \n", + "
| 583 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_SURFACE-1 | \n", + "[[cell signaling, GO:0032502, transcription regulation, GO:0008152, MESH:D049109, MESH:D005786]] | \n", + "[[cell adhesion and migration, cell signaling, GO:0030154, protein kinase and phosphatase activities, transcription and dna metabolism, MESH:D056747, glycosylation and carbohydrate metabolism, cell growth and proliferation]] | \n", + "0.08 | \n", + "
| 584 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_APOPTOSIS-0 | \n", + "[[transcriptional regulation/control, cell cycle/apoptosis, GO:0006955]] | \n", + "[[GO:0006915, transcription regulation, cell cycle progression, GO:0006954, GO:0006260, GO:0006281, oxidative stress response, immune system activation]] | \n", + "0.00 | \n", + "
| 585 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_APOPTOSIS-1 | \n", + "[[the genes listed are mainly involved in the regulation and expression of genes, inflammation pathways and cell cycle regulation. specifically, enriched terms include gene expression and transcriptional regulation, dna damage and repair, GO:0007165, GO:1901987, metabolism and apoptosis.\\n\\nmechanism: the commonality in the function of these genes is likely related to the roles they play in the regulation of gene expression by affecting signal transduction, GO:0008152, cell cycle control and apoptosis. these gene functions may lead to a variety of processes, including inflammation pathways related to immunity, UBERON:2000098, MESH:D002470]] | \n", + "[[cell death regulation, GO:0006954, immune reaction, growth and morphogenesis, UBERON:2000098, GO:0006915, GO:0006281, GO:0030217, GO:0001816, GO:0051726, fast axonal transport, extracellular proteolysis, GO:0007155, GO:0042060, MESH:D009362, MESH:D063646, GO:0016477, regulation of nf-kb pathway]] | \n", + "0.03 | \n", + "
| 586 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[[MESH:M0496924, GO:0006869, development of connective tissues, GO:0006633, GO:0006699, GO:0006805, GO:0006694, cellular transport, MESH:M0023727, connective tissue formation, digit development, GO:0060173]] | \n", + "[[GO:0006629, GO:0006869, organ development, cell signaling, GO:0006412, transport processes]] | \n", + "0.06 | \n", + "
| 587 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[[this set of genes is related to lipid metabolism and lipid transport, protein homeostasis, retinol metabolism, developmental processes, and transportation of lysosomal hydrolases and oxygen-carrying molecules. the set includes genes involved in lipid metabolism (aqp9, atxn1, GO:0033781, abcg4, acsl1, fdxr, aldh8a1, hsd17b11, aldh9a1, aldh1a1, cyp7a1, cp25h, gstk1, MONDO:0100102, acsl5), lipid transport (abca1, abca2, abca3, abca4, abca5, abca8, abca9, abcg8), protein homeostasis (pex12, pex16, pex19, pex11a, pex11g, GO:0005053, pex6, pex26), retinol metabolism (abcd1, abcd2, abcd3), developmental processes (lck, nr3c2, retsat, klf1, ephx2, phyh, bbox1, MONDO:0004277]] | \n", + "[[GO:0006629, GO:0006536, serine metabolism, transcription factor regulation, oxidative stress response]] | \n", + "0.00 | \n", + "
| 588 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[[transcriptional regulation, MESH:D006026, GO:0006629, GO:0005509, GO:0001525, MESH:D016326, receptor signaling; transcription regulators; calcium signaling; glycoside hydrolases; lipid metabolism; cell adhesion; extracellular matrix proteins; signaling receptor molecules.\\n\\nmechanism: this set of genes is likely involved in regulating transcriptional responses, MESH:D006026, GO:0006629, GO:0005509, GO:0001525, MESH:D016326, and receptor signaling. many of these genes interact with each other, forming complex cellular networks and pathways. the particular genes identified in this list are likely related to stimulating or inhibiting the expression of specific genes or pathways, as well as modulating or mediating responses to various environmental signals or stimuli. these gene functions likely interact to maintain homeostasis, contribute to cellular development and processes, promote angiogenesis, and provide a structural and functional framework for the extracellular matrix. furthermore, these genes may be involved in signaling pathways that involve receptor molecules by modulating intracellular calcium levels]] | \n", + "[[GO:0006629, GO:0008203, cell signaling and regulation, GO:0032502, GO:0007155, GO:0006915, GO:0006351]] | \n", + "0.04 | \n", + "
| 589 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[[GO:0006629, transcriptional regulation, cellular adhesion, GO:0032502, GO:0042592]] | \n", + "[[GO:0006629, cholesterol control, GO:0009062, GO:0006699, hmgcr regulation, pmvk regulation, fads2 regulation, srebf2 regulation, s100a11 regulation, mvk regulation]] | \n", + "0.07 | \n", + "
| 590 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_COAGULATION-0 | \n", + "[[inflammatory response regulation, extracellular matrix formation regulation, proteolytic activities]] | \n", + "[[extracellular matrix remodeling; angiogenesis and vascular development; immune response and platelet activation; collagen and fibronectin metabolism and regulation; endocytosis and signal transduction; \\nmechanism: the genes in this list work together to control and regulate multiple relevant processes, such as extracellular matrix remodeling, which is the process of breaking down and reorganizing the components of the extracellular matrix in order to facilitate tissue development and repair, angiogenesis and vascular development, which regulate the formation of new blood vessels and ensure proper blood flow throughout the body, immune response and platelet activation, which are necessary to protect the body from foreign agents and to form healthy blood clots, collagen and fibronectin metabolism and regulation, which are important for tissue integrity and structure, and endocytosis and signal transduction, which are necessary for cellular communication and regulation]] | \n", + "0.00 | \n", + "
| 591 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_COAGULATION-1 | \n", + "[[GO:0007165, GO:0030198, matrix molecular regulation, GO:0006508, GO:0050817, matrix remodeling, GO:0009653]] | \n", + "[[GO:0007155, proteolysis regulation, extracellular protein-cell interaction, migration, GO:0050817, GO:0006956]] | \n", + "0.08 | \n", + "
| 592 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_COMPLEMENT-0 | \n", + "[[GO:0030198, immune system/inflammation/interferon response, GO:0000988]] | \n", + "[[development of tissue and organs, GO:0007165, cell surface receptor binding, GO:0050896, UBERON:0002405, GO:0006955, GO:0005125]] | \n", + "0.00 | \n", + "
| 593 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_COMPLEMENT-1 | \n", + "[[immunoglobulin like domains, GO:0042113, GO:0050852, integrin mediated cell adhesion, GO:0006915, regulation of transcription, GO:0007165, receptor mediated endocytosis and exocytosis, GO:0030198, calcium mediated signaling]] | \n", + "[[cellular signalling, GO:0006954, cell stress response, cell-cell interaction, GO:0007165, GO:0045087, cytoskeletal remodelling, GO:0006457, GO:0050900, GO:0004672, GO:0007155, MESH:D005786, GO:0006260, protein activation, GO:0019763, GO:0002377, GO:0016791]] | \n", + "0.04 | \n", + "
| 594 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_DNA_REPAIR-0 | \n", + "[[GO:0006259, GO:0016070, GO:0006412, dna damage repair, GO:0006351, GO:0006325]] | \n", + "[[GO:0032502, GO:0006260, MESH:D047108, GO:0030154, transcription regulation, GO:0006335, nuclear mrna surveillance pathway, GO:0016070, GO:0006281, GO:0140014, rna-dependent dna replication]] | \n", + "0.06 | \n", + "
| 595 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_DNA_REPAIR-1 | \n", + "[[GO:0006260, transcription regulation, GO:0006412, GO:0043687, nucleic acid metabolism, GO:0010467, GO:0006397, GO:0006412]] | \n", + "[[nucleic acid metabolism, GO:0006351, post-transcriptional modifications, GO:0006338, GO:0000398, GO:0006281, rna polymerization, GO:0006397, GO:0051028, GO:0006413]] | \n", + "0.12 | \n", + "
| 596 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_E2F_TARGETS-0 | \n", + "[[GO:0006260, GO:0006281, gene transcription, GO:0006412, GO:0016569, GO:0007049, GO:0010468]] | \n", + "[[transcriptional regulation, GO:0016569, mitotic division, GO:0051726, MESH:D004268, MESH:D006657, GO:0000981, MESH:D004259, MESH:D012321, chromatin remodeling proteins, ubiquitin ligases, nucleosome assembly proteins, helicases, motor proteins, GO:0000075]] | \n", + "0.05 | \n", + "
| 597 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_E2F_TARGETS-1 | \n", + "[[GO:0006260, GO:0006351, GO:0030261, transcriptional regulation, GO:0006338, GO:0006974, chromatin structure modifications, GO:0006281, GO:0006306, GO:0030163, GO:0007094, GO:1901987, GO:0006468]] | \n", + "[[GO:0006260, GO:0006281, GO:0016569, transcription regulation, translation regulation, protein-protein networks, GO:0051225, kinesin motor proteins, dynein motor proteins]] | \n", + "0.10 | \n", + "
| 598 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[[genes in this list are enriched for functions related to modulating extracellular matrix, cell adhesion and morphogenesis, as well as playing roles in development, growth and signal transduction pathways. enriched terms include:extracellular matrix modulation; cell adhesion; morphogenesis; development; growth; signal transduction.\\n\\nmechanism: many of the genes listed are involved in the signaling, development and maintenance of the extracellular matrix, cell adhesion and morphogenesis, which can be regulated through diverse pathways involving the growth factors (bdnf, MESH:D016222, igfbp2, igfbp3, igfbp4, wnt5a), proteoglycans (comp, cspg4, MONDO:0021055, lamc1, lamc2, dcn, has3, sdc1) and adhesion molecules and receptors (acta2, abi3bp, cadm1, cap2, capg, cd44, cdh11, cdh2, cdh6, fn1, grem1, itga2, itga5, itgav, itgb1, itgb3, itgb5, lrp1, tagl]] | \n", + "[[GO:0031012, GO:0007155, GO:0048870, cell-matrix interaction, growth factor signaling, cytokine signaling, matrix remodeling]] | \n", + "0.00 | \n", + "
| 599 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[[GO:0030198, GO:0009653, collagen production, matrix metalloproteinase activity, GO:0009100, cytoskeletal component organization, regulation of growth and reproduction, regulation of skin morphogenesis]] | \n", + "[[GO:0048705, cell-cell adhesion and motility, extracellular matrix production and remodeling, connective tissue development and differentiation, collagen production and turnover, cytokine and chemokine signaling]] | \n", + "0.00 | \n", + "
| 600 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[[cell morphology; homeostasis & regulation; innervation; cellular metabolism.\\nmechanism: the genes are likely to be involved in various pathways, such as the regulation of gene expression, protein synthesis and structure, cell motility and differentiation, tissue repair regeneration]] | \n", + "[[GO:0006260, GO:0006351, GO:0010467, GO:0016049, differentiation, GO:0016485, trafficking, GO:0060349, cancer-related pathways, GO:0098609, matrix remodeling, intracellular signaling, external signals, internal signals]] | \n", + "0.00 | \n", + "
| 601 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[[immunological response, GO:0007155, transcription regulation, GO:0016477, GO:0008544, GO:0060348, MESH:D024510, GO:0015031, GO:0006915]] | \n", + "[[transcriptional regulation, GO:0007165, protein-protein interactions, GO:0055085, GO:0008610]] | \n", + "0.00 | \n", + "
| 602 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[[MESH:D023281, cytoskeletal processes, GO:0006955, extracellular modification]] | \n", + "[[GO:0030198, GO:0007155, GO:0016477, GO:0048870, growth factor signaling, cytoskeletal organization]] | \n", + "0.00 | \n", + "
| 603 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[[the commonalities in the functions of these genes are involved in transcription, post-transcriptional regulation, GO:0009966, and cell-cycle related processes. the enriched terms are: transcription; post-transcriptional regulation; signal transduction; cell cycle; dna binding; regulation of transcription; regulation of protein abundance; chromatin remodeling; ubiquitination; and protein-protein interaction.\\n\\nmechanism: the underlying mechanism may be related to the regulation of intricate pathways leading to the expression of specific genes in conversion of genetic information into protein-based processes. these genes may be involved in a variety of biological processes, such as transcriptional and post-transcriptional regulation of gene expression, GO:0007165, cell-cycle related processes, GO:0003677, regulation of transcription, regulation of protein abundance, GO:0006338, MESH:D054875, protein-protein interaction]] | \n", + "[[GO:0030198, GO:0000988, receptor signaling pathway, GO:0007269, GO:0019725, GO:0006508, immunological responses, GO:0016049, GO:0003677, GO:0006629]] | \n", + "0.05 | \n", + "
| 604 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[[GO:0006631, oxidation of lipids, GO:0006695, GO:0005977, GO:0009117, GO:0006862, GO:0009165, electron transport activity, enzyme regulation, regulation of metabolic pathways, GO:0006915]] | \n", + "[[metabolic pathways; cellular functions; energy metabolism; lipid metabolism; amino acid metabolism; dna damage repair; cell signaling.\\nmechanism: the genes listed here are likely involved in the various metabolic pathways and cellular functions, perhaps through the production of enzymes, MESH:D011506, or other molecules that contribute to energy metabolism, GO:0006629, amino acid metabolism, dna damage repair, cell signaling]] | \n", + "0.00 | \n", + "
| 605 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[[GO:0008152, energy production and storage, lipid metabolism and transport, acetyl-coa biosynthesis and catalysis, oxidation, GO:0006631]] | \n", + "[[GO:0006629, cell cytoskeleton, GO:0008610, GO:0016042, lipid transportation, GO:0034440, cell membrane biogenesis, GO:0048870, cell traffic, cell signaling]] | \n", + "0.00 | \n", + "
| 606 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-0 | \n", + "[[GO:0051726, GO:0006260, GO:0006338, cyclin b-cdk1 activation, cks1b, cdc25a, wee1, cdc20, apc/]] | \n", + "[[GO:0006260, GO:0006351, GO:0051726, protein binding/interaction, chromatin modifiers/modification, GO:0006281, GO:0000988, GO:0006397, GO:0006915, ubiquitination and proteasomal degradation]] | \n", + "0.12 | \n", + "
| 607 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-1 | \n", + "[[nuclear processes, GO:0006260, gene transcription, GO:0006338, GO:1901987, GO:0006281, GO:0010467, GO:0010468]] | \n", + "[[genes involved in the list are mainly associated with dna replication, cell division and related functions. enriched terms include \"cell cycle\", \"dna replication\", \"chromatin modification\", \"transcription regulation\", \"cell division\", \"dna repair\", \"transcriptional regulation\", \"chromosome segregation\".\\n\\nmechanism: these genes likely play a role in the coordination of the many steps and activities involved in dna replication, GO:0051301, and related cellular processes. the cell cycle is an area of particular interest due to its critical role in the growth and division of cells. dna replication, modification, repair occur during cell division in order to produce maintain copies of genetic information. chromatin modifications occur during cell division in order to package regulate genomic information. transcriptional regulation involves the control of gene expression the production of proteins other materials essential for the maintenance of cellular functions. chromosome segregation cell division serve to divide replicated genetic material into daughter cells]] | \n", + "0.00 | \n", + "
| 608 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_GLYCOLYSIS-0 | \n", + "[[developmental process: digit development, GO:0001525, GO:0030154, GO:0005488, transporting, GO:0008152, GO:0008152, cell signalling]] | \n", + "[[the genes in this list are involved in a variety of cellular processes including protein translation, GO:0070085, regulation of ion channels, gene transcription and dna replication. the enriched terms identified are: translation; glycosylation; ion channels; gene transcription; and dna replication.\\n\\nmechanism: the common underlying mechanisms of the genes in this list likely involve cellular processes such as protein translation, GO:0070085, regulation of ion channels, gene transcription and dna replication. these processes are essential for the regulation of cell functions and the maintenance of a stable organism]] | \n", + "0.00 | \n", + "
| 609 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_GLYCOLYSIS-1 | \n", + "[[GO:0005975, MESH:D004734, GO:0046785, dna binding and replication, actin cytoskeleton dynamics, ion channel regulation, transcriptional regulation, GO:0007155]] | \n", + "[[structural proteins, GO:0006096, GO:0006098, GO:0006099, GO:0007155, GO:0030166, extracellular matrix formation, cytoskeletal assembly]] | \n", + "0.07 | \n", + "
| 610 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[[GO:0009653, GO:0022008, GO:0016049, GO:0030154, GO:0001764, thalamocortical pathway development, GO:0001764, GO:0007399, neural crest migration]] | \n", + "[[the provided genes are involved in a variety of different processes ranging from morphogenesis, development and growth of the digits/limbs, neuronal migration and regulation of cell proliferation. the underlying biological mechanism might be related to the modulation of cell migration, development of neural connections, formation of complex structures, maintenance of body plan and tissue development. enriched terms are: morphogenesis, digit/limb development, GO:0001764, GO:0042127, modulation of cell migration, development of neural connections, formation of complex structures, maintenance of body plan, GO:0009888]] | \n", + "0.06 | \n", + "
| 611 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[[GO:0009653, GO:0007155, GO:0032502, GO:0007268, GO:0008283, GO:0016477, GO:0030154, MESH:D009473]] | \n", + "[[neuron formation, GO:0007155, migration, GO:0007165, GO:0048729, GO:0007399]] | \n", + "0.08 | \n", + "
| 612 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_HEME_METABOLISM-0 | \n", + "[[GO:0055085, MESH:D004734, GO:0003735, GO:0003676, GO:0015031, negative regulation of transcription, regulation of transcription, positive regulation of transcription, GO:0071840, iron metabolism, GO:0007165, GO:0045087, GO:0042803, GO:0051276, GO:0050794, GO:0016569, GO:0008380, GO:0005515, GO:0000075, GO:0006006, GO:0000088, GO:0009116]] | \n", + "[[GO:0044237, energy production and transport, cytoskeleton modification, cytoskeleton remodelling, GO:0007155, MESH:D004735, MESH:M0496924, cellular transport, cellular reorganization]] | \n", + "0.00 | \n", + "
| 613 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_HEME_METABOLISM-1 | \n", + "[[GO:0048468, GO:0010467, GO:0048513, nucleic acid metabolism, transcriptional regulation, GO:0006259, GO:0016070, cytoskeletal dynamics, GO:0007165, GO:0006412]] | \n", + "[[MESH:D047108, GO:0001501, GO:0048513, GO:0009653, GO:0040007, GO:0002376, GO:0048870, GO:0003707, receptor signaling pathway, GO:0006810, GO:0006897, GO:0019725]] | \n", + "0.05 | \n", + "
| 614 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_HYPOXIA-0 | \n", + "[[gene enrichment analysis of the gene list showed that the majority of genes are involved in cellular proliferation, GO:0006915, GO:0006811, GO:0005102, and development. the enriched terms associated with this list include cell proliferation, GO:0006915, GO:0006811, GO:0005102, cell signaling, transcriptional regulation, and development.\\n\\nmechanism: the genes are likely involved in an intricate, interconnected biological network that involves numerous signaling pathways and transcription factors necessary for cellular proliferation, GO:0006915, ion transport and receptor binding. these gene functions result in the regulation of numerous cellular processes and ultimately the development of various diseases. in addition, the genes may be regulating a number of other processes such as metabolism, cell-cell communication, energy production]] | \n", + "[[GO:0007049, remodeling proteins, stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, GO:0000981, chromatin-associated proteins, MESH:D010770]] | \n", + "0.00 | \n", + "
| 615 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_HYPOXIA-1 | \n", + "[[GO:0048468, cell metabolism, transcription regulation, GO:0010468, GO:0006974, GO:0007155, GO:0030154, GO:0042440, MESH:M0352612, GO:0006412, GO:0051726, MESH:D004734]] | \n", + "[[GO:0032502, cell structure and movement, cell cycle and division, GO:0007165, GO:0006810, energy production]] | \n", + "0.00 | \n", + "
| 616 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[[GO:0016049, cell regulation, GO:0009988, MESH:D007109, signal transduction and regulation, GO:0032502, transcriptional regulation, GO:0030198, cytokine-receptor-mediated signaling pathway]] | \n", + "[[immunological function, GO:0030036, MESH:D011956, pro-inflammatory regulation]] | \n", + "0.00 | \n", + "
| 617 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[[this list of genes are involved in developmental processes, GO:0006955, GO:0006954, GO:0007165, and cell adhesion functions. the enriched terms are \"development\"; \"signal transduction\"; \"cell adhesion\"; \"immune response\"; \"inflammation\"; \"transmembrane transport\"; \"protein metabolism\"; \"cardiovascular function\".\\n\\nmechanism: the underlying biological mechanisms involves the coordination of different pathways, genes and proteins. these genes are involved in cellular processes and regulation, including cell proliferation, differentiation, adhesion and migration, GO:0007165, and immunity. the genes also influence signaling pathways, protein metabolism and other functions that have roles in cardiovascular and carcinogenesis. the mechanisms through which these genes affect development, GO:0006954, other immunological responses are complex dependent on the coordination between multiple pathways]] | \n", + "[[MESH:D007109, GO:0006954, GO:0016049, differentiation, GO:0032502, GO:0007165]] | \n", + "0.18 | \n", + "
| 618 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[[pain sensing and signal transduction, GO:0006935, GO:0019221, leukocyte transendothelial migration, GO:0006955, GO:0030168]] | \n", + "[[cell signaling, GO:0001816, cytokine regulation, MESH:D005786, transcription regulation, GO:0007155]] | \n", + "0.00 | \n", + "
| 619 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[[GO:0007165, MESH:D056747, immune signaling, transcription regulation, cytokine regulation, GO:0030155, MESH:D005786, cell growth regulation, metabolism regulation, MESH:D002470, cell death regulation, antifungal immunity]] | \n", + "[[cytokine regulation, chemokine regulation, interleukin regulation, cellular differentiation, cell motility and adhesion, GO:0007165, GO:0006954]] | \n", + "0.12 | \n", + "
| 620 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[[MESH:M0000731, GO:0006954, GO:0007165, transcription regulation, intercellular signaling, GO:0045087, MESH:D056704]] | \n", + "[[this list of genes is significantly enriched for the functions of cell signalling, cytokine mediated immunity, receptor signalling, and tissue morphogenesis. furthermore, the list contains several genes associated with the immune response, including tlrs and ifns, as well as cytokines and chemokines such as ccl17, ccl20, cxcl10, cxcl9, ifnar1, tnfrsf1b, and tnfsf10. in addition, several receptors were found to be enriched on the list, including gpr132, axl, c3ar1, MONDO:0043317, and ccr7. finally, key genes involved in tissue morphogenesis were also found on the list, such as adgre1, edn1, btg2, ccl2, tacr1, and cxcr6.\\n\\nmechanism: \\nthe underlying mechanism for this enrichment of genes is likely related to the common activities of cell signalling, cytokine mediated immunity and tissue morphogenesis. the list of genes is likely regulating common processes such as cell-cell communication and inflammation. additionally, the list of genes may be involved in the development and maintenance of tissue structures, such as muscle tissue]] | \n", + "0.00 | \n", + "
| 621 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[[immune cell signaling, GO:0006928, cell surface receptor activity, GO:0006954, GO:0016477, cell–cell interactions, immune cell receptor-mediated signaling]] | \n", + "[[GO:0006955, cellular activation, receptor-coupled pathways, transcriptional regulation, cytokine and cytokine receptor binding, GO:0006629, GO:0007155]] | \n", + "0.00 | \n", + "
| 622 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[[GO:0006954, neutroph]] | \n", + "[[analysis of this list of genes reveals that they are all involved in the functioning of the immune system in some way, either through regulation of inflammatory response pathways, recognition of foreign agents, or production of molecules defending against potentially harmful intruders. the enriched terms include \"immune system regulation\"; \"inflammatory response\"; \"foreign agent recognition\"; \"antimicrobial defense\"; \"interferon signaling\"; \"antiviral defense\". \\n\\nmechanism: the genes in this list combined likely regulate a wide variety of immune system functions, including modulating inflammation, recognizing and responding to foreign antigens, producing effector molecules against potentially harmful microorganisms, promoting interferon signaling cascades to defend from viral invasion]] | \n", + "0.00 | \n", + "
| 623 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[[interferon signalling pathway, interferon gamma activity, interferon regulatory factor activity, status response to interferon, GO:0006915, GO:0008289, GO:0005509, GO:0002446]] | \n", + "[[GO:0006955, GO:0006954, cytokine signaling, interferon response, GO:0006355, interferon-stimulated genes]] | \n", + "0.00 | \n", + "
| 624 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[[GO:0006955, cell signaling, cytokine response, interferon response, nuclear factor kappab-dependent transcriptional regulation]] | \n", + "[[MESH:M0000731, GO:0019882, GO:0006954, chemokine signaling, GO:0007155, cytokine interactions]] | \n", + "0.00 | \n", + "
| 625 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[[MESH:D007109, interleukin regulation, transcription regulation, GO:0006954, cell signaling, GO:0006915]] | \n", + "[[interferon signaling, antigen processing, presentation, and recognition, cytokine signaling, cell cycle and dna damage response, GO:0006915]] | \n", + "0.10 | \n", + "
| 626 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[[GO:0060348, GO:0009653, growth maintenance, GO:0007267, cell-cell communication, GO:0036211, GO:0006810]] | \n", + "[[digit development, neural development, GO:0002520, transcriptional regulation, g-protein coupled receptors, MESH:D011494, MESH:D020662]] | \n", + "0.00 | \n", + "
| 627 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[[GO:0009653, cell-cell communication, GO:0032502, hormone regulation, cellular differentiation, cell-cycle, cell-signalling]] | \n", + "[[our analysis revealed the enrichment of the gene functions related to development, GO:0007165, transcription and metabolism. specifically, some of the enriched terms include cellular development, GO:0016049, GO:0001501, GO:0048598, cell junction organization and assembly, GO:0007165, GO:0007049, GO:0006351, and cellular metabolism.\\n\\nmechanism: these gene functions may be related to the biological mechanism of growth, differentiation, and development of cells. the signals and transcription are likely involved in regulating and controlling these processes, as well as providing energy through metabolic pathways. additionally, the cell junction processes are likely involved in the coordination and communication between cells, which is essential to development]] | \n", + "0.00 | \n", + "
| 628 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[[GO:0007165, GO:0000902, GO:0050896, GO:0001525, GO:0065009, GO:0030198]] | \n", + "[[GO:0007165, GO:1901987, cell-to-cell adhesion]] | \n", + "0.12 | \n", + "
| 629 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[[GO:0009653, GO:0009888, cell signaling, immune regulation, transcription modulation, GO:0007165, GO:0007155, GO:0016477]] | \n", + "[[integrin, chemokine receptor, MESH:D011494, g-protein-coupled receptor, cytoskeleton proteins, cell-extracellular matrix interaction, type i ifn-mediated innate immunity, wnt signaling, MESH:D020558, MESH:D010740, MESH:D008565, MESH:D016326, receptor tyrosine kinase, toll-like receptor signaling, tlr adaptor proteins]] | \n", + "0.00 | \n", + "
| 630 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[[the human genes abi1, abl1, abr, actn4, akap13, alms1, MONDO:0008780, anln, GO:0005680, arap3, arf6, arfgef1, arfip2, arhgap10, arhgap27, arhgap29, arhgap4, arhgap5, arhgdia, arhgef11, arhgef12, arhgef2, arhgef3, arhgef7, arl8a, atg4b, MESH:D064096, bcar1, bcl2l11, bcr, bin1, birc5, brca2, bub1, capzb, ccdc88a, ccnb2, cd2ap, cdc27, cdc42, cdc42bpa, cdc42ep1, cdc42ep2, cdc42ep4, cdk1, cdk5rap2, cenpe, cenpf, cenpj, cep131, cep192, cep250, cep57, GO:0047849]] | \n", + "[[GO:0007049, GO:0007155, cytoskeletal organization, GO:0004672, GO:0003924]] | \n", + "0.00 | \n", + "
| 631 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[[cytoskeletal organization, GO:0016477, GO:0051301, GO:0006260, GO:0006281, GO:0006605, GO:0065007]] | \n", + "[[GO:0051301, GO:0006468, GO:0006338, GO:0008017, microtubule organization, GO:0051225, GO:0007059, GO:0051305, cell-cycle control, GO:0140014]] | \n", + "0.06 | \n", + "
| 632 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-0 | \n", + "[[the human genes abcf2, acaca, acly, acsl3, actr2, actr3, add3, adipor2, ak4, aldoa, arpc5l, asns, atp2a2, atp5mc1, atp6v1d, MESH:D064096, bcat1, bhlhe40, btg2, bub1, cacybp, calr, canx, ccnf, ccng1, cct6a, cd9, cdc25a, cdkn1a, cfp, cops5, coro1a, cth, ctsc, GO:0038147, cyb5b, cyp51a1, dapp1, ddit3, ddit4, ddx39a, dhcr24, dhcr7, GO:0004146, ebp, edem1, eef1e1, egln3, eif2s2, elovl5, elovl6, eno1, eprs1, ero1a, etf1, MONDO:0100101, MONDO:0100102, fdxr, fgl2, MESH:D010649]] | \n", + "[[genes in this list are involved in various aspects of cellular metabolism, GO:0065007, and development.a number of the genes have roles in energy production and metabolism such as, atp2a2, aldoa, MONDO:0009214, fao1, fgl2, gapdh, gbe1, MONDO:0015408, glrx, MONDO:0005775, me1, phgdh, and pgm1. there is a strong presence of genes involved in protein synthesis and transport, including the ribosomal proteins, the eukaryotic translation factors and initiation factors (eif2s2, eif1e1, elovl5, and elovl6). this gene set is also enriched for a number of ubiquitin and ubiquitin-like proteins (ube2d3, ufm1, uso1, tomm40, hspd1, hspe1, sytl2, nherf1, and hk2). many of these genes are involved in regulation through multiple pathways including regulation of transcription (add3, actr2, actr3, cct6a, gga2, gdh2, mef2b, ykt]] | \n", + "0.08 | \n", + "
| 633 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-1 | \n", + "[[GO:0006412, MESH:D004734, cellular transport, GO:0006955, GO:0035194, mitochondrial oxidative phosphorylation, GO:0006915, GO:0016310, GO:0006096, GO:0006914]] | \n", + "[[GO:0006412, transcription regulation, GO:0009653, GO:0016049, GO:0007165, GO:0008152, GO:0006629, cellular translation]] | \n", + "0.06 | \n", + "
| 634 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-0 | \n", + "[[rna biogenesis, protein synthesis biosynthesis, atp-binding, cytoskeleton organization and assembly, GO:0006351, GO:0006338, GO:0007165, GO:0010467, GO:0006413, MESH:M0439896, GO:0006260]] | \n", + "[[GO:0006412, GO:0036211, GO:0006260, GO:0051726, transcription regulation, GO:0016049, GO:0048468, gene expression.\\nmechanism: the genes may constitute a pathway in which they coordinate together to regulate cell growth, development, and gene expression]] | \n", + "0.06 | \n", + "
| 635 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-1 | \n", + "[[GO:0000394, GO:0051028, MESH:M0439896, GO:0006412, GO:0042254, GO:0035194, GO:0006338]] | \n", + "[[developmental regulation, energy production, GO:0006412, structural maintenance of cell components, GO:0006260, transcription regulation, protein assembly]] | \n", + "0.08 | \n", + "
| 636 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-0 | \n", + "[[genes in this list are primarily involved in cell development, including the processes of rna metabolism, dna replication and cell cycle control. enriched terms include: rna metabolism; dna replication; cell cycle control; chromatin regulation; transcription regulation; cell differentiation; gene expression; and protein synthesis.\\n\\nmechanism: the genes in this list are part of a complex network of molecular pathways involved in regulating the expression, replication and maintenance of genetic material. this includes the transcription, splicing and translation of rnas as well as the replication and repair of dna. the multiple genes in this list suggest coordination and control of various steps in these processes, such as chromatin regulation, which is directly responsible for how genetic material is packaged and regulated. additionally, the genes may be involved in regulating cell cycle progression, transcription regulation and cell differentiation]] | \n", + "[[protein post translational modification, GO:0016310, GO:0006351, GO:0006412, GO:0042254]] | \n", + "0.00 | \n", + "
| 637 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-1 | \n", + "[[GO:0001775, GO:0008283, GO:0006260, dna transcription, rna translation.\\nmechanism: the genes may indicate an underlying biological pathway involving the coordinated expression of these gene sets to regulate the cell cycle, dna replication, transcription, and translation in order to enable cell proliferation]] | \n", + "[[transcription regulation, GO:0006338, nucleosome remodeling, GO:0006260, nuclear localization, GO:0007165, GO:0016567, GO:0006468]] | \n", + "0.08 | \n", + "
| 638 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MYOGENESIS-0 | \n", + "[[gene expression and structure, cytoskeletal structure and dynamics, calcium regulation and signaling, cell adhesion and migration, cell death biochemistry, metabolic regulation]] | \n", + "[[genes in this list are associated with various cellular functions, including cell cycle regulation, developmental pathways, contractile force generation, protein synthesis and degradation, GO:0006915, GO:0000988, and metabolic processes. enriched terms include: cell cycle; cell differentiation; transcriptional regulation; intracellular signaling; muscle contraction; metabolism; apoptosis; protein synthesis; protein degradation.\\n\\nmechanism:\\n\\nthe genes in this list code for proteins involved in a range of cellular processes, including transcription factors that regulate gene expression, receptors that initiate intracellular signaling cascades, enzymes involved in metabolic pathways or apoptosis, and ion channels involved in muscle contraction and cell cycle regulation. these proteins interact to regulate the expression and activity of other proteins, impacting the activity of many important pathways that together coordinate cell growth, differentiation, MESH:D009068, GO:0008152]] | \n", + "0.00 | \n", + "
| 639 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MYOGENESIS-1 | \n", + "[[GO:0031012, GO:0005856, UBERON:0005090, GO:0032502, neuromuscular structure, MESH:D007473, GO:0006811]] | \n", + "[[the genes that were analyzed were related to development, cell signalling, GO:0008152, GO:0065007, GO:0006936, MESH:D055550, and transport. the enriched terms were cellular development, actin cytoskeleton regulation, cell migration and adhesion, GO:0051726, calcium homeostasis and signaling, GO:0006936, GO:0006119, receptor tyrosine kinase signaling, apoptosis and programmed cell death, GO:0030198, GO:0016567, GO:0042632, metabolism and energy production, cell death and apoptosis, cytoskeletal protein binding and regulation of transcription and translation.\\n\\nmechanism: the underlying biological mechanism or pathways involved in these genes include regulation of muscle contraction, cell adhesion and migration, calcium homeostasis, protein ubiquitination and stability, receptor signaling, GO:0051726, GO:0006119, GO:0008219, and regulation of transcription and translation. these mechanisms are essential for cellular development and function, and thus, are enriched in these gene list]] | \n", + "0.00 | \n", + "
| 640 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-0 | \n", + "[[MESH:D047108, GO:0051726, GO:0019722, notch signaling down-regulation, wnt signaling, hedgehog signaling, GO:0000902]] | \n", + "[[GO:0009653, GO:0048513, GO:0009888, GO:0001709, MESH:D002450, notch receptor signaling, wnt signaling, transcription factor signaling]] | \n", + "0.07 | \n", + "
| 641 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-1 | \n", + "[[these genes are involved in a wide range of functions related to signaling, development, and transcriptional regulation, indicating an involvement in a variety of cellular pathways. enriched terms include: cell signaling, GO:0007399, GO:0030154, wnt signaling, notch signaling, hedgehog signaling, transcription factor regulation, GO:0006338, e3 ubiquitin ligase.\\n\\nmechanism: the likely underlying biological mechanism is a complex network of interactions between these genes and their pathways, forming a web of signaling molecules that regulate cell growth, differentiation, apoptosis and other cellular processes. the genes and pathways involved in the network are likely to interact in a dynamic manner]] | \n", + "[[GO:0008283, GO:0009653, GO:0032502, nerve system differentiation, transcription regulation, wnt signalling pathway, GO:0007219]] | \n", + "0.00 | \n", + "
| 642 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[[mitochondrial activity, GO:0022900, GO:0006119, metabolic regulation, MESH:D065767]] | \n", + "[[the list of genes provided are primarily involved in energy metabolism, GO:0007585, and the electron transport chain. specifically, terms such as \"oxidative phosphorylation\", \"mitochondrial electron transport chain\", and \"tricarboxylic acid cycle\" are found to be significantly over-represented.\\n\\nmechanism: the genes provided are involved in the production of atp through metabolic pathways such as oxidative phosphorylation, GO:0005746, and the tricarboxylic acid cycle. these molecules, along with other regulatory proteins, facilitate the flow of electrons to generate energy in the form of atp. this energy is used by cells to carry out metabolic reactions and various cellular processes]] | \n", + "0.00 | \n", + "
| 643 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[[GO:0005746, electron transfer proteins, proton ion transportation proteins, oxidative phosphorylation proteins, metabolite-binding proteins, atp synthesis proteins]] | \n", + "[[mitochondrial electron transport chain complex activity, GO:0006120, GO:0005747]] | \n", + "0.00 | \n", + "
| 644 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_P53_PATHWAY-0 | \n", + "[[cytoskeletal reorganization, calcium homeostasis, ubiquitin-proteasome pathway, GO:1901987, transcriptional regulation, GO:0006397, GO:0006974]] | \n", + "[[analysis of this list of genes suggests a function related to cell cycle regulation, GO:0006915, and protein translation. the enriched terms include 'cell cycle regulation', 'apoptosis', 'protein translation', 'transcription regulation', 'intracellular protein transport', 'protein synthesis', and 'dna repair'.\\n\\nmechanism: the list of genes may be associated with a mechanism related to the regulation of cell cycle transitions and the integration of external signals to regulate gene transcription, protein translation and stability, and cellular apoptosis. this could involve some combination of signal transduction, GO:0006355, GO:0043687, GO:0006281]] | \n", + "0.00 | \n", + "
| 645 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_P53_PATHWAY-1 | \n", + "[[GO:0006351, chromatin dynamics, GO:0007155, MESH:D016207, GO:0007049, dna damage repair, cell signaling, GO:0016049, GO:0006915, immune modulation]] | \n", + "[[gene expression and protein metabolism are likely to be enriched. specifically, the genes are likely involved in protein folding and transport, GO:0016567, transcriptional regulation, GO:0051726, protein-protein interactions, and signal transduction. \\nmechanism: these genes likely play a role in common metabolic, GO:0023052, and regulatory pathways.\\nubiqutination terms: rchy1, hexim1, upp1, pom121, procr, tap1, phlda3, wwp11; \\ntranscription factors:cd81, sat1, ercc5, ralgdh, irak1, aen, tob1, stom, MONDO:0100339, rap2b, tm7sf3, lif, MESH:C058179, ccp110, baiap2, tnfsf9, dcxr, eps8l2, ifi30, fdxr, elp1, itgb4, hbegf, irag2, ccnd2, sertad3, mknk2, retsat, ip6k2, hmox1, zfp36l1, epha2, tpd]] | \n", + "0.00 | \n", + "
| 646 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[[GO:0031016, GO:0006006, GO:0048870, neural development]] | \n", + "[[GO:0031016, GO:0007399, development of neural structures, GO:0048513, transcription regulation, GO:0009653, cell-to-cell adhesion, GO:0006412, hormonal metabolism, hormonal signaling]] | \n", + "0.08 | \n", + "
| 647 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[[GO:0009653, neuronal development, GO:0007165, GO:0030073, transcription regulation, GO:0000988]] | \n", + "[[GO:0022008, GO:0008152, GO:0006355, GO:0006412, GO:0009653, body patterning and organization, neurological system development, GO:0030154]] | \n", + "0.08 | \n", + "
| 648 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PEROXISOME-0 | \n", + "[[enrichment test suggested genes are skewed towards genes involved in development, metabolic control, transport, cell cycle and homeostasis, as well as transcriptional regulation.\\n\\nmechanism: these genes appear to be involved in a diverse range of processes, suggesting multiple pathways contributing to the physiological functions of these genes. for instance, abcb1, abcb4 and abcb9 are involved in medication transport, abcc5 and abcc8 are involved in atp coupling, acaa1 is involved in fatty acid metabolism, alb is involved in heme metabolism, aldh1a1, aldh9a1, atxn1 and bcl10 are involved in transcriptional regulation, ctbp1 and ctps1 are involved in ubiquitination, dhcr24 and dhrs3 are involved in cholesterol biosynthesis, fabp6 is involved in bile acid transport, fads1 is involved in fatty acid desaturase, fis1 and gnpat are involved in lipoic acid synthesis and mitochondrial fatty acid metabolism, gstk1 is involved in gst-mediated detoxification, hmgcl is involved in steroidogenesis, hras, hsd11b2, hsd17b11]] | \n", + "[[GO:0006629, stress response, GO:0009299, GO:0006281, skeletal and cartilage development, GO:0016477, metabolic enzymes, MESH:D002352]] | \n", + "0.00 | \n", + "
| 649 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PEROXISOME-1 | \n", + "[[GO:0006629, GO:0008202, transcription regulation, GO:0051726]] | \n", + "[[GO:0008152, GO:0006351, GO:0065007, GO:0006810, GO:0007165, GO:0006412, GO:0030154, GO:0006260, GO:0036211, membrane trafficking]] | \n", + "0.00 | \n", + "
| 650 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[[GO:0010467, dna repair & maintenance, MESH:M0496065, cellular signaling pathways, GO:0006629]] | \n", + "[[MESH:M0023730, GO:0009653, GO:0030154, tyrosine kinase activity, GO:0038023]] | \n", + "0.00 | \n", + "
| 651 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[[GO:0051726, gene transcription, transcription factor activation, MESH:M0023730, MESH:D011494, receptor proteins, GO:0006412, GO:0016049, GO:0008283, GO:0030154]] | \n", + "[[cell signaling, GO:0019538, GO:0006629, transcription regulation, GO:1901987, GO:0007165, receptor signaling, GO:0070085, GO:0016301, GO:0006915, g-protein interactions, transcriptional regulation]] | \n", + "0.00 | \n", + "
| 652 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-0 | \n", + "[[gene expression regulation; co-translational protein targeting; clathrin-mediated endocytosis; endosomal protein trafficking; vesicle transport; exocytosis; receptor and ligand-mediated signaling; development and organ morphogenesis.\\nmechanism: the identified genes are likely involved in a variety of biological processes related to endocytosis, vesicle trafficking and transport, receptor and ligand-mediated signaling, MESH:D005786, co-translational protein targeting, and organ morphogenesis. these processes can be clustered into several pathways, including the calcineurin-mediated endocytosis pathway, the mapk signaling pathway, the wnt/beta-catenin signaling pathway, the clathrin-mediated endocytosis pathway, the endosomal protein trafficking pathway, the vesicle transport pathway, the exocytosis pathway, the receptor ligand-mediated signaling pathways]] | \n", + "[[cell membrane fusion, GO:0016192, intracellular trafficking, predominant cargo proteins, GO:0006900, membrane remodeling]] | \n", + "0.00 | \n", + "
| 653 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-1 | \n", + "[[genes belonging to this list are mainly involved in endocytosis, GO:0016192, MESH:D021381, and membrane fusion. the enriched terms include: endocytosis; vesicle trafficking; protein trafficking; membrane fusion; membrane transport; cytoskeleton organization; signal transduction; receptor internalization; and protein trafficking pathways.\\n\\nmechanism: the common characteristics shared by the genes suggest that they are all involved in some aspect of the endocytosis pathway. this biological mechanism involves signal transduction by which a signal (chemical or physical) can pass through a cell membrane and allow the cell to take up extracellular substances. through receptor internalization, molecules, like hormones, can be shuttled into intracellular vesicles and undergo further signaling events. the sequential vesicle trafficking steps then enable the cargo to be transported to their final destination. the proteins play various roles in facilitating membrane fusion, GO:0036211, GO:0007010, and vesicle transport. all of these activities act in concert to usher signals, MESH:D011506, other substances into the cell]] | \n", + "[[GO:0043687, GO:0006457, GO:0006412, GO:0006897, GO:0009311, lysosomal trafficking]] | \n", + "0.00 | \n", + "
| 654 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[[redox regulation, antioxidant defense, detoxification of reactive oxygen species, peroxisomal biogenesis, MESH:M0572479, cell metabolism]] | \n", + "[[GO:0008152, oxidative damage resistance, GO:0006281, cellular metabolic regulation, GO:0006915, regulatory pathway, GO:0006457, GO:0006749]] | \n", + "0.00 | \n", + "
| 655 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[[redox balance regulation, GO:0008152, GO:0051726, transcriptional regulation]] | \n", + "[[this list of genes is enriched for terms related to oxidative stress, GO:0008152, and immune system function. specifically, the genes represent proteins involved in oxygen-sensing, anti-oxidation, redox regulation, GO:0006281, the stress response, and cytokine signaling.\\n\\nmechanism:\\nthe underlying biological mechanism of the gene list is likely the cellular response to oxidative stress. oxidative stress is a term used to describe a disruption in the balance of antioxidant molecules and reactive oxygen species. these reactive molecules can cause damage to the cell, and thus the relevant genes likely help the cell to counteract this damage by regulating redox status, mediating oxidant stress, and participating in dna repair and other defense mechanisms. additionally, some of these genes are involved in cytokine signaling, which helps to aid the immune system in defending against potential oxidative insults]] | \n", + "0.06 | \n", + "
| 656 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-0 | \n", + "[[cell signaling, protein regulation, GO:1901987, GO:0009653, GO:0048513, cytoskeletal regulation]] | \n", + "[[GO:1901987, GO:0006338, GO:0016567, GO:0006260, GO:0051225, GO:0006997]] | \n", + "0.09 | \n", + "
| 657 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-1 | \n", + "[[cell cycle checkpoint regulation, GO:0009653, cell signaling, MESH:D003598, organ development]] | \n", + "[[the list of genes provided are involved in diverse processes, such as cell structure and organization, GO:0007165, transcriptional regulation and other metabolic activities. the enriched terms from performing a term enrichment test are cell cycle, GO:0051301, GO:0016569, development and differentiation, cell signaling and signal transduction, GO:0006397, transcriptional regulation, and metabolic processes.\\n\\nmechanism:\\nthe genes provided are believed to be involved in a general mechanism of cell organization and function. the enriched terms are suggestive of the genes being related to fundamental processes such as cell cycle regulation, GO:0051301, transcriptional regulation, GO:0016569, and signal transduction. through the regulation of the genes, they are thought to be capable of controlling the organization and structure of cells, as well as metabolism and other cellular activities. furthermore, these pathways likely interact with each other in a complex manner, thereby allowing for intricate coordination between the genes in order to precisely tune process]] | \n", + "0.00 | \n", + "
| 658 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[[mapk pathway, tgf-β signaling pathway, wnt/β-catenin pathway, GO:0035329, transcriptional regulation, muscle morphogenesis, GO:0048729, regulation of g-protein signaling, GO:0006954]] | \n", + "[[genes in this set are related to morphogenesis, GO:0007155, immune signaling, and transcriptional regulation. enriched terms include: morphogenesis, GO:0007155, immune signaling, transcriptional regulation, digit development, GO:0007049, protein-protein interaction, GO:0008083, and regulation of transcriptional activity.\\n\\nmechanism: morphogenesis can be regulated by the activity of kinases, cell adhesion can be mediated by the expression of cell adhesion molecules, and immune signaling can be regulated by the activity of cytokines, MESH:D018121, and transcription factors. the transcriptional regulation of these genes can be mediated by transcription factors and the regulation of transcriptional activity can be mediated by modulators of tfs, such as kinases and ubiquitin ligases. protein-protein interactions can occur between the different genes, signaling from growth factors can affect the expression of genes in this set]] | \n", + "0.04 | \n", + "
| 659 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[[these genes are involved in processes related to cell development, GO:0009653, calcium and calcium-dependent signaling, MESH:D017978, smad pathway and extracellular matrix proteins.\\n\\nmechanism: the mechanism underlying this gene list is likely related to signal transduction pathways. these may involve cell surface receptors which bind growth factors, such as tgfb1 and bmpr2, and transduce the signal through the smad pathway via the fkbp1a, bmpr1a, smurf1, smad1, ltbp2, thbs1, arid4b, ppm1a, and ctnnb1 proteins to influence the regulation of gene expression and cell fate. moreover, other molecules such as xiap, ube2d3, nog, slc20a1, serpine1, bcar3, rhoa, MESH:D045683, hipk2, ppp1ca, smad7, junb, smad6, ppp1r15a, tjp1, and ifngr2 may be involved in the signal transduction pathway. in addition, the calcium and calcium-dependent signaling by the tg]] | \n", + "[[transcriptional regulation, GO:0007165, GO:0051726, protein kinase pathways, GO:0006412, GO:0048468, GO:0008283, GO:0030054, cytoskeletal organization]] | \n", + "0.00 | \n", + "
| 660 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[[GO:0032502, GO:0006954, MESH:D056747, cell signaling, MESH:M0496924, GO:0009653, GO:0009888, GO:0008283, GO:0006915, immune system response, MESH:M0496924]] | \n", + "[[GO:0002224, GO:0032502, GO:0006954, immune-response regulation, nfkb, GO:0004707, GO:0010467, pro-inflammatory molecules]] | \n", + "0.12 | \n", + "
| 661 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[[gene transcription, actin maturation, cytoskeleton formation, signaling complex assembly, interleukin receptor signaling, GO:0051170, cytokine receptor signaling, nf-kappab signaling pathway, cytokine-mediated signal transduction, GO:0006367, MESH:D005786, cytokine receptor signaling pathway, GO:0010737, GO:0035556]] | \n", + "[[cytokine-mediated signaling, antigen-receptor mediated signaling, GO:0042100, cytokine expression and release, immunoregulatory interactions, GO:0051092, interferon (ifn) signaling]] | \n", + "0.00 | \n", + "
| 662 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[[GO:0009299, GO:0042254, GO:0006457, nucleolar activity, spliceosomal activity, protein production, GO:0015031, GO:0006396, GO:1901987]] | \n", + "[[GO:0006412, GO:0042254, GO:0006413, GO:0006457, GO:0006414, GO:0015833, peptide assembly, chaperone mediated protein folding]] | \n", + "0.13 | \n", + "
| 663 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[[GO:0008152, GO:0006412, GO:0043687, GO:0016310, pepetide binding and metabolism, protein structure and folding, rna synthesis and processing, GO:0000394, GO:0010467, GO:0051726, GO:0006915, GO:0007165, GO:0006281]] | \n", + "[[analysis of this gene list has revealed that the functions enriched in the gene set include translation and translation initiation (exosc2, eif4a3, MESH:D039561, eif4g1, eif4a2); ubiquitination (ern1, skp1, herpud1, ube2g2, ube2l3); and protein folding and stability (atf3, fkbp14, dnajb9, calr, preb, hspa5, hsp90b1).\\n\\nmechanism: the enriched functions imply a complex network of processes that is likely to involve translation initiation of mrna, GO:0016567, and chaperone activity that facilitates protein folding, stability and degradation. it is possible that this gene set is associated with a variety of cellular pathways, including those related to gene expression, GO:0007165, GO:0008152]] | \n", + "0.06 | \n", + "
| 664 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-0 | \n", + "[[MESH:D011494, cellular signaling pathways, GO:0001501, GO:0031012, transcriptional regulation, post-translational phosphorylation, growth regulation, development regulation, remodeling]] | \n", + "[[cell signaling, structural proteins, MESH:D004798, GO:0009653]] | \n", + "0.00 | \n", + "
| 665 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-1 | \n", + "[[mitotic regulation, GO:0060349, morphogenesis of specific organs and tissues, GO:0009966, regulation of transcription, GO:0042127, cellular responses to external stimuli, GO:0006468, GO:0003677]] | \n", + "[[the above list of genes is significantly enriched for terms related to the development of the connective tissue, including morphogenesis, GO:0007049, regulation of transcription, and extracellular matrix organization; as well as the regulation of cell migration, matricellular protein signaling, GO:0007165, and calcium ion binding.\\n\\nmechanism: the enriched terms suggest that these genes work together in a common and interconnected pathway to control the formation, MESH:D009068, and functioning of the connective tissue. this pathway likely involves interactions among signal transduction pathways mediated by protein-protein interactions, transcriptional regulation, and calcium ion binding. these interactions would likely affect the structure and organization of the extracellular matrix, the migration of cells, the cell cycle, signalling through matricellular proteins]] | \n", + "0.04 | \n", + "
| 666 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-0 | \n", + "[[GO:0032502, GO:0016049, gene transcription, GO:0008152, MESH:D011506, GO:0006412, GO:0007049, cell signaling, transcriptional regulation, MESH:D021381, GO:0010468]] | \n", + "[[MESH:D021381, organelle trafficking, GO:0006306, transcription regulation, GO:0003677, GO:0006338, GO:0051726, GO:0008152]] | \n", + "0.12 | \n", + "
| 667 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-1 | \n", + "[[GO:0008283, GO:0051726, dna replication and repair, GO:0007165, GO:0019722, GO:0006915, GO:0006629, oxygen pathway]] | \n", + "[[genes in this list are generally involved in the regulation of cell growth and development, in particular related to apoptosis, signaling and transcriptional pathways. enriched terms include: transcriptional regulation; cell cycle regulation; apoptosis regulation; signal transduction; dna damage response; and cellular metabolism.\\n\\nmechanism: the molecular and cellular mechanisms underlying cell growth and development are complex and interconnected. genes in this list are believed to be involved in several pathways, such as transcriptional regulation, GO:0051726, apoptosis regulation, GO:0007165, GO:0006974, and cellular metabolism. these pathways interact and regulate each other in order to ensure the healthy functioning of cells. transcriptional regulation is key in regulating gene expression, while the cell cycle is tightly regulated by the activation of cell cycle control proteins and anti-apoptotic pathways. signal transduction pathways are essential for the proper coordination of cellular responses to external stimuli, and dna damage response allows for the repair of any irregularities. cellular metabolism is necessary for providing energy for growth and repair, for controlling the production of proteins]] | \n", + "0.11 | \n", + "
| 668 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[[this examination of human genes reveals a number of gene functions that are significantly enriched and related to developmental processes, including cell proliferation and differentiation, GO:0048729, and wnt signalling pathways. \\nmechanism: cell proliferation and differentiation, GO:0048729, wnt signalling pathways are all important in the normal healthy development of cells organs. these genes provide important functions that act in cooperative downstream pathways to enable promote these developmental processes.\\nthe enriched terms are: cellular differentiation; cellular proliferation; digit development; tissue morphogenesis; wnt signalling pathway]] | \n", + "[[the genes in this list are associated with the wnt signaling pathway, modulating cell growth and mophogenesis. the enrichment terms corresponding to this list are wnt signaling, GO:0016049, GO:0009653, transcriptional regulation, and epigenetics.\\n\\nmechanism: the wnt signaling pathway activates nuclear proteins such as lef1 and tcf7, which then activate transcription of genes involved in cell growth and morphogenesis. the genes on the listed are associated with modulating the wnt pathway, including epigenetic regulation and cell cycle regulation]] | \n", + "0.00 | \n", + "
| 669 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[[wnt signaling, notch signaling, transcription regulation, GO:0051726, GO:0009653, GO:0032502]] | \n", + "[[GO:0009653, GO:0006351, GO:0032502, MESH:D060449]] | \n", + "0.25 | \n", + "
| 670 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "T cell proliferation-0 | \n", + "[[cell signalling, protein interaction, GO:0007165, GO:0032502, regulatory role in immunity, GO:0030163, receptor-mediated signaling, GO:0016049, GO:0030154, GO:0006396]] | \n", + "[[GO:0009653, GO:0048468, cell signaling, receptor-mediated signaling, GO:0010468]] | \n", + "0.07 | \n", + "
| 671 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "T cell proliferation-1 | \n", + "[[cell signaling, immune regulation, GO:0007165, growth factor production and response, immune response and modulation, calcium homeostasis, GO:0000981, development and differentiation, GO:0005102, GO:0001816]] | \n", + "[[GO:0005126, GO:0007155, immunoreceptor-antigen complex binding, regulation of the ubiquitin-proteasome pathway, transcription factor regulator activity, gtp-binding protein binding, GO:0030154]] | \n", + "0.00 | \n", + "
| 672 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "Yamanaka-TFs-0 | \n", + "[[the enrichment test results reveal that the list of genes are all involved in stem cell pluripotency and early embryonic development. enriched terms include pluripotency, stem cell morphology, MESH:D047108, GO:0000981, GO:0016049, differentiation, cell proliferation.\\n\\nmechanism: the genes focus on the regulation of the pluripotency and early embryonic developmental program. they regulate various aspects such as transcription factors, cell growth, morphogenesis, differentiation and cell proliferation. by acting in concert, they maintain the pluripotency of stem cells and initiate the processes of early morphogenesis. it is hypothesized that these genes are part of a large regulatory network which facilitates the pluripotency of the progenitor cells and the successful orchestration of early embryonic development]] | \n", + "[[GO:0000988, embryonic stem cell differentiation, cell pluripotency, dna-binding, MESH:D005786, GO:0140110, transcription factor complex formation.\\nmechanism: these genes are known to be involved in the regulation of gene expression, and thus serve an important role in directing the biological activities associated with embryonic stem cell differentiation and pluripotency. they are likely to form complexes, interact with dna, and/or bind to components of the transcription machinery to regulate gene expression at the transcriptional level]] | \n", + "0.00 | \n", + "
| 673 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "Yamanaka-TFs-1 | \n", + "[[GO:0009792, GO:0048864, GO:0000981, GO:0009653]] | \n", + "[[GO:0048863, GO:0048468, embryonic stem cell differentiation, transcriptional regulation, pluripotency, transcription factor regulation.\\n\\nmechanism: the genes klf4, pou5f1, and sox2 act in concert to regulate the expression of developmental proteins that are involved in forming stem cells. this trio of transcription factors plays a key role in regulating cell differentiation and pluripotency, thus influencing the direction of embryonic stem cell development by regulating gene expression of proteins involved in stem cell formation]] | \n", + "0.00 | \n", + "
| 674 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "amigo-example-0 | \n", + "[[GO:0030198, GO:0007155, GO:0009653, cell signaling, cytoskeletal organization, GO:0030154, MESH:D002470]] | \n", + "[[GO:0008283, GO:0048729, motility regulation, vascular development, GO:0098868, UBERON:0002405]] | \n", + "0.00 | \n", + "
| 675 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "amigo-example-1 | \n", + "[[our term enrichment analysis suggests that the human genes jag2, spp1, jag1, vcan, olr1, col5a2, app, UBERON:0003010, postn, tnfrsf21, apoh, pglyrp1, vav2, fstl1, nrp1, s100a4, lrpap1, vtn, timp1, itgav, lum, pf4, cxcl6, col3a1, stc1, kcnj8, msx1, ptk2, prg2, pdgfa, serpina5, and vegfa are related to processes in growth and differentiation, including transcriptional network maintenance, cell adhesion and motility, GO:0006915, and extracellular matrix component formation.\\n\\nmechanism: \\nthese genes may be involved in a complex network of signaling pathways that regulate cell growth and differentiation, cell adhesion and migration, GO:0006915, and matrix component formation. they may be involved in the reception and transduction of growth and differentiation signals, could facilitate the assembly of extracellular matrix components to form the microenvironment necessary to prompt and]] | \n", + "[[GO:0001525, GO:0008283, GO:0016477, matrix remodeling, GO:0048771, jagged-mediated signaling, transcriptional regulation, GO:0030168, GO:0070527, immune regulation, extracellular matrix formation]] | \n", + "0.00 | \n", + "
| 676 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_0-0 | \n", + "[[GO:0009653, GO:0032502, transcription regulation, cell signalling, GO:0006811]] | \n", + "[[GO:0016049, differentiation, migration, chromatin modulation, transcription regulation, cytoskeletal organization, intracellular trafficking, GO:0007155, GO:0007165, dna/rna metabolic processes, GO:0009653, GO:0001525, muscle growth, GO:0032502]] | \n", + "0.19 | \n", + "
| 677 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_0-1 | \n", + "[[GO:0009653, neuronal growth, neuronal system development, cell-cell communication, cell signaling, GO:0009888, organ development]] | \n", + "[[chromatin regulation, GO:0048468, GO:0006412, GO:0006811, GO:0000981, GO:0043687]] | \n", + "0.00 | \n", + "
| 678 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_1002-0 | \n", + "[[analysis of the gene list shows that they are all associated with sarcomere function, MESH:D009119, skeletal muscles and thermogenesis. the enriched terms include sarcomere function, MESH:D009119, UBERON:0001134, MESH:D022722, actin-myosin interaction, calcium handling, muscle development and differentiation, and mitochondrial function. \\n\\nmechanism: the underlying biological mechanism is associated with the activation of genes that are linked to the assembly, maintenance and contraction of the sarcomere, which is the fundamental unit of muscle contraction, as well as muscle development and differentiation, calcium handling, mitochondrial fluctuation, thermogenesis. this contributes to the generation of force within the skeletal muscles]] | \n", + "[[MESH:M0370791, GO:0007015, GO:0006936, z-disc formation, GO:0007097, muscle fiber organization, ion channel influx/efflux]] | \n", + "0.00 | \n", + "
| 679 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_1002-1 | \n", + "[[skeletogenesis, MESH:D024510, GO:0048740, GO:0001501, GO:0006936, GO:0006412, GO:0009058, MESH:D009126]] | \n", + "[[MESH:D024510, GO:0048740, GO:0021675, calcium distribution, actin proteins, cardiac contractile proteins, sarcomeric proteins, membrane protein transport, ion channel proteins, enzyme regulation.\\nmechanism: this list of genes are likely to be involved in the regulation of muscle structures and contractions, organization of calcium distribution throughout the cell, nerve development, and support of membrane protein transport and enzymatic activities. these processes are important for maintaining muscle contraction and activity]] | \n", + "0.12 | \n", + "
| 680 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "endocytosis-0 | \n", + "[[GO:0007165, vesicle/lipid trafficking, cellular adhesion, nutrient regulation, cell metabolism, cytoskeletal organization, endocytosis/exocytosis, intercellular adhesion/motility]] | \n", + "[[GO:0006629, cell signaling, GO:0007049, cytoskeletal dynamics]] | \n", + "0.00 | \n", + "
| 681 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "endocytosis-1 | \n", + "[[membrane trafficking, GO:0007165, protein proteolysis, GO:0006629, receptor signaling, GO:0055088]] | \n", + "[[GO:0006897, intracellular signaling, GO:0016310, protein interactions, receptor trafficking]] | \n", + "0.00 | \n", + "
| 682 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "glycolysis-gocam-0 | \n", + "[[GO:0006096, aerobic glycolysis, GO:0006094]] | \n", + "[[GO:0006754, GO:0006096, MESH:D004734, MESH:M0496924]] | \n", + "0.17 | \n", + "
| 683 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "glycolysis-gocam-1 | \n", + "[[GO:0008152, GO:0006096, GO:0006098, GO:0006006, MESH:D004734]] | \n", + "[[metabolic pathway, GO:0006096, glucose oxidation, pyruvic acid production, GO:0006754]] | \n", + "0.11 | \n", + "
| 684 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "go-postsynapse-calcium-transmembrane-0 | \n", + "[[these genes appear to be involved in the development, functioning and regulation of the nervous system, specifically neurons and their associated pathways and processes. the terms \"neurotransmission\"; \"neuronal cell membrane regulation\"; \"neurotransmitter release\"; \"calcium signaling\"; \"neuronal ion channel regulation\"; and \"neuronal excitability regulation\" are significantly enriched in this gene set.\\n\\nmechanism: it appears that this gene set may be involved in a broad range of processes related to neurophysiology, including the regulation of neuronal membrane excitability and ion channels, neuronal cell membrane regulation, GO:0007269, and calcium signaling. these processes are all complex and interrelated, are likely to have a direct impact on neural development function]] | \n", + "[[summary: the enriched terms of the human genes atp2b1, atp2b2, cacna1c, cacng2, cacng3, cacng4, cacng5, cacng7, cacng8, chrna10, chrna7, chrna9, drd2, f2r, gpm6a, grin1, grin2a, grin2b, grin2c, grin2d, grin3a, grin3b, htr2a, itpr1, ncs1, p2rx4, p2rx7, plcb1, psen1, slc8a1, slc8a2, slc8a3, trpv1 include neuron development; neurotransmitter signaling; signal transduction; transmembrane transport; neural plasticity; ion transport; calcium signaling; glutamate receptor signaling; and synaptic signaling. \\n\\nmechanism: these genes are believed to act in concert to regulate and coordinate the various stages of neuron development, such as neurotransmitter signaling, GO:0007165, GO:0055085, neural]] | \n", + "0.00 | \n", + "
| 685 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "go-postsynapse-calcium-transmembrane-1 | \n", + "[[the term enrichment test reveals that the genes in the list are mainly involved in neuronal ion channels and calcium signalling pathways. enriched terms included calcium channel activity, GO:0005244, GO:0038023, GO:0015276, and g-protein coupled receptor activity. \\n\\nmechanism: the genes in the list form ion channels and g-protein coupled receptors within neuronal cells, which facilitates the communication of neurotransmitters between neurons. several of the genes are involved in calcium signalling pathways, which regulate various cellular pathways involved in the development and maintenance of neurons]] | \n", + "[[neuronal function, GO:0006811, ion channel regulation, neurotransmitter regulation, calcium regulation, potassium regulation, GO:0007268, membrane potential regulation]] | \n", + "0.00 | \n", + "
| 686 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "go-reg-autophagy-pkra-0 | \n", + "[[GO:0016049, GO:0048468, GO:0006915, GO:0006955, GO:0030163, GO:0006508]] | \n", + "[[this set of genes is associated with cellular functions related to metabolic homeostasis and activation of the pi3k/akt signaling pathway. the enriched terms associated with the genes include cell cycle regulation, protein kinase regulation, mitochondrial regulation, and mitochondrial stress response.\\n\\nmechanism: the metabolic homeostasis and activation of the pi3k/akt pathway are mediated by these genes, which affect the regulation of cell cycle, protein kinase regulation, mitochondrial regulation, and mitochondrial stress response. these genes have roles in regulating metabolic processes as well as responding to external stressors. their involvement in cell cycle regulation and protein kinase regulation ensures the healthy development and maintenance of the cell, while their role in mitochondrial regulation and mitochondrial stress response plays an important role in maintaining the cell's energy production]] | \n", + "0.00 | \n", + "
| 687 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "go-reg-autophagy-pkra-1 | \n", + "[[phosphatidylinositol signalling, vascular endothelial growth factor receptor signalling, progesterone-mediated oocyte maturation, nf-kb signaling, GO:0043526]] | \n", + "[[cell signaling, transcription regulation, GO:0006468, ras activation, akt activation, calcium-associated kinases, GO:0019722]] | \n", + "0.00 | \n", + "
| 688 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[[carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomal, GO:0005777, and catabolic processes; digit, skeletal, GO:0035108]] | \n", + "[[MESH:D009113, MESH:D009077, glycosyltransferase, MESH:D006821, GO:0070085, enzyme, MESH:D011506]] | \n", + "0.00 | \n", + "
| 689 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[[glycoside hydrolase (gh) activity, mucin biosynthesis, GO:0006031, MESH:D057056, lysosomal enzyme activity.\\nmechanism: glycoside hydrolase (gh) and lysosomal enzymes play important roles in the process of glycostasis, and are involved in a variety of metabolic activities such as the breakdown of polysaccharides, the synthesis of glycolipids and glycoproteins, and the degradation of other macromolecules. chitin and mucin biosynthesis also involve glycosylation and enzymatic modification of sugars and polysaccharides to form polymeric molecules. cysteine protease are involved in the hydrolysis of proteins, while lysosomal enzymes aid in the breakdown of molecules in the l]] | \n", + "[[the gene functions that were found to be enriched amongst this set of genes were predominantly related to carbohydrate metabolism, including glycosaminoglycan and glycosphingolipid biosynthesis as well as lysosomal enzyme activity.\\n\\nmechanism:\\nthe mechanism most likely lies in the pathway of glycoconjugation, which helps to regulate important processes such as cell adhesion, GO:0006955, and signal transduction. the pathway is integral to the proper formation and function of the extracellular matrix, which is important for cellular differentiation and tissue organization. the enriched terms found here likely represent genes that are involved in the biosynthesis and metabolism of various glycoconjugates, in addition to the regulation of lysosomal enzymes involved in the degradation of complex carbohydrates]] | \n", + "0.00 | \n", + "
| 690 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "ig-receptor-binding-2022-0 | \n", + "[[members of the immunoglobulin (ig) gene superfamily - specifically, igh, GO:0033984, MESH:C014609, GO:0042571, response and maintenance of the adaptive immune system at different levels, likely via antigen binding, signal transduction and b cell activation]] | \n", + "[[immunoglobulin heavy chain combination, immunoglobulin light chain combination, j-chain, antigen-specific receptor, t-lymphocyte receptor, regulation of immune function]] | \n", + "0.00 | \n", + "
| 691 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "ig-receptor-binding-2022-1 | \n", + "[[GO:0003823, b cell receptors, GO:0007596, GO:0005577, MESH:D001779, clec4d]] | \n", + "[[genes related to immunoglobulins, transcripts associated with immunoglobulin transcription and splicing, immunoglobulin gene expression, proteins involved in immunoglobulin regulation and processing, GO:0002637, GO:0002637, mhc class i antigen processing and presentation, cytokine-mediated signaling, GO:0002544, limit degranulation. \\n\\nmechanism: these genes are associated with immunoglobulin production, processing, and regulation. this includes genes related to immunoglobulins, transcripts involved in transcription and splicing, and proteins that are involved in the regulation and processing of immunoglobulins. additionally, genes related to mhc class i antigen processing, cytokine-mediated signaling, chronic inflammatory response, and limit degranulation are also expressed. these genes interact to form an integrated pathway that is involved in the regulation of the immune response and the formation of immunoglobulins]] | \n", + "0.00 | \n", + "
| 692 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "meiosis I-0 | \n", + "[[dna damage recognition, GO:0006281, GO:0006302, meiotic recombination, GO:0007059, GO:0035825, rad51 family proteins, dna end-protection, mus81-mms4 complex, muts family proteins, dna proofreading, spo11-associated pathway]] | \n", + "[[GO:0006260, GO:0006281, replication fidelity, GO:0007049, GO:0071897, dna prioritization]] | \n", + "0.06 | \n", + "
| 693 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "meiosis I-1 | \n", + "[[GO:0006281, GO:0006260, gene splicing]] | \n", + "[[this enrichment test on the list of human genes suggests a central role for dna damage repair and cell cycle regulation in the common functionalities of the genes. enriched terms found include \"dna repair\", \"cell cycle\", \"chromatin remodelling\", \"recombinational repair\", \"steroid hormone receptor\", \"centromere\", GO:0000724]] | \n", + "0.00 | \n", + "
| 694 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "molecular sequestering-0 | \n", + "[[GO:0000075, cell adhesion/motility complex, transcriptional complex, GO:0036211, rna processing complex]] | \n", + "[[GO:0019722, calcium buffering, GO:0006816, regulation of calcification, protection against calcium overload, calcium-v influx/efflux]] | \n", + "0.00 | \n", + "
| 695 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "molecular sequestering-1 | \n", + "[[calcium binding, apoptotic regulation, immune modulation, MESH:D018384, GO:0051726, stress-response regulation]] | \n", + "[[cell morphology regulation, GO:0008152, GO:0006915, GO:0006412, GO:0036211, GO:0006811, GO:0023052, stress response, GO:0006351, cell surface interactions, chromatin regulation]] | \n", + "0.00 | \n", + "
| 696 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "mtorc1-0 | \n", + "[[the human genes abcf2, acaca, acly, acsl3, actr2, actr3, add3, adipor2, ak4, aldoa, arpc5l, asns, atp2a2, atp5mc1, atp6v1d, MESH:D064096, bcat1, bhlhe40, btg2, bub1, cacybp, calr, canx, ccnf, ccng1, cct6a, cd9, cdc25a, cdkn1a, cfp, cops5, coro1a, cth, ctsc, GO:0038147, cyb5b, cyp51a1, dapp1, ddit3, ddit4, ddx39a, dhcr24, dhcr7, GO:0004146, ebp, edem1, eef1e1, egln3, eif2s2, elovl5, elovl6, eno1, eprs1, ero1a, etf1, MONDO:0100101, MONDO:0100102, fdxr, fgl2, MESH:D010649]] | \n", + "[[genes in this list are involved in various aspects of cellular metabolism, GO:0065007, and development.a number of the genes have roles in energy production and metabolism such as, atp2a2, aldoa, MONDO:0009214, fao1, fgl2, gapdh, gbe1, MONDO:0015408, glrx, MONDO:0005775, me1, phgdh, and pgm1. there is a strong presence of genes involved in protein synthesis and transport, including the ribosomal proteins, the eukaryotic translation factors and initiation factors (eif2s2, eif1e1, elovl5, and elovl6). this gene set is also enriched for a number of ubiquitin and ubiquitin-like proteins (ube2d3, ufm1, uso1, tomm40, hspd1, hspe1, sytl2, nherf1, and hk2). many of these genes are involved in regulation through multiple pathways including regulation of transcription (add3, actr2, actr3, cct6a, gga2, gdh2, mef2b, ykt]] | \n", + "0.08 | \n", + "
| 697 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "mtorc1-1 | \n", + "[[energy production, GO:0008152, protein biosynthesis and folding, cell regulation, MESH:D048788, protein turnover]] | \n", + "[[genes related to metabolism and biosynthesis (acly, aldoa, atp2a2, atp6v1d, cacybp, coro1a, dhcr24, MONDO:0100101, MONDO:0100102, gbe1, MESH:C066524, gsr, hmgcs1, hspa9, lgmn, me1, mthfd2l, nampt, pgm1, pgk1, psat1, psma3, psma4, psmg1, psmc2, psmc4, psmd12, psmd13, psmd14, stc1, stip1, and ufm1), protein folding/interaction (act2, actr2, actr3, add3, elovl5, eno1, ero1a, eif2s2, fgl2, insig1, itgb2, map2k3, mcm2, mcm4, nufip1, p4ha1, pdk1, pitpnb, pnp, psme3, sec11a, shmt2, slc2a1, slc2a3]] | \n", + "0.00 | \n", + "
| 698 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "peroxisome-0 | \n", + "[[peroxisome biogenesis, peroxisome formation, membrane protein trafficking, GO:0044255, mitochondrial-peroxisomal crosstalk]] | \n", + "[[protein homeostasis, peroxisome biogenesis, peroxisome assembly, peroxisome maintenance, protein regulation, GO:0050821]] | \n", + "0.10 | \n", + "
| 699 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "peroxisome-1 | \n", + "[[peroxisomal biogenesis, peroxisomal protein transport, oxidative damage resistance]] | \n", + "[[peroxisomal biogenesis, peroxisome assembly, peroxisome regulation, GO:0015031, membrane trafficking]] | \n", + "0.14 | \n", + "
| 700 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "progeria-0 | \n", + "[[cell structural element development, gene transcription, GO:0016070, GO:0006259, transcriptional regulation]] | \n", + "[[after performing the enrichment test on the genes zmpste24, banf1, MONDO:0010196, and lmna, we identified that all of the genes have a role in the regulation of nuclear and chromatin structures. the individual genes are involved in a wide range of processes in these two areas. this includes gene expression, GO:0006260, GO:0006338, GO:0000723, as well as cell cycle checkpoints.\\n\\nthe enriched terms are 'nuclear structure regulation'; 'chromatin structure regulation'; 'gene expression regulation'; 'dna replication regulation'; 'chromatin remodeling'; 'telomere maintenance'; and 'cell cycle checkpoint regulation'. \\n\\nmechanism: the underlying biological mechanism that our gene list points to is one involving the regulation of nuclear and chromatin structures. in order to maintain the stability of the genome and ensure its accurate transmission, molecules encoded by the four genes could be involved in key activities such as gene expression, GO:0006260, GO:0006338, GO:0000723, as well as cell cycle checkpoints]] | \n", + "0.00 | \n", + "
| 701 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "progeria-1 | \n", + "[[dna replication and repair, GO:0006334, GO:0000723, transcriptional regulation]] | \n", + "[[transcriptional regulation, GO:0006281, GO:0051726, GO:0030154]] | \n", + "0.14 | \n", + "
| 702 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "regulation of presynaptic membrane potential-0 | \n", + "[[GO:0007165, GO:0006811, regulation of neurotransmitter release]] | \n", + "[[MESH:D007473, MESH:D008565, synapse formation, GO:0007268, MESH:D009473, neuronal excitability, voltage-gated ion channels, MESH:D058446]] | \n", + "0.00 | \n", + "
| 703 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "regulation of presynaptic membrane potential-1 | \n", + "[[analysis of these genes show that they are involved in human neurological structure and function. enriched terms include neuron activity, GO:0005216, GO:0008066, GO:0004930, MESH:D005680, GO:0005267, MESH:D005680]] | \n", + "[[ion-channel function, neuron excitability, GO:0007268, MESH:D018079, MESH:D017470, MESH:D015221, MESH:D015222]] | \n", + "0.00 | \n", + "
| 704 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "sensory ataxia-0 | \n", + "[[MESH:D024510, neuronal development, GO:0015031, GO:0006629, GO:0009653]] | \n", + "[[GO:0006412, GO:0008152, ion channel transport, GO:0006936, MESH:D024510]] | \n", + "0.11 | \n", + "
| 705 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "sensory ataxia-1 | \n", + "[[GO:0015031, MONDO:0008090, GO:0048705, MESH:D024510, GO:0005783, mitochondrial protein transport, cytoskeletal organization]] | \n", + "[[nucleic acid metabolism, GO:0003676, GO:0050657, GO:0019538, GO:0005515, GO:0015031]] | \n", + "0.08 | \n", + "
| 706 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "term-GO:0007212-0 | \n", + "[[g alpha subunit signaling, gpcr activation and signaling, gpcr function, MESH:D019281]] | \n", + "[[g-protein coupled receptor (gpcr), g-protein subunit, MESH:D000262, MESH:D015220, MESH:D010770]] | \n", + "0.00 | \n", + "
| 707 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "term-GO:0007212-1 | \n", + "[[cellular signaling, g protein signaling pathway, calcium signaling pathway, GO:0007399, GO:0007268, phosphorylation cascade, nerve morphogenesis, indoleamine metabolism]] | \n", + "[[GO:0007165, cellular growth & differentiation, GO:0007010, endocrine system regulation, transcriptional regulation]] | \n", + "0.00 | \n", + "
| 708 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "tf-downreg-colorectal-0 | \n", + "[[nuclear receptor superfamily, transcription regulation, epigenetic regulation, GO:0051726, GO:0003677, GO:0006338, GO:0032502, cell signaling pathways, GO:0005652, GO:0016363]] | \n", + "[[genes such as hira, cebpb, e2f3, hmga1, znf263, tfdp1, trib3, bhlhe40, smarca4, slc26a3, nfe2l3, ssbp2, gtf3a, npm1, trip13, mef2c, nr3c2, foxm1, vdr, hand1, klf4, hexim1, tgif1, med24, tead4, smarcc1, scml1, MESH:D024243, myc, foxa2, bmal2, spib, nme2, phb1, cbx4, runx1, ppargc1a, polr3k, nr5a2, maf, nr1h4, sox9, dnmt1, cbfb, znf593, mta1, zbtb18 are all involved in the regulation of transcription, GO:0006338, GO:0003677, and epigenetics. of this group, genes involved in transcription are significantly enriched (e.g. hira, cebpb, e2f3,]] | \n", + "0.03 | \n", + "
| 709 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "tf-downreg-colorectal-1 | \n", + "[[transcriptional regulation, GO:0016569, GO:0009653, cardiovascular development, differentiation, MESH:M0464910, MESH:M0030450, GO:0048863]] | \n", + "[[GO:0016049, transcriptional regulation, GO:0006338, GO:0051726, GO:0006351, GO:0016569]] | \n", + "0.17 | \n", + "
| 710 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "EDS-0 | \n", + "[[GO:0032963, GO:0030198, GO:0004222, GO:0030206, GO:0008378, GO:0005509, GO:0008270, platelet derived growth factor binding, GO:0002020, GO:0035987, GO:0007266, GO:0007160, hypoxia response, epidrmis development, peptidyl-lysine hydroxyl]] | \n", + "[[collagen or extracellular matrix structural constituent, collagen metabolic process or biosynthetic process, proteoglycan metabolic process or biosynthetic process, GO:0006024, dna-binding transcription factor binding activity, GO:0001217, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, metal ion binding activity, GO:0003755, GO:0035987, GO:0004252, GO:1904028, protein peptidyl-prolyl is]] | \n", + "0.04 | \n", + "
| 711 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "EDS-1 | \n", + "[[GO:0030198, GO:0030199, GO:0043589, GO:0042060, GO:0043588, GO:0032964, GO:0006024, GO:0003755, GO:0035987]] | \n", + "[[GO:0030198, GO:0030199, GO:0032964, GO:0030166, GO:0006024]] | \n", + "0.40 | \n", + "
| 712 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "FA-0 | \n", + "[[analysis of the above genes shows that they are all involved in dna repair and involved in the fanconi anaemia nuclear complex, which is a critical part of the fanconi anaemia disease pathway. the list of enriched terms includes \"protein monoubiquitination\", \"dna repair complex\", \"fanconi anaemia nuclear complex\", \"double-strand break repair via homologous recombination\", \"response to intra-s dna damage checkpoint signaling\", \"telomere maintenance\", \"positive regulation of g2/m transition of mitotic cell cycle\", \"regulation of transcription by rna polymerase ii\".\\n\\nmechanism: the underlying biological mechanism is the fanconi anaemia pathway, where the defective genes of the path have the potential to lead to cancer or other fanconi anaemia-related illnesses. this dna repair pathway relies heavily on the fanconi anaemia nuclear complex, which involves the processes of monoubiquitination, involving the above genes, double-strbreak repair via homologous recombination. in addition, the regulation of telomere maintenance, positive regulation of g2/m transition of mitotic cell cycle regulation of transcription by rna polymerase ii are essential for proper dna repair]] | \n", + "[[GO:0006281, GO:0006513, GO:0043240, GO:0000785, GO:0005634, GO:0005829]] | \n", + "0.00 | \n", + "
| 713 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "FA-1 | \n", + "[[this group of genes are involved in a range of dna repair processes, including protein monoubiquitination and double-strand break repair via homologous recombination. they are all localized in different components of the cell (e.g. chromatin, GO:0005634, GO:0005829, GO:0005657, GO:0005694, etc.) and are part of several complexes/hierarchies (e.g. fanconi anaemia nuclear complex, GO:0033063, GO:0048476, GO:0033557, GO:0033593, etc.). enriched terms includes: dna repair; protein monoubiquitination; double-strand break repair via homologous recombination; regulation of dna metabolic process; negative regulation of double-stranded telomeric dna binding activity; response to gamma radiation; regulation of telomere maintenance; establishment of protein localization to telomere; and regulation of protein metabolic process.\\n\\nmechanism: these genes are involved in a range of complex and interrelated biochemical pathways, which utilize a variety of enzymatic activities (e.g. ubiqu]] | \n", + "[[GO:0006513, GO:0006281, GO:0003682, GO:0000400, GO:0003684, GO:0003697, GO:1990599, GO:0004520, GO:0006310, GO:0005524, GO:0006259, GO:0072757, GO:0051052, GO:0003691, GO:0000723, GO:0019219, GO:0051246, GO:0070200, GO:0016573, GO:0004402, gamma-tubulin binding activity, identical protein binding activity, jun kinase binding activity, rna polymerase ii-specific dna-binding transcription factor binding activity, GO:0061630, GO:0031386]] | \n", + "0.00 | \n", + "
| 714 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ADIPOGENESIS-0 | \n", + "[[GO:0005515, protein homodimerization, GO:0005524, GO:0003677, GO:0003824, MONDO:0016019]] | \n", + "[[protein binding activity, MESH:D010758, atp binding activity, gtp binding activity, GO:0022857, dna binding activity, receptor binding activity, GO:0004869, caspase binding activity, rna binding activity]] | \n", + "0.00 | \n", + "
| 715 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ADIPOGENESIS-1 | \n", + "[[protein homodimerization, GO:0019899, GO:0140657, GO:0005102, ligase binding, GO:0003924, GO:0046872, dna-binding, rna-binding, oxidase activity, MESH:D010758, GO:0120227, transportase activity, dehydrogenase activity, GO:0016791, GO:0016301, GO:0004175, GO:0022857, chemotactic receptor activity, GO:0017077]] | \n", + "[[protein binding activity, enzyme binding activity, atp binding activity, rna binding activity, gtp binding activity, identical protein binding activity, gtp-dependent protein binding activity, transition metal ion binding activity, GO:0016615, aldehyde dehydrogenase activity, GO:0008097, GO:0052650, fad binding activity, MESH:D010758, heme binding activity, GO:0003872, GO:0004609, GO:0003873, GO:0004144, GO:0003994, GO:0004784, GO:0004129, molybdenum ion binding activity]] | \n", + "0.02 | \n", + "
| 716 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[[receptor binding activity, signaling receptor binding activity, protein binding activity, dna-binding, GO:0016563, GO:0005125, GO:0008083, GO:0042605, enzyme binding activity, chemical binding activity, protein complex binding activity]] | \n", + "[[protein homodimerization, protein heterodimerization, GO:0042802, GO:0019901, dna-binding, rna-binding, GO:0017124, GO:0019958, GO:0008201, ubiquitin-protein ligase binding]] | \n", + "0.05 | \n", + "
| 717 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[[enzyme binding activity, rna binding activity, protein binding activity, chemokine receptor binding activity, GO:0004712, GO:0042803, identical protein binding activity, GO:0008083, interleukin binding activity, cell-cell adhesion mediation, dna-binding transcription activity, GO:0015026, cytoplasmic factor activity, metal ion binding activity, polypeptide antigen transporter activity]] | \n", + "[[GO:0007155, GO:0005102, GO:0007165, GO:0001228, chemokine receptor binding activity, enzyme binding activity, GO:0008083, GO:0005125, degradation of redundant or damaged proteins and peptides, GO:0046983, metal ion binding activity, peptide antigen binding activity, GO:0004888, GO:0004712, GO:0042803, ubiquitin binding activity]] | \n", + "0.24 | \n", + "
| 718 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[[protein binding activity, enzyme binding activity, transcription factor binding activity, GO:0016787, GO:0004721, GO:0003714, GO:0003713, atp binding activity, GO:0004672, GO:0016563, GO:0003924, nad+ binding activity, ring-like zinc finger domain binding activity, GO:0061656, small protein activating enzyme binding activity, GO:0000224, GO:0062076, GO:0004383, GO:0004222, 17-beta-dehydrogen]] | \n", + "[[GO:0005215, GO:0005515, GO:0004672, GO:0038023, GO:0006351, GO:0044237, GO:0006974, GO:0007010, GO:0016787, GO:0046872, GO:0003924]] | \n", + "0.11 | \n", + "
| 719 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[[protein binding activity, GO:0004672, GO:0006351, GO:0038023, enzymatic activity, GO:0016310, GO:0097472, GO:0003677, GO:0006351, postsynaptic organization, GO:0016887, nucleic acid binding activity, ubiquitin protein ligase binding activity, fad binding activity, MESH:D009249, GO:0061665, enzyme binding activity, GO:0022857, endopeptidase activator]] | \n", + "[[GO:0005515, GO:0016887, GO:0016563, GO:0003677, GO:0004674, GO:0022857, GO:0016787, GO:0061631, cis-regulatory region sequence-specific dna binding activity, GO:0061665, GO:0034594, GO:0007165, GO:0043027, GO:0003924, GO:0042803, nucleic acid binding activity, GO:0003713, GO:0003714, enzyme binding activity, calmodulin binding activity, metalloendope]] | \n", + "0.18 | \n", + "
| 720 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ANGIOGENESIS-0 | \n", + "[[GO:0030021, collagen binding activity, integrin binding activity, GO:0060090, identical protein binding activity, fibronectin binding activity, GO:0046983, heparan sulfate proteoglycan binding activity, GO:0007160, GO:0010810]] | \n", + "[[summary: the list of genes provided appear to be involved in a variety of unrelated processes, but when grouped by shared activities, several functions in common can be identified. these common functions include protein binding activity, GO:0060230, phospholipid binding activity, platelet-derived growth factor binding activity, GO:0046983, signaling receptor binding activity, collagen binding activity, atp activated inward rectifier potassium channel activity, voltage gated monoatomic ion channel activity, GO:0005249, GO:0016298, heparan sulfate proteoglycan binding activity, heparin binding activity, multiple growth factor activities, peptidoglycan binding activity, GO:0016019, platelet derived growth factor binding activity, non membrane spanning protein tyrosine kinase activity, GO:0005096, vascular endothelial growth factor binding activity, metal ion binding activity, small molecule binding activity, enzyme binding activity, retinoic acid binding activity, cxcr3 chemokine receptor binding activity, prostaglandin transmembrane transporter activity and sodium-independent organic anion transmembrane transporter activity. \\nmechanism: the genes in the list appear]] | \n", + "0.09 | \n", + "
| 721 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ANGIOGENESIS-1 | \n", + "[[GO:0007166, GO:0006468, GO:0045861, GO:0007160, GO:1902533, GO:0010604, transmem]] | \n", + "[[GO:0005515, GO:0006468, GO:0016477, GO:0008283, GO:0045861, GO:1902533, GO:0009966, GO:0010604, GO:0019901, GO:0008191, ion binding activity, small molecule binding activity, GO:0035987, GO:0005096, platelet-derived growth factor binding activity, GO:0046983, calcium ion binding activity, sympathetic nerve activity, GO:0051336]] | \n", + "0.18 | \n", + "
| 722 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-0 | \n", + "[[GO:0098609, agonist binding activity, cytoplasmic matrix binding, protein homodimerization, GO:0005102]] | \n", + "[[GO:0007155, GO:0005178, gtp binding activity, collagen binding activity, atp binding activity, phospholipase binding activity, GO:0007160, GO:0050839, GO:0017124]] | \n", + "0.00 | \n", + "
| 723 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-1 | \n", + "[[binding activities, GO:0003824, involvement in biological processes, structural roles]] | \n", + "[[extracellular matrix structure, GO:0038023, cell adhesion molecule binding activity, small gtpase binding activity, GO:0042803, identical protein binding activity, collagen binding activity, actin binding activity, atp binding activity, protein kinase binding activity, sh3 domain binding activity, integrin binding activity, GO:0005096]] | \n", + "0.00 | \n", + "
| 724 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_SURFACE-0 | \n", + "[[GO:0061024, protein organization, GO:0036211, GO:0015031, GO:0006897, GO:0007165, GO:0006915]] | \n", + "[[GO:0005480, cell structure maintenance, GO:0046872, GO:0016477, plasmamembrane transport, GO:0005515, GO:0043170, GO:0030296, endolemmal transport, GO:0016485, GO:0010467, GO:0006915, lipoprotein particle receptor catabolic process, peptide chain release, protein homodimerization, GO:0007165, GO:0048870, GO:1902600, GO:0000785, GO:0005654, GO:0031410, GO:0042552, GO:0044183]] | \n", + "0.07 | \n", + "
| 725 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_SURFACE-1 | \n", + "[[GO:0007155, protein folding and regulation, GO:0050801, MESH:D005786]] | \n", + "[[genes in this list are primarily involved in regulation of transcription, GO:0007165, membrane management, protein folding and binding, cell surface receptor signaling and adhesion, and cellular extravasation. enriched terms include: transcription, GO:0007165, protein-folding and binding, cell-surface receptor signaling, adhesion, GO:0045123, GO:0061024, extracellular matrix structural components, genetic expression, apoptotic pathways, and intracellular ion homeostasis. \\n\\nmechanism: genes on this list are primarily involved in several processes that coordinate essential cellular functions by dynamically managing activity of proteins at the surface of the cell, within underlying membrane layers, extracellularly and within dna. these genes manage the way cells communicate within their environment, interact with extracellular components, respond to stimuli, and extravasate. they code for proteins involved in transcription, GO:0007165, protein folding and binding, adhesion, apoptotic pathways, intracellular ion homeostasis, extracellular matrix structural components that have pleiotropic roles in modulating gene expression functioning of cellular components]] | \n", + "0.00 | \n", + "
| 726 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_APOPTOSIS-0 | \n", + "[[dna binding activity, protein binding activity, enzyme binding activity, GO:0004197, identical protein binding activity, signaling receptor binding activity, calcium ion binding activity, protein kinase binding activity, GO:0000988, bh3 domain binding activity]] | \n", + "[[dna binding activity, GO:0046983, protein binding activity, enzyme binding activity, protein kinase binding activity, GO:0004197, GO:0003714, phosphoprotein binding activity, mhc class i protein binding activity, GO:0003700, signaling receptor binding activity, GO:0042803]] | \n", + "0.38 | \n", + "
| 727 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_APOPTOSIS-1 | \n", + "[[calcium ion binding activity, protein binding activity, identical protein binding activity, chromatin dna binding activity, dna-binding transcription factor binding activity, ig domain binding activity, sh2 domain binding activity, bh3 domain binding activity, cyclin binding activity, rna binding activity, GO:0004197, metalloprotease inhibitor activity, phospholipid binding activity, lipopeptide binding activity, lysophosphatidic acid binding activity, sulfatide binding activity, atpase binding activity, pdz domain binding activity]] | \n", + "[[protein binding activity, identical protein binding activity, enzyme binding activity, GO:0003700, rna polymerase ii-specific transcriptional activity, GO:0004197, GO:0004896]] | \n", + "0.14 | \n", + "
| 728 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[[atp binding activity, GO:0016887, protein binding activity, signaling receptor binding activity, enzyme binding activity, GO:0042803, GO:0016791, GO:0000988, GO:0022857, ubiquitin-dependent protein binding activity, cholesterol binding activity, GO:0019871, phosphotyrosine residue binding activity]] | \n", + "[[atp binding activity, GO:0016887, cholesterol binding activity, GO:0022857, GO:0046982, GO:0000981, enzyme binding activity, GO:0016491, peptide antifungal protein binding activity, acyl-coa hydroxyacyltransferase activity, GO:0019145]] | \n", + "0.26 | \n", + "
| 729 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[[GO:0140657, GO:0016887, GO:0008233, enzyme binding activity, GO:0003700, GO:0042803, identical protein binding activity, signaling receptor binding activity]] | \n", + "[[this gene list is associated with multiple functions in various metabolic processes, from binding and transporter activity to atpase activity, homodimerization activity, and various hydrolytic activities. enriched terms include: protein binding activity; atp hydrolysis activity; protein homodimerization activity; atpase binding activity; atpase-coupled transmembrane transporter activity; transcription regulatory region sequence-specific dna binding activity; and transmembrane transporter activity. mechanism: this set of genes acts as part of multiple metabolic processes, such as lipid and fatty acid metabolism, GO:0042632, GO:0140327, and hormone regulation. these genes facilitate enzymatic activity and activity in transporting molecules, such as fatty acids, MESH:D002784, MESH:D014815, hormones. the processes activities these genes are involved in suggest a coordination of metabolic cell stimulation processes]] | \n", + "0.00 | \n", + "
| 730 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[[atp binding activity, protein kinase binding activity, GO:0042803, GO:0003700, low-density lipoprotein particle binding activity, GO:0005041, GO:0030229, GO:0004602, GO:0004364, GO:0016491, GO:0004496, GO:0004631, GO:0047598, GO:0047024, MESH:D010758, GO:0060090, cholesterol binding activity, GO:0120020, isopentenyl]] | \n", + "[[atp binding activity, protein binding activity, GO:0007155, GO:0007165, GO:0006915, dna-binding, GO:0006695, cell structure organization, GO:0003985, GO:0008610, GO:0000988, GO:0015631, protein homodimerization]] | \n", + "0.03 | \n", + "
| 731 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[[GO:0042632, MESH:D055438, GO:0005515, GO:0006351, GO:0010468, dna-binding, GO:0007165, negative regulation, positive regulation, GO:0016491, GO:0008610, GO:0003723, ldl particle binding, GO:0019901, phosphotransferase activity, acetyl-coa ligase activity, endopeptidase activity, etc]] | \n", + "[[GO:0006695, GO:0008610, positive regulation of transcription, GO:2001234, GO:0031647, regulation of cell adhesion/migration, atp binding activity, transcription factor binding activity, protein binding activity, protein kinase binding activity, signaling receptor binding activity, ion/metal binding activity, endopeptidase regulator activity, etc]] | \n", + "0.03 | \n", + "
| 732 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_COAGULATION-0 | \n", + "[[the provided list of human genes are mainly involved in metabolism, adjustment of the immune system and coagulation, and development of cells and organs. in particular, they are found to be involved in binding activities and endopeptidase activities such as post-translational modification, transcription and regulation of protein. the enriched terms include calcium-dependent protein/phospholipid/lipoprotein binding activity, GO:0004197, protein homodimerization/homooligomerization activity, identical protein binding activity, and serine-type endopeptidase activity. \\n\\nmechanism: the expression and activities of these genes may play important roles in the development and metabolism of cells and organs by facilitating protein folding, GO:0043687, cell-matrix adhesion and crosstalk between proteins. the binding activities of these genes towards phospholipid, lipoprotein and other molecules mediate the interaction between cells and extracellular environment, and regulate blood coagulation and formation of extracellular matrix. the endopeptidase activities of these genes degrade and modulate proteins, which are essential for various biological processes]] | \n", + "[[protein binding activity, collagen binding activity, identical protein binding activity, integrin binding activity, phospholipid binding activity, atp binding activity, fibronectin binding activity, GO:0008237, GO:0004252, metaloendopeptidase activity, calcium ion binding activity]] | \n", + "0.04 | \n", + "
| 733 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_COAGULATION-1 | \n", + "[[protein binding activity, domain specific binding activity, disordered domain specific binding activity, GO:0008233, GO:0004252, GO:0005125, signaling receptor binding activity, identical protein binding activity, GO:0004222, GO:0003924, receptor tyrosine kinase binding activity, GO:0004421, phospholipid binding activity, amyloid-beta]] | \n", + "[[the genes in this list are predicted to enable various calcium-dependent functions related to protein binding, GO:0019899, and peptidase activity, typically related to blood coagulation, GO:0007155, endodermal cell fate, and negative regulation of protein-regulating processes. these genes are involved in various activities across multiple cellular pathways, including cellular response to uv-a, GO:0030155, and blood coagulation. the enriched terms include “calcium-dependent functions”, “protein binding activity”, “enzme binding activity”, “peptidase activity”, “blood coagulation”, “cell adhesion”, “endodermal cell fate”, “negative regulation of protein-regulating processes”, “cellular response to uv-a”, and “regulation of cell adhesion”.\\n\\nmechanism: the mechanism underlying this list of genes is likely related to calcium-dependent regulation of proteins and peptides, which acts to control various cellular processes. calcium can act as a negative regulator of proteins, through calcium binding to proteins and preventing their activity, or as a]] | \n", + "0.00 | \n", + "
| 734 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_COMPLEMENT-0 | \n", + "[[enriched functions observed in the genes include binding activitiy (for various ligands, such as dna, GO:0005562, MESH:C062738, calcium ions, heparin/heparan sulphate, MESH:D019204, c5l2 anaphylatiotaxin, MESH:M0028275, mhc, amyloid-beta, cytokine, opsonin, MESH:D005227, MESH:D011494, etc.), enzyme activity (such as deubiquitinase, lck, atpase, aminopeptidase, peptidase, etc.), GO:0044183, cysteine type endopeptidase inhibitor activity and endopeptidase activity, phospholipid binding activity, transcription factor activity and transcription regulatory region sequence-specific dna binding activitiy. the underlying mechanism could be related to signal transduction, functional process, dna/rna transcription, protein degradation and signalling pathways such as cell killing and apoptotic signalling pathways.\\n\\nsummary: enriched functions include multiple binding activities, GO:0003824, and transcription regulatory activities for signal transduction, functional processes, and signalling pathways. \\nmechanism: signal transduction, functional processes, dna/rna transcription, protein degradation,]] | \n", + "[[protein binding activity, GO:0001216, enzyme binding activity, metal ion binding activity, sh2 domain binding activity, GO:0004197, phosphoprotein binding activity, actin binding activity, cation binding activity, lipid binding activity, GO:0004252, GO:0008092, cell killing activity, protein kinase binding activity]] | \n", + "0.00 | \n", + "
| 735 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_COMPLEMENT-1 | \n", + "[[enzyme binding activity, GO:0101005, GO:0004197, GO:0005102, GO:0019901, sh2 domain binding activity, GO:0004435, GO:0003924, GO:0004222, atpase binding activity, integrin binding activity, dna binding activity, lipoprotein receptor binding activity, GO:0007165, GO:0006915, MESH:D015850]] | \n", + "[[dna-binding, GO:0005543, GO:0005515, GO:0005102, GO:0019899, inhibitor activities, GO:0003924, GO:0046872, protein activities, GO:0023052, transcription regulation, GO:0006281, GO:0008219, GO:0006955]] | \n", + "0.07 | \n", + "
| 736 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_DNA_REPAIR-0 | \n", + "[[the given list of human genes are primarily involved in dna binding, transcription and translational activities, rna binding, enzyme binding activities, and identical protein and nucleic acid binding activities. there is also evidence of involvement in activities such as transcription co-activator activity, nuclear localization, cytochrome-c oxidase activity, atp-dependent activities and endopeptidase activator activity. enriched terms include dna binding, GO:0003723, GO:0003887, GO:0046983, identical protein binding activity, transcription factor binding activity, GO:0003700, zinc ion binding activity, atp binding activity, protein binding activity]] | \n", + "[[dna binding activity, rna binding activity, enzyme binding activity, protein binding activity, calcium ion binding activity, GO:0140612, GO:0003713, zinc ion binding activity]] | \n", + "0.12 | \n", + "
| 737 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_DNA_REPAIR-1 | \n", + "[[dna binding activity, rna binding activity, transcription activity, enzyme binding activity, GO:0042803]] | \n", + "[[dna binding activity, enzyme binding activity, GO:0016887, rna binding activity, protein binding activity, GO:0003887, GO:0004518, mrna regulatory element binding]] | \n", + "0.30 | \n", + "
| 738 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_E2F_TARGETS-0 | \n", + "[[GO:0007049, GO:0006260, transcriptional regulation, post-transcriptional regulation, GO:0003682, GO:0140014, GO:0051169, GO:0046931]] | \n", + "[[chromatin binding activity, GO:0006260, GO:0006281, GO:0006351, GO:0016570, nuclear import/export, dna/rna binding, protein-macromolecule binding, GO:0051726, protein homodimerization, GO:0006200, GO:0000287, MESH:D011494, GO:0004518]] | \n", + "0.05 | \n", + "
| 739 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_E2F_TARGETS-1 | \n", + "[[dna binding activity, protein binding activity, histone binding activity, GO:0016887, enzyme binding activity, GO:0006260, GO:0006306, chromatin binding activity, GO:0042803, GO:0003887, rna binding activity]] | \n", + "[[nuclear pore remodeling, GO:0065003, GO:0003677, transcriptional regulation, GO:0006260, GO:0006913, chromatin modification and repair, cell cycle progression, GO:0140014, GO:0019899, GO:0042393, protein homod]] | \n", + "0.05 | \n", + "
| 740 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[[extracellular matrix structural components, GO:0007160, protein domain specific binding activity, identical protein binding activity, GO:0048018, signaling receptor binding activity, metal ion binding activity, peptide hormone receptor binding activity, heparin binding activity, collagen binding activity, GO:0007165, GO:0005125]] | \n", + "[[protein binding activity, identical protein binding activity, collagen binding activity, integrin binding activity, heparin binding activity, phosphatidylinositol binding activity, cell adhesion molecule binding activity, extracellular matrix binding activity, signaling receptor binding activity, GO:0008009, gene transcriotion activity, metal ion binding activity]] | \n", + "0.26 | \n", + "
| 741 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[[protein binding activity, identical protein binding activity, metal ion binding activity, ion binding activity, actin binding activity, small molecule binding activity, fibronectin binding activity, collagen binding activity, integrin binding activity, procollagen binding activity, cadherin binding activity, phosphatidylinositol-3,4,5-trisphosphate binding activity, substrate-binding activity, GO:0005096, GO:0004867, GO:0005006, GO:0005024, GO:0004896, platelet-derived growth factor binding activity, nucleotide-binding transcription factor activity]] | \n", + "[[GO:0005201, collagen binding activity, cell adhesion molecule binding activity, dna binding activity, gtp binding activity, GO:0042803, platelet-derived growth factor binding activity, platelet-derived growth factor binding activity, calcium ion binding activity, signaling receptor binding activity, identical protein binding activity]] | \n", + "0.11 | \n", + "
| 742 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[[binding activity, transport activity, GO:0003824, adhesion activity, intracellular signaling, GO:0006351, neuronal development]] | \n", + "[[dna binding activity, protein binding activity, enzyme binding activity, GO:0022857, transcription activity, GO:0003924, atpase binding activity, mrna binding activity, protein homodimerization, GO:0042169, GO:0016922, GO:0030165]] | \n", + "0.00 | \n", + "
| 743 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[[GO:0003677, GO:0051117, GO:0005515, GO:0016791, dehydrogenase activity, GO:0004016, GO:0055085, transcriptional regulation, GO:0007155, GO:0006915]] | \n", + "[[GO:0003677, GO:0000981, GO:0003723, protein binding/dimerization, transmembrane transporter, GO:0005509, GO:0019899, GO:0003924]] | \n", + "0.06 | \n", + "
| 744 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[[protein binding activity, dna-binding, domain binding activity, carbohydrate binding activity, enzyme binding activity, ligand binding activity, transmembr]] | \n", + "[[GO:0050839, GO:0003677, transfacmembrane receptor protein tyrosine kinase activity, ligand binding, ca2+ ion binding, GO:0005543, GO:0019899, GO:0016563, GO:0005243, GO:0003682, GO:0032794, GO:0048018, GO:0005242, GO:0004930, GO:0060089, calcium-dependent exonuclease activity, GO:0003779, GO:0007165, GO:0004672, GO:0016310, sh2 domain binding activity, heme binding activity, GO:0042803, hsp90 protein binding activity, GO:0017002, GO:0004957, ww domain binding activity, pdz domain binding activity, sh3 domain binding activity]] | \n", + "0.00 | \n", + "
| 745 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[[dna-binding, GO:0016563, GO:0005515, membrane transporter activity, GO:0016787, GO:0016310, ligand-mediated activity]] | \n", + "[[GO:0008134, GO:0019899, GO:0005515, GO:0007155, ligand-gated ion transporter activity, GO:0001216, GO:0050839, protein domain specificity, GO:0030742, GO:0003677, GO:0019003, GO:0005525, GO:0051117, GO:0030165, GO:0005509, phosphotransfer, GO:0031490, GO:0001217]] | \n", + "0.04 | \n", + "
| 746 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[[GO:0006631, GO:0006629, GO:0005975, GO:0003677, GO:0003723, protein homodimerization, GO:0000287, GO:0005524, GO:0046872, GO:0047617, GO:0003995, fad binding activity, nadph binding activity, homodimerization activity, GO:0000774, GO:0015254, GO:0004497, 5alpha-androstane-3alpha,17beta-diol dehydrogenase activity, GO:0008170, identical protein binding activity, GO:0016860, enzyme binding activity, GO:0004674, GO:0042803, GO:0004351, GO:0004222, ubiquitin binding activity, dna-binding]] | \n", + "[[protein binding activity, identical protein binding activity, metal ion binding activity, atp binding activity;lipid transport activity, fatty acid binding activity, fad binding activity, pdz domain binding activity;transmembrane transporter activity, ubiquitin binding activity, nucleotide binding activity, GO:0004080, GO:0004738, enoyl-coa hydratase activity;amino-acid oxidase activity, GO:0003979, GO:0009055, GO:0004853, 5alpha-reductase activity, rna-binding]] | \n", + "0.07 | \n", + "
| 747 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[[GO:0016491, enzyme binding activity, dna binding activity, GO:0004090, GO:0052650, GO:0015245, nadph binding activity, GO:0042803, atp binding activity, receptor ligand binding activity, nad+ binding activity, smad binding activity, rna polymerase ii-specific transcription factor activity, atp-dependent protease activity, GO:0016404, GO:0004672, ubiquitin conjugating]] | \n", + "[[GO:0003824, GO:0016491, protein binding activity, hydratase activity, GO:0003997, lipid binding activity, dna binding activity, ubiquitin binding activity, atp binding activity, flavine adenine dinucleotide binding activity, nadp+ binding activity, GO:0042803, smad binding activity, GO:0004466]] | \n", + "0.19 | \n", + "
| 748 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-0 | \n", + "[[GO:0003677, transcription binding, GO:0046872, GO:0005515, GO:0019899, MESH:D020558, GO:0003682, GO:0042826, GO:0046983, sumo-dependent ubiquitination, GO:0003723, GO:0005524, GO:0042054, GO:0008017, GO:0010997, boxh/aca snorna binding, GO:0043515, GO:0070840, m7gpppn-cap structure binding, GO:0008270, GO:0003697, GO:0038024, GO:0006200, GO:0051536, GO:0005884]] | \n", + "[[dna binding activity, rna binding activity, protein kinase binding activity, protein folding activity, enzyme binding activity, transcription factor binding activity, chromatin binding activity, protein domain specific binding activity, nucleic acid binding activity, atp binding activity, identical protein binding activity, GO:0140110, GO:0046983, histone binding activity, anaphase-promoting complex binding activity, cytoplasmic release activity, metal ion binding activity, GO:0016887, histone deacetylase binding activity, telomere binding activity]] | \n", + "0.02 | \n", + "
| 749 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-1 | \n", + "[[GO:0005515, GO:0003677, GO:0006351, GO:0019904, GO:0042054, GO:0004402, GO:0004674, GO:0030374, GO:0005049, GO:0016887, zinc ion binding activity, GO:0140037, GO:0036310, sumo polymer binding activity, nuclear receptor binding activity, dna topoisomerase binding activity, GO:0010997, GO:0000774, GO:0005096, microtubule binding activity, dna replication origin binding activity, GO:0000987, rna polymerase ii-specific transcription]] | \n", + "[[GO:0005515, GO:0003677, GO:0008134, MESH:D019098, GO:0003723, GO:0006260, GO:0051726, GO:0003682, GO:0010467, GO:0006457, regulation of chromosome structure, GO:0019904, GO:0005524, GO:0019900, GO:0035402, GO:0031267, MESH:M0518050, protein homodimerization, GO:0043130, atp-dependent dna/dna annealing]] | \n", + "0.07 | \n", + "
| 750 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_GLYCOLYSIS-0 | \n", + "[[GO:0003676, GO:0005515, GO:0005524, metabolic activity, GO:0016310, MESH:D010084, GO:0005975, GO:0005125, GO:0008083]] | \n", + "[[the list of genes represent a range of molecular, metabolic, and protein regulatory processes, including atpase activity, glucose binding activity, GO:0004672, transcriptional activity and activity from receptors, transporters, and enzymes. the enriched terms are \"protein binding activity\"; \"atpase activity\"; \"transcriptional activity\"; \"receptor activity\"; \"transporter activity\"; \"enzyme activity\"; and \"glucose binding activity\".\\n\\nmechanism: the genes in the list encode proteins involved in a range of processes, such as structural support, GO:0007165, regulation of transcription, metabolic pathways and transport of molecules. the underlying biological mechanism is likely related to the coordinated expression of these genes in response to a particular stimulus, or to maintain cellular homeostasis]] | \n", + "0.00 | \n", + "
| 751 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_GLYCOLYSIS-1 | \n", + "[[protein binding activity, identical protein binding activity, enzyme binding activity, atp binding activity, transcription activation activity, dna-binding transcription activity, heparin binding activity, cytoplasmic protein binding activity, signalling receptor binding activity, cytoskeletal protein binding activity, GO:0042803, GO:0060422, rna binding activity, GO:0140677, GO:0004689, phosphotransferase activity, heme binding activity, calcium ion binding activity]] | \n", + "[[enzyme binding activity, identical protein binding activity, dna binding activity, GO:0042803, heparin binding activity, atp binding activity, protein kinase binding activity, phosphatase binding activity, cyclin binding activity, protein phosphatase binding activity, GO:0004722, actin binding activity, lbd domain binding activity, actin filament binding activity, GO:0008083, chromatin binding activity, hyaluronic acid binding activity, GO:0004197, ubiquitin binding activity, cyclosporin a binding activity, mannose-binding activity, heparan sulfate binding activity, heme binding activity, GO:0016887, transition metal ion binding activity, GO:0031545, GO:0016615, GO:0004148, GO:0004784, transcription core]] | \n", + "0.14 | \n", + "
| 752 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[[GO:0007155, GO:0007165, epithelial-mesenchymal interaction, GO:0006898, GO:0001525, GO:0001843]] | \n", + "[[protein/lipid binding activity, GO:0003700, GO:0010468, GO:0051246, positive/negative regulation of cellular component organization, GO:0030036, GO:0030833, GO:0001525, GO:0090630, GO:0019219, GO:0007160]] | \n", + "0.06 | \n", + "
| 753 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[[GO:0003700, rna polymerase ii transcription regulatory region sequence-specific dna binding activity, chromatin binding activity, receptor binding activity, GO:0005096, gtpase binding activity, phospholipid binding activity, calcium ion binding activity, zinc ion binding activity, identical protein binding activity, apolipoprotein binding activity, phosphotyrosine residue binding activity, very-low-density lipoprotein particle binding activity, phosphatidylcholine binding activity, phosphatidylethanolamine binding activity, adenyl ribonucleotide]] | \n", + "[[acetylcholine binding activity, GO:0003990, GO:0005096, rna polymerase ii-specific dna-binding transcription factor binding activity, GO:0003714, GO:0017053, GO:0007165, GO:0006351, GO:0007155, GO:0016477, GO:0001525, GO:0035556, GO:0019219, GO:0006468]] | \n", + "0.03 | \n", + "
| 754 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_HEME_METABOLISM-0 | \n", + "[[identical protein binding activity, dna binding activity, rna binding activity, GO:0000988, GO:0003714, GO:0016564, GO:0016563, GO:0016791, protein kinase binding activity, GO:0006865, GO:0006811, heme binding activity, oxygen binding activity, protein-fructose gamma-glutamyltransferase activity, GO:0042803, lamin binding activity, chromatin binding activity and ubiquitin ligase activity]] | \n", + "[[dna-binding, rna-binding, GO:0019899, GO:0019901, GO:0019903, protein homodimerization, GO:0048729, GO:0006468]] | \n", + "0.00 | \n", + "
| 755 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_HEME_METABOLISM-1 | \n", + "[[transcription activity, dna binding activity;rna binding activity, protein kinase binding activity, atp binding activity, protein binding activity, identical protein binding activity, GO:0042803, GO:0004197, GO:0015075, protein domain specific binding activity, GO:0032452, GO:0004674, GO:0016564, GO:0061630, lamin binding activity, GO:0004521, GO:0038023, GO:0004602, phosphoprotein binding activity, molecule adaptation, enzyme binding activity, protein phosphatase binding activity, GO:0004418, ubiquitin conjugating enzyme binding activity, GO:0004842, ap-2 adapt]] | \n", + "[[GO:0003677, GO:0005515, GO:0016310, GO:0003824, GO:0005215, MESH:M0496924, vesicular pathways, cytoskeletal pathways, GO:0046872, GO:0003723, GO:0030544, GO:0042802, GO:0008013, phosphatidylinositol-4 binding, GO:0035612, rna polymerase ii dna binding, GO:0042393, GO:0019901, tyrosine-protein kinase activity, GO:0061630, GO:0003713, fibronectin leucine-rich-repeat sense-specific binding, endothelial differentiation-specific factor binding, fatty-acid binding, heme-binding, GO:0051537, GO:0050661, GO:0070742, MESH:D012330]] | \n", + "0.02 | \n", + "
| 756 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_HYPOXIA-0 | \n", + "[[dna-binding transcription activity, enzyme binding activity, protein binding activity, ligand-binding activity, atp binding activity, nadp binding activity, metal ion binding activity, carbohydrate binding activity, signaling receptor binding activity, GO:0003714, GO:0001217, GO:0008160, heparin binding activity, n-acetylglucosamine n-sulfotransferase activity, MESH:D006497]] | \n", + "[[this is a list of genes of known or suspected functions in a variety of processes, ranging from dna binding and transcription regulation to enzyme binding, metabolic activity, GO:0005102, and structural protein formation. commonly enriched terms include dna binding, transcription regulation, GO:0019899, and protein binding. mechanism: a variety of processes are involved in these gene functions, including dna replication and repair, protein folding and conformational change, receptor binding and signal transduction, metabolic activity, structural protein formation]] | \n", + "0.00 | \n", + "
| 757 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_HYPOXIA-1 | \n", + "[[dna binding activity, rna binding activity, protein binding activity, GO:0004672, GO:0019887, GO:0016407, GO:0016301, GO:0008233, GO:0004197, GO:0004252, ubiquitin binding activity, GO:0042803, GO:0000988, GO:0016563, GO:0016564, apolipoprotein binding activity, phosphatase binding activity, disordered domain specific binding activity, chromatin binding activity, GO:0016303, GO:0030701, GO:0004693, GO:0004396, actinin binding activity, 14-3-3 protein binding activity, gtp binding activity, MESH:D009584]] | \n", + "[[dna-binding transcription activity, GO:0003714, GO:0016564, GO:0016563, rna polymerase ii-specific, protein binding activity, GO:0042803, platelet-derived growth factor binding activity, GO:0030291, GO:0046982, GO:0004197, protein kinase binding activity, GO:0019887, GO:0004725, cyclin binding activity, GO:0004693, GO:0035403, phosphatidylinositol-3-kinase activity, nad+]] | \n", + "0.18 | \n", + "
| 758 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[[ligand binding, GO:0019899, GO:0005102, MESH:M0518050, GO:0003700, rna-binding, protein homodimerization, protein-kinase binding activity, identical protein binding activity, GO:0004896, c-c chemokine binding activity, GO:0004197, GO:0022857, gtp binding activity, protease binding activity]] | \n", + "[[GO:0005096, dna-binding transcription activator/repressor activity, protein binding activity, ligand binding activity, identical protein binding activity, bh3 domain binding activity, phosphatidylinositol binding activity, GO:0016787, atp binding activity, atpase-coupled intramembrane lipid transport activity, amyloid-beta binding activity, hsp90 protein binding activity, s100 protein binding activity, cadherin binding activity, GO:0038023, GO:0005125, GO:0005021, GO:0004896, identical protein binding activity, GO:0008233, heat shock protein]] | \n", + "0.06 | \n", + "
| 759 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[[dna-binding, transcriptional activity, GO:0006355, GO:0005515, protein homodimerization, GO:0003924, GO:0005102, ligand-activated transcription, GO:0019900, GO:0002020, GO:0004674, GO:0004175, cystein-type endopeptidase activity, GO:0005102, GO:0061630, GO:0005125, GO:0008083, leukemia inhibitory factor activity, 5'-deoxyn]] | \n", + "[[dna-binding transcription activity, protein kinase binding activity, small gtpase binding activity, interleukin-binding activity, GO:0004896, signaling receptor binding activity, rna binding activity, gtp binding activity, GO:0004197, identical protein binding activity, protein domain specific binding activity, GO:0046982]] | \n", + "0.00 | \n", + "
| 760 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[[GO:0038023, binding activity, MESH:D016207, MESH:M0496065, MESH:D008074, MESH:D010455, MESH:D011506, GO:0019900, GO:0005524]] | \n", + "[[cytokine binding activity, protein binding activity, kinase binding activity, signaling receptor binding activity, GO:0004675, cell adhesion molecule binding activity, interleukin-receptor activity, GO:0004725, tir domain binding activity, ubiquitin protein ligase binding activity, GO:0008284, GO:0032768, GO:0009966, GO:0090276, GO:0045597, GO:0010604, GO:0098542, GO:0009612, GO:0001819, GO:0031349]] | \n", + "0.00 | \n", + "
| 761 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[[GO:0004896, cxcr chemokine receptor binding activity, interleukin-binding activity, GO:0006952, GO:0010605, GO:0051247]] | \n", + "[[cytokine binding activity, GO:0004896, GO:0008083, cell adhesion molecule binding activity, chemokine (c-x3-c) binding activity, GO:0006952, signaling receptor binding activity, GO:0000988, identical protein binding activity, phosphatidylinositol binding activity, heparin binding activity, lipid binding activity, c-c chemokine binding activity, dna binding activity, GO:0005096, sh3 domain binding activity, ephrin receptor binding activity, transforming growth factor beta receptor binding activity, ubiquitin-like protein ligase binding activity, enzyme binding activity, calcium-dependent protein binding activity, protease binding activity]] | \n", + "0.08 | \n", + "
| 762 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[[protein binding activity, GO:0005125, GO:0004930, dna-binding transcription activity, lipopolysaccharide binding activity, atp binding activity, integrin binding activity, GO:0048018, GO:0022857, signaling receptor binding activity, extracellular atp-gated channel activity, phosphatidylinositol- 3-kinase activity, metallod]] | \n", + "[[GO:0004930, GO:0005125, GO:0003700, GO:0005216, receptor binding activity, GO:0008083, cell adhesion molecule binding activity, signalling receptor binding activity, GO:0003714, enzymatic activity, phospholipid binding activity, peptide hormone receptor binding activity, GO:0003924]] | \n", + "0.08 | \n", + "
| 763 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[[GO:0038023, binding activity, GO:0003824, GO:0008083, GO:0005215, GO:0000988]] | \n", + "[[atp binding activity, chemokine/chemokine receptor/chemokine receptor binding activity, cytokine/cytokine binding activity/cytokine receptor activity, dna binding activity/dna-binding transcription factor activity, GO:0004930, identical protein binding activity, ion transport/ion transporter activity, peptide/peptide receptor binding activity, phospholipid binding activity, GO:0019887, signaling receptor binding activity, GO:0000988, GO:0022857]] | \n", + "0.06 | \n", + "
| 764 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[[signaling receptor binding activity, GO:0003713, regulation of transcription, dna-binding activity, rna binding activity, metal ion binding activity, identical protein binding activity, GO:0042803]] | \n", + "[[immunologic processes, GO:0098609, GO:0006952, cellular response, positive regulation, rna polymerase ii specific, GO:0003677, GO:0003723, protein homodimer]] | \n", + "0.00 | \n", + "
| 765 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[[GO:0098542, GO:0006955, GO:0046718, GO:0032020, GO:0019882, GO:0019221, GO:0045087, GO:0007166, GO:0030225, GO:0032722, GO:0001961, cell-cell adhesion mediated by plasma membrane cell adhesion molecules]] | \n", + "[[GO:0003713, rna binding activity, dna binding activity, identical protein binding activity, GO:0061630, zinc ion binding activity, GO:0042803, double-stranded rna binding activity, heparin binding activity, GO:0030701, GO:0004175, cxcr chemokine receptor binding activity, tap binding activity, peptide antigen binding activity, gtp binding activity, GO:0033862, GO:0004197, amyloid-beta binding activity, macrophage migration inhibitory factor binding activity, GO:0004550, GO:0016064, GO:0140374, GO:0071345, GO:0046597, positive regulation of]] | \n", + "0.00 | \n", + "
| 766 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[[the list of genes are discovered to be enriched in terms like dna binding activities, GO:0042803, GO:0000988, GO:0004672, GO:0004725, GO:0016887, enzyme binding activity, phosphatidylinositol phosphate binding activity, GO:0030528, GO:0008009, and cytokine receptor activity.\\n\\nmechanism: the biological mechanism underlying the enriched terms is most likely associated with cell and immune response. these genes are involved in various processes related to cell signaling, detection, recognition, GO:0006351, and expression. through these processes, the genes regulate important functions such as cell adhesion, GO:0005515, GO:0019899, GO:0005125, and transcription factor activation. in addition, several of these genes are also involved in apoptotic and other cell regulation pathways]] | \n", + "[[protein binding activity, enzyme binding activity, dna-binding transcription activity, GO:0006200, protein homodimerization, kinase regulation, protein dimerization.\\nmechanism: these genes are likely involved in the regulation of gene expression cell signaling pathways, enabling an array of signaling activities that help to maintain cellular homeostasis]] | \n", + "0.04 | \n", + "
| 767 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[[binding activity, GO:0003824, protein activity, GO:0000981]] | \n", + "[[GO:0016887, dna binding activity, gtp binding activity, peptide antigen binding activity, GO:0004252, dna-binding transcription activity, GO:0005125, GO:0008009, GO:0004896, GO:0038023, GO:0004930, rna binding activity, enzyme binding activity, GO:0046983, phosphorylation-dependent protein binding activity, GO:0019887, GO:0140311, toll-interleukin receptor (tir) domain binding activity, signaling receptor binding activity, and]] | \n", + "0.00 | \n", + "
| 768 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[[protein binding activity, transmembrane activity, GO:0003700, sequence-specific double-stranded dna binding activity, GO:0004930, identical protein binding activity, calcium ion binding activity, scaffold protein binding activity, transcription cis-regulatory region binding activity]] | \n", + "[[GO:0004930, GO:0042803, calcium ion binding activity, sodium:potassium:chloride transporter activity, GO:0004683, platelet-derived growth factor activity, GO:0005007, cytoskeletal protein binding activity, GO:0015171, n6-threonylcarbamylade adenine dinucleotide synthetase activity, GO:0043273, intracellular transport activity, signal transduction activity, GO:0016887, GO:0004175, GO:0016491, GO:1990817, GO:0004958, beta-caten]] | \n", + "0.08 | \n", + "
| 769 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[[dna-binding activity, transcription activity, calcium ion binding activity, atp-binding activity, protein binding activity, GO:0004930, cell death regulation, GO:0009653, GO:0042445]] | \n", + "[[the list of genes is significantly enriched for dna-binding activities, calcium ion binding activities, identical protein-binding activities, GO:0046982, GO:0016887, and g protein-coupled receptor activities.\\n\\nmechanism:\\nthe underlying biological mechanism likely involves a complex, dynamic interaction between various proteins, MESH:D004798, and ions, driven by a variety of dna-binding, calcium-binding, and atp-binding activities, resulting in the recruitment of additional proteins to form heterodimers, thereby leading to protein synapsis cell signaling]] | \n", + "0.00 | \n", + "
| 770 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[[cell adhesion molecule binding activity, atpase-coupled intramembrane transport, GO:0004222, GO:0042803, signal receptor binding activity, GO:0003700, MESH:D006493]] | \n", + "[[atp binding activity, atpase-coupled intramembrane transport, GO:0048018, dna-binding transcription regulation, protein domain binding activity, enzyme binding activity, GO:0005125, GO:0007165, GO:0007155, GO:0016477, GO:0030154, MESH:D048788]] | \n", + "0.06 | \n", + "
| 771 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[[GO:0005125, protein domain specific binding activity, protein kinase binding activity, cell adhesion molecule binding activity, signaling receptor binding activity, GO:0004222, GO:0001217, rna binding activity, gtpase binding activity, structural proteins, atp binding activity]] | \n", + "[[receptor binding activity, identical protein binding activity, GO:0001216, enzyme binding activity, protein domain specific binding activity, protein kinase binding activity, ligand binding activity, atp binding activity, cytoskeletal protein binding activity, cell adhesion molecule binding activity, GO:0004930, transmembrane transporter binding activity, GO:0008233, dna binding activity, GO:0004252, histone binding activity, signal transduction activity]] | \n", + "0.17 | \n", + "
| 772 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[[protein binding activity, cytoskeleton binding activity, GO:0005096, atpase binding activity, GO:0042030, adenyl ribonucleotide binding activity, calmodulin binding activity, cadherin binding activity, gamma-tubulin binding activity, integrin binding activity, kinetochore binding activity, molecular function adaptor activity, GO:0042803, protein kinase binding activity, protein phosphatase binding activity, sh2 domain binding activity, sh3 domain binding activity, small gtpase binding activity, beta-catenin binding activity, beta-tubulin binding activity, dynein complex binding activity, identical protein binding activity, phosphatidylcholine binding activity, protein domain specific binding activity, protein tyrosine kinase binding activity]] | \n", + "[[actin binding activity, atp binding activity, atpase binding activity, GO:0098632, dynein complex binding activity, gamma-tubulin binding activity, gtp binding activity, gtpase binding activity, guanyl ribonucleotide binding activity, GO:0003924, GO:0005085, kinetochore binding activity, GO:0060090, GO:0140677, myosin binding activity, phosphatidylcholine binding activity, GO:0019904, GO:0042803, GO:0004672, GO:0004674, small gtpase binding activity]] | \n", + "0.18 | \n", + "
| 773 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[[MESH:D020558, atpase, tubulin binding activity, microtubule binding activity, actin filament binding activity, kinesin binding activity, dynein binding activity, g protein-coupled receptor binding activity]] | \n", + "[[this set of genes are involved in activities, processes and signaling pathways related to intracellular motion such as transport within cells (microtubule/kinesin/dynein binding, GO:0005096, GO:0008092, motor protein activity), cell cycle activities (centrosome duplication, GO:0019899, protein homodimerization, GO:0019902, GO:0003682, GO:0043515, GO:0005516, formin binding, atpase/atp hydrolysis regulatory activity), and cell-cell signaling (jun kinase kinase kinase activity, map-kinase scaffolding, GO:0042608, GO:0045296, GO:0051879, GO:0097016, GO:0005680, GO:0051059, rna binding).\\n\\nmechanism: these genes enable a wide range of activities and processes related to intracellular motion and cell-cell signaling that are either directly or indirectly connected to the assembly, MESH:M0030663, and disassembly of cytoskeletal structures, MESH:D014404, and cellular organelles. these activities can promote cell cycle progression, GO:0008283, and/or cell-cell signaling]] | \n", + "0.00 | \n", + "
| 774 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-0 | \n", + "[[enzyme binding activity, acid binding activity, molecule transport, adapter binding activity, receptor binding activity, dna binding activity, protein binding activity, GO:0003824, GO:0016787, GO:0016491, anion binding activity, GO:0008233, GO:0140657, thioredoxin activity, translocation, GO:0061630, cysteine endopeptidase activity, GO:0004738, GO:0004618, magnesium ion binding activity, GO:0004340, GO:0003924]] | \n", + "[[protein binding activity, dna binding activity, enzyme binding activity, GO:0060090, GO:0140677, GO:0042803, domain binding activity, GO:0016491, protein kinase binding activity, phosphatidylinositol binding activity, GO:0016504, GO:0003714, nuclear androgen receptor binding activity, nf-kappab binding activity, ubiquitin protein ligase binding activity, phosphotyrosine residue binding activity, GO:0016564, GO:0003743, peptidyl-proinalyl cistrans isomerase activity]] | \n", + "0.11 | \n", + "
| 775 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-1 | \n", + "[[protein binding activity, identical protein binding activity, GO:0008233, GO:0003824, GO:0005884, dna-binding, rna-binding, GO:0016922, MESH:D054875, anion binding activity, atp binding activity, GO:0016887, protein kinase binding activity, phosphotyrosine residue binding activity, e3 ubiquitin-protein ligase binding activity, mdm2 binding activity, GO:0060090, GO:0140677, GO:0098772, GO:0003713, GO:0003714, GO:0016564, GO:0042803, k63]] | \n", + "[[protein-protein interaction, atp binding activity, GO:0042803, GO:0016887, protein kinase binding activity, ubiquitin protein ligase binding activity, GO:0060090, anion binding activity, chemical oxidoreductase activity, protein domain specific binding activity, gtp binding activity, dna binding activity, rna binding activity, transcription regulation activity, GO:0007165, chromatin binding activity, phospholipid binding activity, GO:0004017, lipoprotein particle binding activity, GO:0008233, actin filament binding activity, fad binding activity, steroid hydrolase activity, rna stem-loop binding activity, GO:0022857, nf-kappab binding activity, coenzyme a binding activity, protein n-terminal phospho-seryl-prolyl pept]] | \n", + "0.16 | \n", + "
| 776 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-0 | \n", + "[[GO:0003677, GO:0003723, GO:0003682, GO:0006351, GO:0006412, GO:0045292, atpase binding activity, enzyme binding activity, GO:0044183, ubiquitin protein ligase, MESH:C021362, nf-kappab binding activity, GO:0140693, nucleic acid binding activity, heparan sulfate binding activity, biopolymer binding activity, GO:0060090, GO:0140678, g-protein beta-subunit binding activity, molecular sequence recognition, complementary rna strand recognition, mrna 3'-utr]] | \n", + "[[GO:0003723, GO:0044183, dna binding/recognition, protein homodimerization, GO:0003678, GO:0019904, MONDO:0000179, GO:0042393, cytoplasmic protein binding, GO:0005524, GO:0006281]] | \n", + "0.06 | \n", + "
| 777 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-1 | \n", + "[[rna binding activity, identical protein binding activity, mrna 3' utr binding activity, GO:0000900, dna binding activity, ubiquitin protein ligase binding activity, protein domain specific binding activity, GO:0006457, dna replication origin binding activity, dna-binding transcription factor binding activity, GO:0042803]] | \n", + "[[GO:0003677, GO:0003723, GO:0019904, GO:0003682, GO:0019899, protein folding chaperone activities, atp binding activity, mrna 3'-utr binding activity, identical protein binding activity, GO:0004869, GO:0140693, GO:0140713, heparan sulfate binding activity, peptidyl-prolyl isomerase activity, cyclin binding activity, GO:0004693, nuclear localization sequence binding activity, magnetic ion binding activity, histone methyltransferase binding activity, mrna 5'-utr binding activity, GO:0033677, MESH:D012321]] | \n", + "0.03 | \n", + "
| 778 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-0 | \n", + "[[GO:0006351, GO:0006351, GO:0008284, GO:0071824, GO:0019219, rna binding activity, GO:0010468, GO:0006364]] | \n", + "[[rna-binding, GO:0036211, GO:0015031, cell signaling, GO:0006412, genetic information regulation, protein bridging, chromatin regulation, transcription regulation, GO:0003676, mitochondrial functions]] | \n", + "0.00 | \n", + "
| 779 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-1 | \n", + "[[rna binding activity, dna binding activity, protein binding activity, GO:0006364, GO:0019538, GO:0006351, transcription coregulator binding activity, GO:0022402, GO:0003682, mitochondria regulation, cyclin binding activity, cyclin-dependent protein serine/threonine kin]] | \n", + "[[rna binding activity, ribosomal rrna processing, mrna and/or rrna catabolism/stability, regulation of transcription/translation, regulation of signal transduction and metabolism processes, regulation of cell cycle/proliferation, protein modification/regulation, GO:0005634, GO:0005829, GO:0005840, GO:0005739]] | \n", + "0.05 | \n", + "
| 780 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MYOGENESIS-0 | \n", + "[[GO:0008092, GO:0005201, GO:0044325, ion channel regulator, GO:0003779, GO:0005096, GO:0051879, GO:0017046, GO:0003677, signalling receptor binding, GO:0042802, GO:0048306, GO:0019899, GO:0005509, GO:0005524, GO:0006200, GO:0051117, GO:0004017, GO:0008195, GO:0051015, microfilament binding, GO:0003872, GO:0043138, GO:0004517, MESH:D009243]] | \n", + "[[calcium ion binding activity, identical protein binding activity, actin filament binding activity, GO:0042803, signaling receptor binding activity, atp binding activity, gtp binding activity, dna binding activity, GO:0019887]] | \n", + "0.00 | \n", + "
| 781 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MYOGENESIS-1 | \n", + "[[GO:0005509, GO:0004129, GO:0003677, GO:0005524, GO:0003779, abnormal growth and development, GO:0002020, structural constituent]] | \n", + "[[calcium binding activity, enzyme binding activity, dna binding activity, atp binding activity, GO:0042803, protein domain-specific binding activity, gtp binding activity, actin binding activity, GO:0008160, small gtpase activator activity, transmembrane transporter binding activity, GO:0004016, c3hc4-type ring finger domain-binding activity, GO:0060090, GO:0005096]] | \n", + "0.00 | \n", + "
| 782 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-0 | \n", + "[[GO:0036211, MESH:D005786, signal transduction regulation, dna-templated transcription regulation, GO:0007219, GO:0016567, GO:0031146, GO:0045893]] | \n", + "[[this list of genes is associated with several biological processes related to the regulation of gene expression, such as notch receptor processing, amyloid-beta formation, proteolysis, regulation of cell differentiation, canonical wnt signaling pathway, protein ubiquitination, scf-dependent proteasomal ubiquitin-dependent protein catabolic process, and positive regulation of transcription by rna polymerase ii. the underlying biological mechanism is likely related to the role of these genes in transcription and post-transcriptional gene regulation. enriched terms include: gene expression regulation, GO:0007220, GO:0034205, GO:0006508, GO:0045595, GO:0060070, GO:0016567, GO:0031146, GO:0045944]] | \n", + "0.13 | \n", + "
| 783 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-1 | \n", + "[[GO:0006351, GO:0036211, MESH:D054875, GO:0065007, GO:0007219, GO:0031146, wnt, GO:0016567, GO:0043543, GO:0004879, GO:0003714, transcription corepressor binding activity, GO:0006351, rna polymerase ii-specific dna-binding transcription repressor activity, GO:0045893, GO:0000122, GO:0045737, GO:0010604, GO:0010628, negative regulation of cell different]] | \n", + "[[GO:0016567, GO:0031146, GO:0007219, GO:0036211, GO:0010468, GO:0030335, GO:0008284, GO:0045596]] | \n", + "0.17 | \n", + "
| 784 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[[GO:0006118, GO:0020037, GO:0005515, GO:0016491, atpase activity & binding activity, GO:0060090, acyl binding activity, GO:0003954, gtp binding activity, iron-sulfur cluster binding activity, fad binding activity, MESH:D010758, GO:0019395, rna binding activity, 4 iron, 4 sulfur cluster binding activity, ubiquitin protein ligase binding activity, GO:0004129, proton-transporting atp synthase activity, lipoic acid binding activity, mhc class i protein binding activity, angiostatin binding activity, deltarasin binding activity, ubiquitin protein binding activity, nadp binding activity]] | \n", + "[[acetyl-coa transferase activity, GO:0003995, aldehyde dehydrogenase activity, atpase binding activity, GO:0004129, GO:0009055, GO:0004300, fad binding activity, GO:0003924, heme binding activity, identical protein binding activity, lipid binding activity, metal ion binding activity, GO:0003958, GO:0016491, GO:0004738, pro]] | \n", + "0.08 | \n", + "
| 785 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[[GO:0140657, GO:0009055, GO:0008553, ubiquitin protein ligase binding activity, MESH:D014451, heme binding activity, protein homodimerization, mhc class i protein binding activity, metal ion binding activity, angiostatin binding activity, mitochondrion targeting sequence binding activity, GO:0015227, rna binding activity, 4 iron, 4 sulfur cluster binding activity, GO:0000295, GO:0004129, fatselytranstransferase activity, GO:0003925, acyl-coa c-acetyltransferase activity, GO:0004774, GO:0003994, GO:0004095, GO:0003958, acetate coa-transfer]] | \n", + "[[GO:0009055, protein homodimerization, GO:0003924, GO:0000295, phosphoprotein binding activity, mitochondrial respiratory chain activity, proton-transporting atp synthase activity, mitochondrial ribosome binding activity]] | \n", + "0.10 | \n", + "
| 786 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_P53_PATHWAY-0 | \n", + "[[GO:0003700, protein binding activity, protein kinase binding activity, GO:0042803, enzyme binding activity, GO:0098631, signaling receptor binding activity, actin binding activity, cyclin binding activity, GO:0005198, GO:0030695]] | \n", + "[[dna binding activity, rna polymerase ii-specific dna-binding transcription factor binding activity, transcription regulation, protein binding activity, enzyme binding activity]] | \n", + "0.14 | \n", + "
| 787 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_P53_PATHWAY-1 | \n", + "[[dna binding activity, rna binding activity, rna polymerase binding activity, GO:0004672, GO:0042803, protein kinase binding activity, GO:0000988, GO:0003924, GO:0098631, cell signaling receptor binding activity, enzyme binding activity, heme binding activity, collagen binding activity, GO:0004392, GO:0060090, GO:0004527, GO:0042803, g protein-coupled receptor binding activity, GO:0022857, identical protein binding activity, GO:0016787, GO:0008083]] | \n", + "[[GO:0007165, MESH:D005786, GO:0005515, GO:0019899, GO:0016791, GO:0000988, GO:0007155, growth factor binding. \\nmechanism: these genes are involved in the regulation of gene expression and cellular processes by modulating signal transduction, binding proteins, and enzymes, as well as activating phosphatase activity, transcription factor activity and growth factor binding]] | \n", + "0.03 | \n", + "
| 788 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[[GO:0006351, GO:0016563, atpase-coupled ion transport, GO:0004672, GO:0008233, dna binding activity, GO:0017156, GO:1903530]] | \n", + "[[atp binding activity, GO:0019829, GO:0016477, GO:0044249, GO:0071333, GO:0090398, GO:0042742, GO:0005789, e-box binding activity, GO:0015149, GO:0002551, GO:0043303, GO:0008233, GO:0008607, GO:0045597, positively regulation of cellular biosynthetic process, positively regulation of glycolytic process, positively regulation of insulin secretion, positively regulation of macromolecule metabolic process, positively regulation of type b pancreatic cell development, positive regulation of cellular]] | \n", + "0.04 | \n", + "
| 789 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[[transcription regulation, GO:0098609, GO:0007165, GO:0045047, GO:0030041, GO:0051594, GO:0060291, GO:1903561, GO:0030027, GO:0005881, GO:0043195, GO:0005829, GO:0030425, MESH:D012319, dna-templated trans]] | \n", + "[[GO:0098609, GO:0032502, differentiation, UBERON:0000061, transcription regulation, MESH:D012319, GO:0007165, GO:0043170, protein expression, cell signaling, protein production]] | \n", + "0.18 | \n", + "
| 790 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PEROXISOME-0 | \n", + "[[molecular binding activity, GO:0003824, GO:0005215, domain binding activity, GO:0006869, GO:0015031, GO:0006259, GO:0016070]] | \n", + "[[after term enrichment analysis on the gene summaries, the following terms were found to be enriched: atp binding activity, atpase-coupled activity, GO:0042803, identical protein binding activity, enzyme binding activity, GO:0005319, GO:0016887, and metal ion binding activity.\\n\\nmechanism: the enriched terms suggest a biological mechanism that involves energy production and transport, GO:0007165, and protein interactions and formation of protein complexes. these processes are necessary for various cellular processes such as metabolism, GO:0007585, GO:0098754, GO:0040007]] | \n", + "0.00 | \n", + "
| 791 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PEROXISOME-1 | \n", + "[[genes involved in this list are primarily associated with the metabolic or structural processes needed for cellular development and homeostasis. enriched terms include fatty acid metabolism, protein homodimerization, MESH:D010084, dna and rna binding, enzyme/acyl-coa/gtpase binding/hydrolase activity, transport/export/import, and regulation of transcription by rna polymerase ii. mechanism: these genes act together to provide a plethora of functions that are integral to the growth, maintenance and protection of cells. fatty acids are transported, oxidized, and bound to proteins or phospholipids in the membrane, proteins interact with atp and gtp and undergo homodimerization, transcriptional activity is regulated by heterodimerizing with transcription factor proteins]] | \n", + "[[cell metabolic process, GO:0090304, GO:0005515, GO:0003677, GO:0016485, GO:0042446, GO:0006694, GO:0005524, GO:0006200, protein homodimerization, GO:0019901, GO:0003714, GO:0003712, cyclin binding activity, rna binding activity, protein phosphatase binding activity, sulphatide binding activity, magnesium ion binding activity, GO:0043621, MESH:M0518050, protein transmembrane]] | \n", + "0.03 | \n", + "
| 792 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[[protein binding activity, GO:0016301, GO:0005048, GO:0005102, GO:0051726, apoptosis regulation, GO:0007165, rna binding activity, GO:0004721, GO:0004620, GO:0003924, 1-phosphatidylinositol phospholipase activity, phosphotyrosine residue binding activity, GO:0000774, guanyl ribonucleotide binding activity, GO:0004869, GO:0051219, GO:0044325, GO:0008092, GO:0050750, GO:0003713, GO:0050681, nuclear receptor coactiv]] | \n", + "[[cellular process regulations, GO:0003824, protein and peptide regulation, protein domain modification]] | \n", + "0.00 | \n", + "
| 793 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[[the genes in this list are involved in several biological functions, including signal transduction, GO:0006915, cellular response to stimuli, response to dna damage, GO:0051726, and regulation of protein phosphorylation and ubiquitination. the terms \"protein phosphorylation\"; \"ubiquitination\"; \"signal transduction\"; \"cellular response to stimulus\"; \"dna damage response\"; \"regulation of cell cycle\"; \"intrinsic apoptosis\"; and \"scaffold protein\" are all statistically over-represented.\\n\\nmechanism: signaling pathways and cellular processes are intricately regulated and require the coordinated participation of different proteins. by performing a term enrichment analysis, we see that the genes in this list are involved in a variety of molecular pathways, including signal transduction, GO:0006915, cellular response to stimuli, response to dna damage, GO:0051726, and regulation of protein phosphorylation and ubiquitination. this suggests that the gene products help coordinate these pathways by forming complexes, binding to signaling molecules, or carrying out the necessary enzyme activities. this suggests the underlying biological mechanism may involve interplay between specific gene products, MESH:D011506, signaling molecules to ensure efficient functioning of the cell]] | \n", + "[[GO:0007165, GO:0019900, GO:0003924, GO:0004721, transcription factor activation, GO:0004620, GO:0005102, MESH:D054875, MESH:D000107, GO:0006915, GO:0016477, negative regulation of proliferation]] | \n", + "0.03 | \n", + "
| 794 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-0 | \n", + "[[protein binding activity, GO:0003924, gtp-dependent protein binding activity, snare binding activity, enzyme binding activity, protein kinase binding activity, clathrin binding activity, GO:0006897, retrograde transport, GO:0006893, GO:0006888, GO:0006622]] | \n", + "[[protein binding activity, atp binding activity, gtp-dependent protein binding activity, GO:0003924, signal sequence binding activity, clathrin binding activity, small gtpase binding activity]] | \n", + "0.27 | \n", + "
| 795 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-1 | \n", + "[[protein binding activity, activity, GO:0042803, enzyme binding activity, scaffold protein binding activity, snare receptor activity, syntaxin binding activity, GO:0016887, GO:0008553, GO:0008320, metal ion binding activity, protein foldinactivity, GO:0003924, protein kinase binding activity, phosphat]] | \n", + "[[atp binding activity, GO:0042803, smarc protein binding activity, GO:0003924, gtp binding activity, GO:0005096, enzyme binding activity, GO:0004197, protein domain specific binding activity, phosphatidylinositol-4-phosphate binding activity, protein kinase binding activity, GO:0008320, calcium-dependent protein binding activity, metal ion binding activity, dopaminergic receptor binding activity, ubiquitin-like protein ligase binding activity, GO:0005484, phosphatidylinositol-3,4,5-trisphosphate binding activity, phosphatidylinositol-3,5-bisphosphate binding activity, signaling receptor binding activity, GO:0005198, syntaxin binding activity, GO:0005484]] | \n", + "0.23 | \n", + "
| 796 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[[oxidative stress defense, GO:0098754, dna/rna binding, GO:0006351, GO:0098609, GO:0016043, GO:0019722, GO:0006468, GO:0010731, GO:0004392, GO:0019511, GO:0061621, GO:0005886, GO:0006750, GO:0006082]] | \n", + "[[the human genes provided are mostly involved in redox homeostasis, GO:0006952, and cell organization. there is also involvement in processes related to the maintenance of the blood-brain barrier, GO:0009650, and metabolism of hormones, MESH:D008055, and glucose. there are an abundance of terms related to transmembrane transport, MESH:D010088, heme and iron metabolism, GO:0019511, and gluthathione metabolism.\\n\\nmechanism:\\nredox homeostasis is regulated by a network of enzymatic and substrate-dependent processes. these processes include cellular antioxidant defense, removal of superoxide radicals and peroxides, GO:0061691, and regulation of the balance between oxidant production and scavenging. transport genes are employed to promote transmembrane transport of xenobiotics and lipids, like abcc1, atox1, and glrx. iron and heme metabolism is facilitated by genes like ftl, hmox2, and mpo. peptidyl-proline hydroxylation is regulated by genes like egln2 and mgst1, while glutathione metabolism is controlled by genes like g]] | \n", + "0.03 | \n", + "
| 797 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[[MESH:D004734, oxidative stress response, GO:0042803, protein phosphatase 2a binding activity, GO:0004601, GO:0004602, GO:0047499, GO:0003954, chromatin dna binding activity, GO:0004861, GO:0004784, GO:0047184, GO:0015038, GO:0015035, phosphatidylinositol binding activity, GO:0004096, heme binding activity]] | \n", + "[[GO:0045454, GO:0019899, protein homodimerization, GO:0015035, GO:0004602, GO:0003954, atp binding activity, identical protein binding activity, transition metal ion binding activity, GO:0016209, heme binding activity, ubiquitin-specific protease binding activity, GO:0047499, heparin binding activity, GO:0004601, GO:0004784, GO:0008811, GO:0004096]] | \n", + "0.30 | \n", + "
| 798 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-0 | \n", + "[[GO:0003723, GO:0031491, transcription and regulation, GO:0003677, GO:0004672, protein folding and chaperoning, metabolic regulation, MESH:D054875]] | \n", + "[[GO:0140677, GO:0004672, cellular component activity, binding activity, GO:0008233, nucleosome binding activity, ion binding activity, phosphatase binding activity, GO:0051726, apoptosis regulation, GO:0007155, GO:0007399, transcription regulation, GO:0015031, GO:0009988, MESH:D005786]] | \n", + "0.04 | \n", + "
| 799 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-1 | \n", + "[[GO:0019899, GO:0005515, ligand binding, GO:0005509, GO:0000166, GO:0008134, GO:0003677, GO:0005525, GO:0042562, GO:0006200, GO:0004672, GO:0003723, GO:0008047, GO:0044183, GO:0003682, GO:0019903, GO:0019212, GO:0008233, GO:0022890]] | \n", + "[[all of the genes are involved in regulation of various metabolic processes and signaling pathways, with most of them associated with binding activities and regulation of protein activities. enriched terms include: protein binding activity, atp binding activity, protein-folding chaperone binding activity, chromatin binding activity, GO:0046976, transcription corepressor binding activity, GO:0004672, GO:0060090, enzyme binding activity, GO:0140677, GO:0098632, GO:0004888, gtp binding activity, signaling receptor binding activity, ribonucleoprotein complex binding activity, myosin light chain binding activity, GO:0017116, GO:0003689, GO:0051131, peptide alpha-n-acetyltransferase activity. mechanism: the genes are involved in various metabolic processes and signaling pathways, by regulating protein activities through different binding activities and histone methyltransferase activity. some of these activities regulate certain processes based on gtp binding, while others are involved in cell-cell adhesion, transmembrane signaling and chaperone-mediated protein complex assembly]] | \n", + "0.03 | \n", + "
| 800 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[[GO:0007165, regulation of transcription, GO:0051246, regulation of macromolecule metabolism, GO:0050794, interaction with transcription factors, interaction with smad proteins]] | \n", + "[[GO:0005524, GO:0048185, GO:0046332, protein phosphatase/kinase activity, smad signaling, bmp signaling, GO:0006351, MESH:D012319, GO:0005515, GO:0007165, GO:0007049, GO:0008152, GO:0007155]] | \n", + "0.05 | \n", + "
| 801 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[[tgf binding activity, dna-binding transcription factor binding activity, smad binding activity, GO:0019211, GO:0004674, GO:0004869, GO:0061631, myosin binding activity, r-smad binding activity, beta-catenin binding activity, cadherin binding activity, gtp binding activity, i-smad binding activity, GO:0003924, GO:0003714, GO:0042803, nucleic acid binding activity, serine-type endope]] | \n", + "[[dna-binding activity, transcription regulation, GO:0035556, GO:0004674, smad binding activity, positive/negative regulation of rna/protein metabolic process, GO:0006468, receptor tyrosine kinase binding activity, GO:0007165, GO:0042803, GO:0061630, GO:0031326, GO:0009966, GO:0006357, GO:0090092]] | \n", + "0.10 | \n", + "
| 802 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[[dna binding transcription factor, GO:0005102, GO:0019899, GO:0005126, growth factor, transmembrane receptor]] | \n", + "[[the list of genes provided are involved in a broad set of functions related to gene transcription or regulation of transcription factors, cell signaling, binding activities and metabolic processes. the enriched terms for this gene set include dna-binding transcription factor activity, rna polymerase ii transcription regulatory region sequence-specific binding, GO:0003924, chemokine receptor binding activity, signaling receptor binding activity, protein kinase binding activity, enzyme binding activity, identical protein binding activity and protease binding activity.\\n\\nmechanism: the underlying biological mechanism for this list of genes is likely related to control of gene expression, as well as control of protein interactions that mediate cell signaling and metabolic processes. additionally, the functions related to binding activities suggest many of the genes are involved in cell-to-cell communication and cell adhesion]] | \n", + "0.00 | \n", + "
| 803 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[[GO:0000988, rna polymerase ii-specific, dna-binding, identical protein binding activity, enzyme binding activity, signaling receptor binding activity, GO:0004672, GO:0005125, GO:0008083, GO:0098631, GO:0022857, GO:0016791, gtp binding activity, GO:0140657]] | \n", + "[[GO:0001216, transcription regulatory region sequence-specific dna-binding, gtp binding activity, enzyme binding activity, identical protein binding activity, signal receptor binding activity, GO:0016791, protein kinase binding activity, GO:0005125, GO:0008083]] | \n", + "0.33 | \n", + "
| 804 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[[GO:0006457, GO:0003723, transcription activator, GO:0003677, GO:0051082, GO:0003720, GO:0003676, GO:0044325, GO:0005524, GO:0006402, translation regulation, GO:0003755, GO:0035925]] | \n", + "[[rna binding activity, dna binding activity, protein binding activity, GO:0140693, identical protein binding activity, dna-binding transcription factor binding activity, GO:0042803, atpase binding activity, GO:0016887, enzymatic activity, GO:0003713, GO:0008494, protein phosphatase binding activity, peptidyl-prolyl primase activity, transcription cis-regulatory region sequence-specific activity]] | \n", + "0.00 | \n", + "
| 805 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[[atp binding activity, GO:0016887, enzyme binding activity, identical protein binding activity, GO:0060090, GO:0140678, nucleic acid binding activity, GO:0046983, protein folding chaperone binding activity, ribosome binding activity, rna binding activity, snare binding activity, transcription corepressor binding activity, transcription regulator]] | \n", + "[[enzyme binding activity, rna binding activity, protein binding activity, transmembrane transporter binding activity, dna binding activity, protein kinase binding activity, box h/aca snorna binding activity, protein phosphatase binding activity, telomerase rna binding activity, GO:0042803, GO:0046982, transcription factor binding activity, atp binding activity, GO:0016887, GO:0003724, GO:0003756, ubiquitin protein ligase binding activity, GO:0004518, adenyl ribonucleotide binding activity, heat shock protein binding activity]] | \n", + "0.13 | \n", + "
| 806 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-0 | \n", + "[[genes included in this set are involved in various cellular functions such as enzyme binding activity, GO:0003924, lipoprotein binding activity, GO:0004620, and other related activities. common enriched terms across these genes include protein binding activity, smad binding activity, dna-binding activity, phosphotyrosine residue binding activity, GO:0003824, GO:0003924, and enzymatic inhibitor activity. mechanism: these genes are likely to be involved in regulation and control of cellular functions and processes through various proteins. this regulation and control is likely being done through interaction of the proteins encoded by these genes with other proteins and structurally with dna, as well as through the enzymatic activities of the encoded proteins]] | \n", + "[[gtp binding activity, enzyme binding activity, dna-binding transcription factor binding activity, phosphotyrosine residue binding activity, cyclin binding activity, receptor-ligand interaction, protein-protein interaction, smad binding protein, nf-kappab binding protein, growth factor binding protein]] | \n", + "0.05 | \n", + "
| 807 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-1 | \n", + "[[dna binding activity, GO:0000988, protein binding activity, smad binding activity, GO:0005096, MESH:C062738]] | \n", + "[[GO:0001216, rna polymerase ii-specific activity, nf-kappab binding activity, microtubule binding activity, actin binding activity, identical protein binding activity, smad binding activity, GO:0005243, GO:0005388, receptor binding activity, GO:0005096, histone binding activity, ap-1 transcription factor binding activity, vitamin d receptor binding activity, cytoplasmic protein binding activity, GO:0004930, platelet-derived growth factor binding activity, enzyme binding activity, protease binding activity, phospholipid binding activity, GO:0004672, GO:0004674, intracellular protein binding activity]] | \n", + "0.07 | \n", + "
| 808 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-0 | \n", + "[[GO:0005515, GO:0003677, binding activity, receptor binding activity, GO:0004672, GO:0007155, GO:0023052, GO:0010468]] | \n", + "[[protein binding activity, atp binding activity, rna binding activity, dna binding activity, receptor binding activity, enzyme binding activity, GO:0005548, GO:0098609, GO:0007268, GO:0097190, GO:0005138, GO:0042110, overall cellular metabolism, MESH:D005786]] | \n", + "0.05 | \n", + "
| 809 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-1 | \n", + "[[gtp binding activity, dna binding activity, GO:0016563, protein kinase binding activity, GO:0004175]] | \n", + "[[enzyme binding activity, GO:0016787, GO:0016740, GO:0038023, dna binding activity, rna binding activity, GO:0000988, protein binding activity]] | \n", + "0.08 | \n", + "
| 810 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[[the genes summarized above are all involved in developmental processes, such as organizing and regulating cell adhesion, components of the wnt pathway and regulation of gene expression. the enriched terms for these genes would be development-related terms, such as cell adhesion, GO:0060070, GO:0006468, GO:0016567, GO:0006351, GO:0006476, GO:0006351, and protein stability.\\n\\nmechanism: the underlying biological mechanism involves the involvement of many of these genes in the wnt pathway, which is a conserved signaling pathway involved in cell-cell communication and a variety of developmental processes. another mechanism involves the regulation of gene expression and the binding of dna-binding transcription factors, as well as protein ubiquitination and deacetylation which also control gene expression]] | \n", + "[[protein binding activity, GO:0003700, rna polymerase ii-specific dna-binding transcription factor binding activity, notch binding activity, pdz domain binding activity, GO:0042813, ubiquitin protein ligase binding activity, beta-catenin binding activity, GO:0003713, histone deacetylase binding activity, GO:0048019, transcription corepressor binding activity, GO:0060090, GO:0004407, cholesterol binding activity]] | \n", + "0.00 | \n", + "
| 811 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[[GO:0005515, transcription regulation, GO:0051726, GO:0007165, response pathways]] | \n", + "[[GO:0007165, GO:0010468, GO:0006351, GO:0001932, GO:0031647, GO:0016477, GO:0008283, GO:0032502, GO:0006508]] | \n", + "0.08 | \n", + "
| 812 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "T cell proliferation-0 | \n", + "[[signaling receptor binding activity, protein kinase binding activity, GO:0061630, GO:0035556, GO:0001816, GO:0010467]] | \n", + "[[protein binding activity, enzyme binding activity, protein kinase binding activity, interleukin binding activity, phosphorylation-dependent protein binding activity, GO:0001216, GO:0042803, nucleic acid binding activity, GO:0005001, GO:0048018, GO:0004725, GO:0005125, cytoskeletal protein binding activity, cytokin receptor activity, GO:0030335]] | \n", + "0.05 | \n", + "
| 813 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "T cell proliferation-1 | \n", + "[[GO:0048018, phosphotyrosine residue binding activity, cytoskeletal protein binding activity, GO:0005574]] | \n", + "[[cation binding activity, diacylglycerol binding activity, enzyme binding activity, GO:0046982, receptor binding activity, protein kinase binding activity, phosphorylation-dependent protein binding activity, phosphotyrosine residue binding activity, GO:0005001, protease binding activity, cytoskeletal protein binding activity, phosphatidylinositol 3-kinase binding activity, GO:0061630, GO:0004888, GO:0043621, GO:0004697, zinc ion binding activity, transmembrane atp-gated monoatomic cation channel activity, purin]] | \n", + "0.10 | \n", + "
| 814 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "Yamanaka-TFs-0 | \n", + "[[transcription repressor and activator activities, rna polymerase ii-specific, nucleic acid binding activity, GO:0009889, GO:0009966, GO:0010468, GO:0045765, and protein-dna complex organization, GO:0042127]] | \n", + "[[dna-binding, GO:0000988, rna polymerase ii-specific, nucleic acid binding activity, transcription cis-regulatory region binding activity, GO:0010468, GO:0009889]] | \n", + "0.33 | \n", + "
| 815 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "Yamanaka-TFs-1 | \n", + "[[dna-binding, GO:0016563, GO:0016564, GO:0000988, rna binding activity, ubiquitin protein ligase binding activity, GO:0010628, GO:0010629, GO:0009889, GO:0045765, GO:0060828, GO:0009966, transcription cis-regulatory region binding activity, GO:0045944, GO:0003130, GO:0001714]] | \n", + "[[GO:0006351, GO:0010468, dna-binding, GO:0000785, GO:0005829, GO:0005654, GO:0005667, GO:0009966, GO:0045944, GO:0001714]] | \n", + "0.18 | \n", + "
| 816 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "amigo-example-0 | \n", + "[[GO:0005515, GO:0060230, GO:0005543, MESH:M0518050, GO:0050804]] | \n", + "[[the list of genes provided is involved in multiple processes related to cell adhesion, growth factor binding, protein phosphorylation, tissue development, and regulation of cholesterol homeostatis and transcytosis. the underlying biological mechanism likely involves multiple pathways, including cellular response to lipopolysaccharide, cell-matrix adhesion, and negative regulation of low-density lipoprotein. enriched terms include cell adhesion, cell surface receptor signaling, collagen binding activity, GO:0019838, GO:0042157, GO:1902533, GO:0046983, GO:0006468, regulation of bmp signaling, GO:0042127, GO:0010468, GO:0009966, regulation of very-low-density lipoproten particle clearance, GO:0045056]] | \n", + "0.00 | \n", + "
| 817 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "amigo-example-1 | \n", + "[[GO:0005515, GO:0043167, GO:0008009, GO:0019838, signal receptor binding, GO:0019902, GO:0016477, GO:0086009, GO:0007165, GO:0065007, GO:0006952]] | \n", + "[[GO:0051246, GO:0001952, GO:0042127, GO:0042981, GO:0043269, GO:0030193, GO:0007166, GO:0050804, GO:0005201, GO:0007160, organ development and differentiation, regulation of hormone pathways]] | \n", + "0.00 | \n", + "
| 818 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_0-0 | \n", + "[[GO:0005509, double-stranded dna-binding, cell adhesion and migration, transcriptional regulation]] | \n", + "[[genes in this list are involved in a range of activities, including calcium ion binding activity, metal ion binding activity, protein domain specific binding activity, identical protein binding activity, dna-binding transcription factor activity, and several others. the underlying biological mechanism appears to be related to structural support and regulation of cellular processes. enriched terms include: metal ion binding, GO:0005509, GO:0005515, GO:0000988, dna-binding, GO:0042802, domain specific protein binding]] | \n", + "0.10 | \n", + "
| 819 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_0-1 | \n", + "[[metal ion binding activity, protein binding activity, rna binding activity, GO:0019208, GO:0005243, GO:0042803, calcium ion binding activity, MESH:C086554]] | \n", + "[[GO:0001216, protein kinase binding activity, metal ion binding activity, calcium ion binding activity, transcription co-regulator activity, responsive to stimuli]] | \n", + "0.17 | \n", + "
| 820 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_1002-0 | \n", + "[[UBERON:0001134, GO:0006936, GO:0016567, GO:0045010, calcium-dependent signaling, GO:0010468, GO:0006468, GO:0043687, GO:0042692, GO:0060537, MONDO:0020121, muscle organelle organization]] | \n", + "[[GO:0051015, GO:0000146, GO:0051371, GO:0003785, GO:0005523, GO:0017022, GO:0031432, GO:0004111]] | \n", + "0.00 | \n", + "
| 821 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_1002-1 | \n", + "[[actin binding activity, GO:0007015, muscle alpha-actinin binding activity, GO:0006936, GO:0060415, GO:0071689, GO:0004672, protein phosphatase binding activity, GO:0043502, tropomyosin binding activity, troponin binding activity, troponin complex activities]] | \n", + "[[calcium-dependent protein binding activity, atp binding activity, actin filament binding activity, actin monomer binding activity, transmembrane transporter binding activity, GO:0016567, GO:0061630, tropomyosin binding activity, identical protein binding activity, GO:0008375, protein phosphatase 1 binding activity, zinc ion binding activity, troponin c binding activity, troponin i binding activity, actin binding activity, tropomyosin binding activity, GO:0001216, sequence-specific double-stranded dna binding activity]] | \n", + "0.07 | \n", + "
| 822 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "endocytosis-0 | \n", + "[[protein signaling, GO:0006468, GO:0016567, GO:0015031, GO:0030030, GO:0006897, GO:0006898, GO:0035091, GO:0001766, GO:0097320]] | \n", + "[[GO:0004674, lysophosphatidic acid binding activity, sulfatide binding activity, GO:0016790, cadherin binding activity, GO:0032456, sh3 domain binding activity, GO:0051260, macropinosome formation, GO:0031623, transferring transport, t cell receptor binding activity, GO:0005085, GO:0044351, GO:0001773, GO:0007520, GO:0018105, GO:0010468, vascular endothelial growth factor receptor signalling pathway, GO:0051128, GO:0007042, GO:0045807, GO:0051090]] | \n", + "0.00 | \n", + "
| 823 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "endocytosis-1 | \n", + "[[GO:0006897, GO:0005515, GO:0006869, GO:0016567, GO:0042632, GO:0035727]] | \n", + "[[GO:0006468, GO:0051260, cell signaling, GO:0005480, GO:0016567, endocytosis/exocytosis, GO:0005102, GO:0010468, vesicle buddying, GO:0007165, GO:0050727, GO:0035556, gtp-dependent pathways, receptor signaling, canonical inflammasome signaling]] | \n", + "0.05 | \n", + "
| 824 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "glycolysis-gocam-0 | \n", + "[[GO:0019538, enzymatic activity, protein transcription, cell metabolism, carbohydrate phosphorylation and metabolism, protein homeostasis, cell signaling, GO:0008104, cell homeostasis, cellular energy production]] | \n", + "[[protein binding activity, atp binding activity, peptidoglycan binding activity, GO:0051156, GO:0002639, GO:0010595, GO:0006002, GO:0061615, GO:0030388, GO:0046166, fructose binding activity, GO:0004332, MONDO:0009295, GO:0004807, disordered domain specific binding activity, GO:0004866, GO:0046835, GO:0072655, maintenance of protein location in]] | \n", + "0.00 | \n", + "
| 825 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "glycolysis-gocam-1 | \n", + "[[GO:0003824, GO:0031625, protein homodimerization, GO:0016310, GO:0006096, GO:1904659, GO:0070061, GO:0004332, GO:0004618, GO:0004619, GO:0004396, peptidoglycan binding activity, GO:0003872, GO:0004807, GO:0004347, GO:0021762, binding activity of sperm to zona pellucida, GO:0030388, GO:0019725, GO:0046716, GO:0071456, GO:0016525, UBERON:2005050]] | \n", + "[[protein binding activity, atp binding activity, ubiquitin protein ligase binding activity, fructose binding activity, GO:0042803, GO:0004618, GO:0004619, GO:0004807, GO:0004396, GO:0004332, GO:0004634, GO:0003872, GO:0004347, GO:0006096, GO:0006002, GO:0046166, GO:0046835, GO:0072655, GO:0072656, GO:0071456, negative regulation of]] | \n", + "0.26 | \n", + "
| 826 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "go-postsynapse-calcium-transmembrane-0 | \n", + "[[GO:0097553, GO:1990034, GO:0071318, GO:0007186, GO:0035235, GO:1990454, GO:0017146, GO:0014066, GO:1900274, GO:0099509, GO:2000300, GO:0032680, GO:0005245, GO:2000311, GO:0080164]] | \n", + "[[GO:0005262, GO:0005245, regulation of intracellular calcium concentrations, GO:0098960, GO:2000311, g protein-coupled receptor signaling, GO:0070588, GO:0015276]] | \n", + "0.10 | \n", + "
| 827 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "go-postsynapse-calcium-transmembrane-1 | \n", + "[[GO:0006816, regulation of calcium]] | \n", + "[[GO:0005261, acetylcholine-gated channel activity, GO:0022849, nmda selective glutamate receptor activity, GO:0005245, GO:1990454, GO:0035235, GO:0071318, regulation of]] | \n", + "0.00 | \n", + "
| 828 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "go-reg-autophagy-pkra-0 | \n", + "[[these genes are involved in several cellular activities, primarily in their roles in signal transduction pathways, GO:0036211, protein folding and stability, GO:0051726, and apoptosis. the terms enriched are: signaling receptor activity; protein phosphorylation; regulation of macromolecule biosynthetic process; autophagy; g2/m transition of mitotic cell cycle; chromosome segregation; cytoplasmic stress granule; torc1 signaling; defense response; anoikis; protein folding chaperone; histone acetylation; i-kappab kinase/nf-kappab signaling; k63-linked polyubiquitin modification-dependent protein binding activity.\\n\\nmechanism: these genes participate in a variety of biological processes, including signal transduction pathways, GO:0036211, GO:0051726, apoptosis and dna-templated transcription, answering to different external and internal stimuli as well as aiding in cell survival and death. the enriched terms involve protein-protein interactions and modifications, as well as involvement in akt/pi3k, tor, and nf-kb pathways that are essential for cell signaling, typical in response to bacterial infection and the activation of pro-survival mechanisms]] | \n", + "[[protein kinase binding activity, GO:0004672, GO:0004674, GO:0001934, GO:0010556]] | \n", + "0.00 | \n", + "
| 829 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "go-reg-autophagy-pkra-1 | \n", + "[[protein binding activity, metal ion binding activity, protein kinase binding activity, GO:0030295, protein folding chaperone activity, GO:0042803, chromatin binding activity, GO:0003713, GO:0016410, GO:0016538, GO:0016303, card domain binding activity, heat shock protein binding activity, muramyl dipeptide binding activity, 14-3-3 protein binding activity, rna polymerase iii cis-regulatory region sequence-specific dna binding activity]] | \n", + "[[the genes listed above are involved in a variety of processes, including negative and positive regulation of transport, GO:0051246, cell surface receptor signaling, and regulation of gene expression. these genes also have a variety of functions, including protein kinase binding activity, chromatin binding activity, GO:0030295, and metal ion binding activity. the enriched terms that describe these genes include: protein binding activity; protein kinase binding activity; signal transduction; positive and negative regulation of transport; chromatin binding activity; and protein serine/threonine kinase activity.\\n\\nmechanism: these gene products are part of, or act upstream of a variety of signaling pathways, all of which are involved in cell growth, MESH:D008283, and response to environmental stimuli. the pathways typically involve post-translational modifications of target proteins by phosphorylation, as well as formation or breakdown of protein-containing complexes. these signaling pathways ultimately affect gene expression and determine the type of output which a particular cell will produce]] | \n", + "0.07 | \n", + "
| 830 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[[the genes in this list share functions involving glycoprotein and carbohydrate metabolic processes and structural functions related to extracellular matrix organization. enriched terms include: dihydroceramidase activity, GO:0017040, GO:0061463, GO:0004134, GO:0004135, GO:0004556, hyaluronic acid binding activity, GO:0004415, GO:0004568, GO:0008843, clathrin heavy chain binding activity, GO:0008422, GO:0004348, GO:0004336, GO:0004553, GO:0008375, GO:0004563, identical protein binding activity, syndecan binding activity, heparan sulfate proteoglycan binding activity, GO:0003796, GO:0004567]] | \n", + "[[the genes in the list are involved in many processes relating to glycan metabolism and synthesis, such as glycoside catabolic process, GO:0006027, GO:0019377, GO:0005980, and sucrose catabolic process. other enriched terms are dihydroceramidase activity, hyaluronic acid binding activity, GO:0004415, GO:0030212, GO:0046373, GO:0004571, GO:0006487, and protein homodimerization activity.\\n\\nmechanism: glycan metabolism and synthesis involves several enzymes with diverse activities such as alpha-glucosidases, MESH:D043323, MESH:D001617, MESH:D001619, n-acetylglucosaminyltransferases. these enzymes hydrolyze transfer carbohydrate building blocks to form modify carbohydrates for a variety of cellular functions]] | \n", + "0.05 | \n", + "
| 831 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[[GO:0006516, GO:0006027, heparan sulfate catabolism, glucoside catabolism, GO:0036508, GO:0006517, GO:0005975, GO:0006869, GO:0030214, receptor signaling, GO:0031589, GO:0009313, GO:0004672, GO:0008283, GO:0019915, GO:0050885, GO:0042742, GO:0005989, GO:0008344, GO:0007605, GO:0006487, GO:0006281, GO:0071451, peptidyl-serine]] | \n", + "[[GO:0005975, GO:0046477, GO:0006516, oligo-saccharide catabolic process, GO:0006869, GO:0015144, GO:0046982, protein domain specific binding activity, GO:0006629, GO:0016139, GO:0030214, GO:0006032]] | \n", + "0.12 | \n", + "
| 832 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "ig-receptor-binding-2022-0 | \n", + "[[immunoglobulin receptor binding activity, antigen binding activity, fc-gamma receptor i complex binding activity, GO:0004715, phosphotyrosine residue binding activity, peptidoglycan binding activity, phosphatidylcholine binding activity. mechanism: the genes listed appear to be involved in the regulation of the immune response. they likely aid in the recognition of pathogens, binding to the appropriate receptors, triggering a signal for an immune response. they may also play a role in enabling the recognition of self-antigens inhibiting a response to them]] | \n", + "[[immunoglobulin receptor binding activity, antigen binding activity, GO:0004715, phosphatidylcholine binding activity, phosphotyrosine residue binding activity]] | \n", + "0.50 | \n", + "
| 833 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "ig-receptor-binding-2022-1 | \n", + "[[antigen binding activity, immunoglobulin receptor binding activity, GO:0098542, GO:0002253, fc-gamma receptor i complex binding activity, GO:0004715, peptidoglycan binding activity, phosphatidylcholine binding activity, GO:0007229, GO:0038187, mannose binding activity, phosphotyrosine residue binding activity, GO:0051130, GO:0045657, protection of host from foreign agent]] | \n", + "[[GO:0042803, GO:0007160, phosphorylation-dependent signaling, GO:0019901, GO:0034988, GO:0030098, GO:0098609, GO:0001784, GO:0042834, integrin signaling, GO:0006909]] | \n", + "0.00 | \n", + "
| 834 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "meiosis I-0 | \n", + "[[these genes are involved in processes related to dna binding, repair, replication, recombination, and regulation thereof. the enriched terms would be: dna binding, GO:0003690, dna damage repair, GO:0006310, GO:0005515, meiotic recombination, GO:0007059, GO:0000278, GO:0071173, GO:0051289, GO:0003682, resolution of meiotic recombination intermediates. \\nmechanism: the underlying biological mechanism is that these proteins work together to maintain genomic stability, regulate gene expression, promote proper cell division, germline cell development, meiosis]] | \n", + "[[GO:0003677, atp dependent activity, GO:0003682, GO:0005634, protein export, transcriptional regulation, GO:0003690, GO:0003697, GO:0006281, GO:0004518, MESH:D011995, GO:0007059, GO:0000278, intrinsic apoptotic signaling, regulation of telomere maintenance.\\nmechanism: the genes identified are likely playing roles in a variety of dna metabolic pathways, including dna repair, double-stranded dna break repair, homologous recombination, transcriptional regulation, and mitotic cell cycle processes. these pathways likely enable cellular replication and maintenance of genomic integrity, as well as control of gene expression and apoptosis]] | \n", + "0.17 | \n", + "
| 835 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "meiosis I-1 | \n", + "[[GO:0140013, dna binding activity, GO:0006259, GO:0035825, telomere attachment, GO:0000785, GO:0000795, GO:0005694, GO:0005737]] | \n", + "[[GO:0003677, GO:0003690, GO:0042802, GO:0006259, GO:0006302, GO:0007131, meiotic chromosome segregation and pairing, GO:0007283, GO:0000712, GO:0051026, GO:0016925, GO:0007130]] | \n", + "0.05 | \n", + "
| 836 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "molecular sequestering-0 | \n", + "[[calcium ion binding activity, identical protein binding activity, GO:0004252, GO:0140314, calcium-dependent protein binding activity, arginine binding activity, GO:0140313, enzyme binding activity, GO:0019887, nf-κb binding activity, nuclear localization sequence binding activity, oxysterol binding activity, rage receptor binding activity, ubiquitin protein ligase binding activity, actin binding activity, rig-i binding activity, GO:0003713, zinc ion binding activity, GO:1903231]] | \n", + "[[calcium ion binding activity, identical protein binding activity, GO:0140311, ubiquitin protein ligase binding activity, cellular response, GO:0001932, GO:0010359, GO:0097214, GO:0010468, GO:0035456]] | \n", + "0.12 | \n", + "
| 837 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "molecular sequestering-1 | \n", + "[[protein binding activity, GO:0140313, GO:0000988, GO:0019887, calcium ion binding activity, dna-binding activity, ubiquitin protein ligase binding activity, tumor necrosis factor binding activity, regulatory pathway activity]] | \n", + "[[GO:0005515, GO:0046872, GO:0043167, GO:0010468, GO:0001932, cell death pathways, GO:0009059, GO:0046907, cellular response to infection and inflammation]] | \n", + "0.00 | \n", + "
| 838 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "mtorc1-0 | \n", + "[[enzyme binding activity, acid binding activity, molecule transport, adapter binding activity, receptor binding activity, dna binding activity, protein binding activity, GO:0003824, GO:0016787, GO:0016491, anion binding activity, GO:0008233, GO:0140657, thioredoxin activity, translocation, GO:0061630, cysteine endopeptidase activity, GO:0004738, GO:0004618, magnesium ion binding activity, GO:0004340, GO:0003924]] | \n", + "[[protein binding activity, dna binding activity, enzyme binding activity, GO:0060090, GO:0140677, GO:0042803, domain binding activity, GO:0016491, protein kinase binding activity, phosphatidylinositol binding activity, GO:0016504, GO:0003714, nuclear androgen receptor binding activity, nf-kappab binding activity, ubiquitin protein ligase binding activity, phosphotyrosine residue binding activity, GO:0016564, GO:0003743, peptidyl-proinalyl cistrans isomerase activity]] | \n", + "0.11 | \n", + "
| 839 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "mtorc1-1 | \n", + "[[cytoskeleton protein binding, phosphatase binding activity, GO:0016491, cell development and signaling activity, dna binding activity, cellular transporter activity, protein kinase binding activity]] | \n", + "[[protein binding activity, GO:0005215, dna binding activity, rna binding activity, atp binding activity, peptide activity, GO:0003824, enzyme binding activity, phosphoprotein binding activity, GO:0016563, GO:0016787, GO:0016491, GO:0004017, identical protein binding activity, GO:0060090, GO:0007165, signal receiving activity, GO:1901987, metabolism regulation, cell growth control]] | \n", + "0.08 | \n", + "
| 840 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "peroxisome-0 | \n", + "[[peroxisome biogenesis, protein import into peroxisome, GO:0000425, GO:0000268, GO:0140036, GO:0006631, protein homodimerization, enzyme binding activity, GO:0050821, GO:0043335]] | \n", + "[[peroxisome biogenesis, atp binding activity, GO:0016887, ubiquitin-dependent protein binding activity, GO:0016558, GO:0050821, GO:0043335, GO:0000425, GO:0006625, protein tetramerization.\\n\\nmechanism: these gene functions are involved in a complex process involving the biogenesis and maintenance of peroxisomes, which are subcellular organelles that contain a variety of enzymes involved in metabolic processes. this process entails the function of multiple proteins working together to ferry important proteins into the peroxisomal membrane, where these proteins will become functional components of the organelle]] | \n", + "0.25 | \n", + "
| 841 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "peroxisome-1 | \n", + "[[GO:0016558, GO:0050821, GO:0042127, protein-lipid binding, GO:0007031, GO:0008611, GO:0001881, GO:0006631]] | \n", + "[[protein binding activity, GO:0016558, peroxisome matrix targeting signal-2 binding activity, GO:0042803, GO:0008611, GO:0006631, GO:0008285, GO:0000425, GO:0032994, microtubule-based peroxisome localization.\\nmechanism: based on the functions that these genes carry out, it is likely that the genes are involved in a mechanism whereby proteins are imported into the peroxisome matrix, and the peroxisome matrix is organized, stabilized, and/or maintained in order to carry out fatty acid metabolism and pexophagy. the receptor recycling and microtubule-based localization also likely play a role in this mechanism]] | \n", + "0.20 | \n", + "
| 842 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "progeria-0 | \n", + "[[GO:0003677, GO:0005515, GO:0046872, cellular response to radiation, hypoxia, and starvation, GO:0042981, GO:0032204, GO:0010835, GO:0045069]] | \n", + "[[protein binding activity, dna binding activity, metal ion binding activity, GO:0003678, GO:0042803, GO:0071480, GO:0010836, GO:0007084, GO:0045071, GO:0032392, GO:0006259, GO:0009267, GO:1902570, GO:0042981, GO:0071456, GO:0032204, GO:0004222, GO:0050688, with a positive effect]] | \n", + "0.08 | \n", + "
| 843 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "progeria-1 | \n", + "[[dna damage and repair, GO:0005515, GO:0046872, homodimerization, GO:0006915, MESH:D016922, GO:0001666]] | \n", + "[[GO:2000772, dna binding and metabolic processes, dna helicase and metal ion binding activities, protein localization to nucleolus and regulation of apoptotic processes appear to be enriched terms common to the three genes given.\\n\\nmechanism: the three genes appear to be involved in similar nucleic acid binding and regulation activities that enable the maintenance and regulation of cellular processes. this suggests an underlying molecular mechanism in which these genes interact directly to modulate a variety of cellular processes related to senescence, GO:0003677, GO:0008152, GO:0006915]] | \n", + "0.08 | \n", + "
| 844 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "regulation of presynaptic membrane potential-0 | \n", + "[[GO:0005216, GO:0016917, GO:0008066, GO:0007186, GO:0007214, GO:0006836, GO:0005249, GO:0005248, GO:0007193]] | \n", + "[[voltage-gated potassium/sodium channel activity, GO:0015276, transmembrane transporter binding activity, GO:0004930, GO:0004971, GO:0015277, GO:0035235, GO:1902476, GO:0007214, GO:0019228, GO:0042391, GO:0007268, regulation of]] | \n", + "0.05 | \n", + "
| 845 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "regulation of presynaptic membrane potential-1 | \n", + "[[GO:0005216, membrane potential regulation, GO:0015276, g protein-coupled receptor signaling, GO:1902476, GO:0007214, GO:0071805]] | \n", + "[[GO:0005216, GO:0015276, membrane potential regulation, GO:0005249, GO:0005248, GO:0008066, GO:0004890, GO:0055074, GO:0022851, ionotropic glutamate receptor signaling, GO:1902476, GO:0051932, GO:0048167, negative regulation of smooth muscle apoptotic process, GO:0051924, GO:0086009, GO:0035249, GO:0060292, GO:0006836, GO:0050804, GO:0034220, GO:0051205, GO:0060079]] | \n", + "0.15 | \n", + "
| 846 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "sensory ataxia-0 | \n", + "[[dna-binding, rna polymerase ii-specific activity, GO:0046872, GO:0031625, GO:0045944, GO:0002639, GO:1901184, GO:0033157, monoatomic cation]] | \n", + "[[transcription regulation, GO:0031625, GO:0003677, GO:0006027, GO:0043583, GO:0045475, GO:0007399, GO:0006457, GO:0043066, GO:0010595, GO:0002639, GO:0034214, GO:0050974, GO:0006812, GO:0015886, GO:0071260, GO:0042552, GO:0098742, GO:0006839, GO:0019226, GO:0008380, GO:0003774, GO:0061608, nuclear localization sequence binding activity, GO:0006607, GO:0003887, GO:0006284, gap-filling, protein ubiquitination.\\n\\nmechanism: analysis of the given list of genes suggests that there]] | \n", + "0.06 | \n", + "
| 847 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "sensory ataxia-1 | \n", + "[[transcription regulation, nucleic acid metabol]] | \n", + "[[MESH:D015533, dna-binding, rna polymrease ii-specific, dna binding activity, GO:0034214, GO:0061608, protein folding chaperone binding activity, GO:0016567, cell aggregration, GO:0098609, GO:0042552, GO:0005886, GO:0034220, GO:0030218, GO:0015886, mitochondrial transport.\\nmechanism: the eighteen human genes are involved in a variety of complex biological processes, from transcriptional regulation, through to cellular adhesion and the transport of macromolecules, including proteins, nucleic acids and heme. there is likely significant cross-talk between these various processes, particularly at the level of dna binding proteins, transcription activators, and nuclear receptor activities. this suggests that these genes are likely playing a role in the coordination of cellular processes to facilitate proper neural development and maintenance of peripheral nerve function]] | \n", + "0.00 | \n", + "
| 848 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "term-GO:0007212-0 | \n", + "[[g protein-coupled receptor binding activity, GO:0003924, enzyme binding activity, GO:0042803, signaling receptor binding activity, GO:0004016, g-protein beta/gamma-subunit complex binding activity, signaling receptor binding activity, clathrin light chain binding activity, sequence-specific double-stranded dna binding activity, GO:0004672, nf-kappab binding activity, protein kinase a catalytic subunit binding activity, GO:0004674]] | \n", + "[[GO:0007186, GO:0051480, GO:0006357, GO:1901214, GO:0006915, GO:0006171, GO:0006468]] | \n", + "0.00 | \n", + "
| 849 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "term-GO:0007212-1 | \n", + "[[GO:0004672, g-protein activity, g-protein beta/gamma- subunit complex binding activity, atpase binding activity, GO:0004016, protein-folding chaperone binding activity, signal receptor binding activity, GO:0071333, GO:0007165, negative regulation of nf-kappa b transcription factor activity, GO:2000394, GO:0007212, cellular response to prostaglandin e, GO:0007204]] | \n", + "[[GO:0007186, GO:0043087, GO:0060170, GO:0006171, GO:0005783, membrane localization, transcriptional regulation, GO:0007212, GO:0006874, GO:0046039, GO:0098843, protein kinase activity. \\n\\nmechanism:\\nthe g protein-coupled receptor signaling pathway is a general pathway that mediates the effects of hormones, neurotransmitters other extracellular signals in cells across a variety of tissues organs. signaling through gpcrs involves activation of g proteins, which in turn activate or inhibit effector enzymes ion channels. the commonality among these genes is that they are involved in mechanisms of gpcr signaling downstream processes such as regulation of gtpase activity, camp synthesis regulation of calcium ion concentration. the genes may also participate in membrane localization, transcriptional regulation postsynaptic endocytic zone functions. other associated activities]] | \n", + "0.04 | \n", + "
| 850 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "tf-downreg-colorectal-0 | \n", + "[[GO:0003677, GO:0003723, GO:0003682, GO:0008134, GO:0003713, GO:0016564, MESH:M0518050, GO:0019899]] | \n", + "[[transcription activation/repression, GO:0007165, GO:0006351, GO:0007049, MESH:D012319, GO:0003682, GO:0008270, GO:0016575, protein ligase/cofactor binding]] | \n", + "0.06 | \n", + "
| 851 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "tf-downreg-colorectal-1 | \n", + "[[GO:0006351, dna-binding, rna polymerase ii-specific, transcription activator/transcription repressor, cis-regulatory region sequence-specific, GO:0001221, GO:0006355, GO:0006337, GO:0009966]] | \n", + "[[dna-binding transcription, GO:0016563, rna polymerase ii-specific, GO:0016564, positive/negative regulation of transcription, GO:0006351, GO:0010468, nucleic acid binding activity, sequence-specific double-stranded dna binding activity, protein kinase binding activity]] | \n", + "0.12 | \n", + "
| \n", + " | count | \n", + "mean | \n", + "std | \n", + "min | \n", + "25% | \n", + "50% | \n", + "75% | \n", + "max | \n", + "
|---|---|---|---|---|---|---|---|---|
| model | \n", + "\n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " | \n", + " |
| gpt-3.5-turbo | \n", + "426.0 | \n", + "0.14 | \n", + "0.15 | \n", + "0.0 | \n", + "0.0 | \n", + "0.11 | \n", + "0.22 | \n", + "0.8 | \n", + "
| text-davinci-003 | \n", + "426.0 | \n", + "0.06 | \n", + "0.08 | \n", + "0.0 | \n", + "0.0 | \n", + "0.04 | \n", + "0.08 | \n", + "0.5 | \n", + "
| \n", + " | \n", + " | count | \n", + "mean | \n", + "std | \n", + "min | \n", + "max | \n", + "
|---|---|---|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " | \n", + " | \n", + " | \n", + " |
| gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "142.000 | \n", + "0.152 | \n", + "0.143 | \n", + "0.000 | \n", + "0.750 | \n", + "
| no_synopsis | \n", + "142.000 | \n", + "0.123 | \n", + "0.129 | \n", + "0.000 | \n", + "0.500 | \n", + "|
| ontological_synopsis | \n", + "142.000 | \n", + "0.160 | \n", + "0.185 | \n", + "0.000 | \n", + "0.800 | \n", + "|
| text-davinci-003 | \n", + "narrative_synopsis | \n", + "142.000 | \n", + "0.061 | \n", + "0.070 | \n", + "0.000 | \n", + "0.333 | \n", + "
| no_synopsis | \n", + "142.000 | \n", + "0.038 | \n", + "0.052 | \n", + "0.000 | \n", + "0.250 | \n", + "|
| ontological_synopsis | \n", + "142.000 | \n", + "0.084 | \n", + "0.095 | \n", + "0.000 | \n", + "0.500 | \n", + "
| prompt_variant | \n", + "model | \n", + "method | \n", + "geneset | \n", + "v1 | \n", + "v2 | \n", + "sim | \n", + "length_diff | \n", + "
|---|---|---|---|---|---|---|---|
| 0 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "EDS-0 | \n", + "[Summary: Genes involved in connective tissue disorders, specifically Ehlers-Danlos syndrome, are enriched for terms related to collagen and extracellular matrix organization.\\nMechanism: The genes encode proteins that play roles in collagen synthesis, modification, and organization, as well as extracellular matrix maturation.\\n] | \n", + "[Summary: Genes associated with connective tissue disorder Ehlers-Danlos syndrome.\\nMechanism: Collagen synthesis and matrix maturation.\\n\\nHypothesis: The enriched terms suggest that Ehlers-Danlos syndrome is caused by disruptions in collagen synthesis and the maturation of matrix organization. The genes identified appear to play critical roles in these processes, including collagen synthesis, extracellular matrix organization, and proteolytic subunits and serine proteases that may degrade or modify collagen fibers. Additionally, the presence of sulfotransferases and zinc finger proteins may suggest additional regulatory pathways for collagen synthesis and modification. The disruption of these pathways likely leads to reduced collagen strength and increased tissue laxity, two key hallmarks of Ehlers-Danlos syndrome.] | \n", + "0.97 | \n", + "498 | \n", + "
| 1 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "EDS-1 | \n", + "[Summary: Several of the genes listed are involved in the biosynthesis and regulation of collagen, a key component of connective tissue. Mutations in these genes are associated with Ehlers-Danlos syndrome, a group of genetic disorders that affect collagen production and cause hypermobility of joints, skin elasticity, and tissue fragility.\\n\\nMechanism: The genes listed are involved in collagen biosynthesis and regulation, suggesting that deficiencies or mutations in these genes could lead to abnormal or insufficient collagen production, ultimately resulting in connective tissue disorders such as Ehlers-Danlos syndrome.\\n\\n\\nHypothesis: The genes listed may converge on a pathway that regulates the synthesis, assembly, and remodeling of the extracellular matrix, particularly with respect to collagen and other fibrillar components. Defects or deficiencies in this pathway could lead to dysregulation of tissue remodeling and repair, resulting in connective tissue disorders such as Ehlers-Danlos syndrome.] | \n", + "[Summary: Genes associated with Ehlers-Danlos syndrome (EDS) are involved in the biosynthesis, assembly, and organization of collagen and extracellular matrix, as well as immune response and protein folding.\\n\\nMechanism: The genes identified are involved in the process of collagen biosynthesis and assembly, including post-translational modifications such as lysyl hydroxylation and glycosylation. Disruptions in these processes can lead to the connective tissue disorder Ehlers-Danlos syndrome. \\n\\n] | \n", + "0.95 | \n", + "512 | \n", + "
| 2 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "FA-0 | \n", + "[Summary: Genes related to the Fanconi anemia complementation group and other DNA repair components\\nMechanism: DNA repair \\n] | \n", + "[Summary: The common function of the listed genes is DNA damage repair and maintenance of genome stability, particularly through homologous recombination and the Fanconi anemia pathway.\\nMechanism: The genes share a role in maintaining genomic integrity and preventing the onset of cancer through coordinated DNA repair functions.\\n] | \n", + "0.91 | \n", + "207 | \n", + "
| 3 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "FA-1 | \n", + "[Summary: The genes in this list are predominantly involved in DNA repair, specifically in the Fanconi anemia (FA) pathway and homologous recombination (HR) pathway. \\n\\nMechanism: The FA pathway is a complex pathway involved in the repair of DNA interstrand crosslinks and other forms of DNA damage. The HR pathway is involved in the repair of double-strand breaks in DNA.\\n\\n] | \n", + "[Summary: The enriched terms are related to DNA repair and maintenance of genome stability.\\n\\n\\nHypothesis: Mutations or dysregulation in these genes may lead to a higher susceptibility to DNA damage, defects in DNA repair, and could potentially lead to tumorigenesis. They may also be potential targets for therapeutic intervention in certain cancers.] | \n", + "0.85 | \n", + "22 | \n", + "
| 4 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ADIPOGENESIS-0 | \n", + "[Summary: Genes involved in energy metabolism and mitochondrial function are over-represented.\\n\\nMechanism: These genes likely play a role in regulating cellular energy metabolism, particularly through mitochondrial function.\\n\\n] | \n", + "[Summary: Genes involved in mitochondrial function and metabolism are enriched.\\n\\nMechanism: These genes are involved in various metabolic and mitochondrial processes, including fatty acid metabolism, electron transport chain function, and redox reactions. The common theme among these functions is energy production and regulation within the mitochondria.\\n\\n] | \n", + "0.95 | \n", + "131 | \n", + "
| 5 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ADIPOGENESIS-1 | \n", + "[Summary: Many of the genes in the list are involved in mitochondrial function, specifically in the respiratory chain and energy production. Other common functions include lipid metabolism and transport, protein binding, and regulation of cell growth and division.\\n\\n\\nHypothesis: These genes may be involved in maintaining cell and mitochondrial function, particularly in energy production and membrane transport. Many are also involved in regulating oxidative stress, which can damage cells and contribute to a range of diseases. Overall, the commonalities suggest that these genes play important roles in maintaining cellular and mitochondrial health, and dysregulation of these genes may contribute to metabolic disorders, neurodegenerative diseases, and other health problems.] | \n", + "[Summary: Many of the genes in this list are involved in mitochondrial function and energy metabolism, specifically in processes related to lipid metabolism and the electron transport chain. \\n\\n] | \n", + "0.95 | \n", + "587 | \n", + "
| 6 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[Summary: Immune response and cytokine signaling pathways are enriched in this set of genes.\\nMechanism: These genes are involved in the regulation of immune response and activation of cytokine signaling pathways.\\n] | \n", + "[Summary: Immune system function and cytokine signaling\\nMechanism: Immune response and cytokine pathways\\n\\nHypothesis: The overrepresented terms suggest that these genes play a role in the immune system function and cytokine signaling. This could involve the activation of T cells, leukocyte migration, and cytokine production to regulate the immune response and fight against pathogens. The cytokine pathways produced by these genes could also influence T cell differentiation and antigen processing/presentation via MHC class II, leading to the production of interleukin-2 and interferon-gamma. The chemokine-mediated signaling pathway could also play a role in leukocyte migration and immune response activation.] | \n", + "0.94 | \n", + "502 | \n", + "
| 7 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[Summary: Immune response and cytokine signaling\\nMechanism: Regulation of immune response through cytokine signaling pathways\\n\\nHypothesis: The enriched terms all relate to the regulation of immune response through cytokine signaling pathways. The genes in this list are involved in the production and function of chemokines and cytokines, which play key roles in immune system communication and response. Toll-like receptors, interferon signaling, and TNF signaling pathways are important components of the innate immune response, while TGF-beta signaling plays a role in immune tolerance and regulation. Overall, this gene list suggests a strong focus on immune response and regulation.] | \n", + "[Summary: The common function of the genes listed is related to the immune system, specifically cytokine signaling, chemotaxis, and antigen presentation.\\nMechanism: The genes are involved in various aspects of immune response, including the production and signaling of cytokines, chemotaxis of immune cells, and antigen presentation to T cells.\\n] | \n", + "0.90 | \n", + "343 | \n", + "
| 8 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[Summary: Signal transduction and cellular metabolism\\n\\nHypothesis: These genes may be involved in a signaling pathway that regulates cellular metabolism in response to extracellular signals. They may work together to modulate the activity of various enzymes and transporters, leading to changes in the levels of key metabolic intermediates and ultimately contributing to the regulation of cellular metabolism.] | \n", + "[Summary: Genes involved in various aspects of cellular processes, including transport, metabolism, cytoskeleton organization, and signaling pathways, are over-represented.\\n\\nMechanism: These genes are involved in diverse biological pathways, and thus do not share a single common mechanism.\\n\\n] | \n", + "0.89 | \n", + "118 | \n", + "
| 9 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[Summary: Protein regulation and cellular signaling pathways\\nMechanism: Enzyme-catalyzed reactions and protein-protein interactions\\n] | \n", + "[Summary: Regulation of protein activity, transport, and metabolism\\nMechanism:hypothesize that these genes are involved in regulating protein activity, transport, and metabolism through various processes such as binding to regulatory subunits, transcribing DNA, catalyzing enzymatic reactions, and transporting molecules across cellular membranes.\\n] | \n", + "0.87 | \n", + "216 | \n", + "
| 10 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ANGIOGENESIS-0 | \n", + "[Summary: Extracellular matrix proteins and signaling molecules are enriched among the listed genes.\\nMechanism: These genes may be involved in the regulation of tissue development and regeneration, as well as cell growth, migration, and adhesion. \\n] | \n", + "[Summary: Extracellular matrix organization and cellular adhesion\\nMechanism: Extracellular matrix synthesis and remodeling by integrins and proteoglycans\\n] | \n", + "0.88 | \n", + "94 | \n", + "
| 11 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ANGIOGENESIS-1 | \n", + "[Summary: Extracellular matrix (ECM) organization and cell adhesion/migration are enriched functions among the listed genes.\\nMechanism: The listed genes are involved in regulating ECM integrity and cell adhesion/migration, which are critical processes in development and tissue homeostasis. Dysregulation of these processes can contribute to pathogenesis of a variety of diseases, including cancer.\\n] | \n", + "[Summary: Extracellular matrix organization and cell adhesion\\n\\nHypothesis: These genes may be involved in the regulation of tissue remodeling and repair, as well as in the maintenance of cell integrity and differentiation. Dysregulation of these genes could potentially lead to pathological processes such as fibrosis or cancer metastasis.] | \n", + "0.93 | \n", + "59 | \n", + "
| 12 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-0 | \n", + "[Summary: Genes involved in cytoskeleton organization, cell adhesion, and signal transduction.\\nMechanism: These genes likely play a role in the maintenance of cellular morphology, adhesion, and proper communication between cells.\\n] | \n", + "[Summary: Genes involved in cell adhesion and cytoskeletal organization are enriched.\\n\\nMechanism: These genes are involved in the organization and regulation of cellular structures such as the cytoskeleton, focal adhesions, and tight junctions, which are critical for cell adhesion and migration.\\n\\n] | \n", + "0.94 | \n", + "68 | \n", + "
| 13 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-1 | \n", + "[Summary: Genes involved in cell adhesion, specifically with roles in tight junction formation and maintenance, as well as extracellular matrix interactions.\\n\\nMechanism: These genes are involved in various molecular mechanisms related to cell adhesion, including tight junction formation/maintenance, extracellular matrix interactions and basement membrane organization.\\n\\n] | \n", + "[Summary: Cell adhesion and signaling\\nMechanism: Tight junction formation\\n\\nHypothesis: The genes in this list all play a role in cell adhesion and signaling, with a particular focus on the formation of tight junctions. Tight junctions represent a mode of cell-to-cell adhesion in epithelial or endothelial cells and are crucial for the maintenance of cellular polarity and barrier function. The enriched terms suggest that the genes in this list are involved in various signaling pathways, including those mediated by cadherins, integrins, GPCRs, and PTKs. They also regulate the actin cytoskeleton and ECM, which are important for cell adhesion and migration. Furthermore, the involvement of PI3K, MAPK, and TGF-beta signaling pathways indicates that these genes likely play a] | \n", + "0.93 | \n", + "406 | \n", + "
| 14 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_SURFACE-0 | \n", + "[Summary: This list includes genes with diverse functions such as cell signaling, growth inhibition, and ion transport. However, common enriched terms suggest involvement in cell adhesion and regulation.\\nMechanism: The genes appear to be involved in molecular networks responsible for the regulation and maintenance of the cell membrane, particularly in receptor-mediated cell signaling and cell adhesion.\\n] | \n", + "[Summary: Membrane-bound proteins involved in signal transduction and cell adhesion\\n\\n] | \n", + "0.88 | \n", + "321 | \n", + "
| 15 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_SURFACE-1 | \n", + "[Summary: Cell adhesion and signaling pathways are enriched among the given set of human genes.\\n\\nMechanism: The enriched genes are involved in various processes, including transport, development, and regulation of the immune system, and these processes are intertwined in signaling pathways that affect cell adhesion.\\n\\n] | \n", + "[Summary: Cell surface proteins and membrane transporters involved in various cellular processes, including cell adhesion, signal transduction, and ion transport.\\n\\nMechanism: These gene products are involved in the regulation of cellular functions at the cell membrane and play a critical role in maintaining proper cellular signaling and transport mechanisms.\\n\\n] | \n", + "0.90 | \n", + "43 | \n", + "
| 16 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_APOPTOSIS-0 | \n", + "[Summary: Apoptotic processes and regulation of cell death are enriched terms in the gene list.\\n\\n] | \n", + "[Summary: Apoptosis, cell death, and signaling pathways are enriched terms in these genes.\\nMechanism: The genes are involved in regulating various aspects of apoptosis and cell death, as well as signaling pathways that control these processes.\\n] | \n", + "0.93 | \n", + "147 | \n", + "
| 17 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_APOPTOSIS-1 | \n", + "[Summary: Genes involved in apoptosis, cytokine signaling, and growth factor regulation.\\n\\nMechanism: These genes all play a role in regulating cell survival and growth, primarily through apoptosis, cytokine signaling, and growth factor regulation.\\n\\n] | \n", + "[Summary: Apoptosis and cell death related genes.\\n\\nMechanism: Activation of caspases, which are a family of cysteine-aspartic acid proteases that play a central role in executing apoptosis.\\n\\n\\nHypothesis: These genes are involved in the regulation and execution of apoptotic pathways, which play an important role in development, tissue homeostasis and elimination of damaged cells. The activation of caspases leads to the cleavage of a variety of structural and regulatory proteins, resulting in cytoskeletal rearrangements, DNA fragmentation, and ultimately, cell death. The over-representation of terms related to caspase activity and apoptosis regulation suggests that these genes are strongly linked to this biological process.] | \n", + "0.91 | \n", + "483 | \n", + "
| 18 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[Summary: Membrane-associated proteins that are members of the superfamily of ATP-binding cassette (ABC) transporters, as well as enzymes involved in lipid metabolism, are over-represented in this gene list. \\n\\nMechanism: Several of the enriched terms relate to lipid metabolism, suggesting that these genes may be involved in the transport or regulation of various lipids within the body. \\n\\n] | \n", + "[Summary: Transport and metabolism of lipids and cholesterol\\nMechanism: ABC transporters and cytochrome P450 enzymes play a key role in the transport and metabolism of lipids and cholesterol.\\n] | \n", + "0.88 | \n", + "199 | \n", + "
| 19 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[Summary: Peroxisomal biogenesis and lipid metabolism are enriched functions among the given genes.\\nMechanism: Peroxins (PEXs) are essential proteins for functional peroxisome assembly. Peroxisomes are organelles involved in lipid metabolism, fatty acid beta-oxidation, and bile acid synthesis.\\n\\n] | \n", + "[Summary: Peroxisome biogenesis and lipid metabolism are enriched functions among the listed genes.\\n\\n\\nHypothesis: It is possible that dysregulation of these genes could lead to metabolic disorders such as peroxisome biogenesis disorders or abnormal cholesterol and fatty acid metabolism. Further research is needed to fully understand the underlying biological mechanisms and potential clinical implications of these enriched functions.] | \n", + "0.95 | \n", + "141 | \n", + "
| 20 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[Summary: Lipid metabolism and cholesterol homeostasis are over-represented functions amongst the list of genes.\\n\\nMechanism: These genes are involved in the regulation of cholesterol levels in cells, lipid metabolism and transport of various molecules across cell membranes. \\n\\n] | \n", + "[Summary: Genes involved in lipid metabolism, transport, and synthesis are enriched.\\nMechanism: Lipids are essential components of cellular structure, energy storage, and signaling. These genes contribute to the regulation of lipid metabolism and transport, as well as the synthesis of lipids necessary for these processes.\\n] | \n", + "0.94 | \n", + "47 | \n", + "
| 21 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[Summary: Genes involved in cholesterol biosynthesis, lipid metabolism, and signal transduction.\\nMechanism: Biosynthesis and regulation of cholesterol and lipids.\\n\\nHypothesis: These genes are involved in the complex pathways of cholesterol biosynthesis and lipid metabolism, which are tightly regulated processes where disturbances can lead to a wide range of diseases. The genes identified here may play key roles in these pathways, including enzymes involved in the conversion of mevalonate to cholesterol, fatty acid desaturases regulating lipid unsaturation, and phospholipid-binding proteins regulating signal transduction. Further research into these mechanisms could aid in the development of therapies for metabolic disorders such as atherosclerosis and hyperlipidemia.] | \n", + "[Summary: Cholesterol biosynthesis and metabolism\\nMechanism: Regulation of cholesterol levels via enzymatic activity\\n\\nHypothesis: The enriched terms suggest a common biological mechanism involving the regulation of cholesterol levels and metabolism through various enzymatic pathways, including those responsible for cholesterol biosynthesis, phospholipid metabolism, fatty acid biosynthesis, and sterol metabolism. The genes in this list likely play a role in maintaining proper cholesterol levels and homeostasis, and dysregulation of these pathways may lead to various diseases such as hypercholesterolemia, atherosclerosis, and other metabolic disorders.] | \n", + "0.93 | \n", + "119 | \n", + "
| 22 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_COAGULATION-0 | \n", + "[Summary: Many of the genes in this list are involved in blood clotting and complement activation, while others are proteases, lipoproteins, or involved in extracellular matrix regulation.\\nMechanism: These genes are involved in regulating or participating in protease activities, blood clotting, and complement activation, as well as extracellular matrix regulation.\\n\\nHypothesis: The enriched terms suggest that these genes may be involved in a regulatory network that balances protease activities, blood clotting, complement activation, and extracellular matrix regulation. Dysregulation of this network may lead to pathologies such as thrombosis, inflammation, and tissue remodeling. The specific biological mechanisms involved can include protease activation and inhibition, substrate recognition, signal transduction, and gene expression regulation.] | \n", + "[Summary: Several genes are involved in blood coagulation, extracellular matrix remodeling, and regulation of the complement pathway. \\nMechanism: These genes are likely involved in various aspects of tissue homeostasis and response to injury, including wound healing and inflammation.\\n] | \n", + "0.94 | \n", + "569 | \n", + "
| 23 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_COAGULATION-1 | \n", + "[Summary: The enriched terms are related to blood coagulation and complement pathway, as well as extracellular matrix degradation and calcium-binding proteins.\\n\\n\\nHypothesis: The coagulation, complement, and extracellular matrix remodelling pathways are interconnected through multiple mechanisms and play crucial roles in maintaining tissue homeostasis and repair. Dysregulation of these pathways is associated with several human diseases, such as thrombosis, autoimmune disorders, and cancer. Calcium ions are essential for mediating] | \n", + "[Summary: Extracellular matrix breakdown, blood coagulation, and protein inhibition are enriched functions shared by these genes.\\nMechanism: These genes are involved in regulating the extracellular matrix, blood coagulation, and protease activity through protein inhibition.\\n] | \n", + "0.88 | \n", + "260 | \n", + "
| 24 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_COMPLEMENT-0 | \n", + "[Summary: Genes enriched in immune system functions and regulation of complement activity.\\n\\nMechanism: These genes are involved in the regulation and function of the immune system and the complement cascade, including regulation of proteolytic enzymes, regulation of cytokine and growth factor signaling, and maintenance of cell surface glycoproteins.\\n\\n] | \n", + "[Summary: Proteases and their inhibitors are enriched among these genes, as well as genes involved in blood clotting and complement activation.\\n\\nMechanism: These genes are involved in proteolytic and inflammatory pathways, including complement activation and blood clotting.\\n\\n] | \n", + "0.91 | \n", + "77 | \n", + "
| 25 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_COMPLEMENT-1 | \n", + "[Summary: Genes involved in inflammation, immunity, and blood coagulation are enriched in this list.\\n\\nMechanism: These genes are involved in various processes related to the regulation of the immune response, blood coagulation, and inflammation. Many of these genes play a role in the complement cascade, cytokine signaling, and protein phosphorylation.\\n\\n] | \n", + "[Summary: Genes involved in regulation of immune response and blood coagulation are statistically over-represented.\\n\\n] | \n", + "0.91 | \n", + "238 | \n", + "
| 26 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_DNA_REPAIR-0 | \n", + "[Summary: Genes involved in DNA repair, transcription initiation, RNA processing, and nucleotide metabolism.\\n\\nMechanism: These genes are all involved in various cellular processes that are crucial for maintaining genomic stability and integrity, including DNA repair, transcription initiation, RNA processing, and nucleotide metabolism. \\n\\n] | \n", + "[Summary: Genes are involved in DNA repair, transcription, and nucleotide metabolism.\\n\\nMechanism: These genes are involved in essential cellular processes, including DNA repair, transcription initiation, and nucleotide metabolism. Many of these genes encode subunits of DNA polymerases or transcription factor complexes. Their shared function in DNA repair may suggest a common biological pathway in maintaining genomic stability.\\n\\n] | \n", + "0.98 | \n", + "93 | \n", + "
| 27 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_DNA_REPAIR-1 | \n", + "[Summary: The enriched terms suggest that these genes are involved in DNA replication, repair, and transcription.\\n\\nMechanism: These genes are involved in various aspects of DNA metabolism, including DNA replication, repair, and transcription. \\n\\n\\nHypothesis: These genes are all involved in fundamental cellular processes in which DNA is duplicated, transcribed, and repaired. They likely work together to ensure the accuracy and stability of genetic information.] | \n", + "[Summary: Genes involved in DNA repair and transcription regulation.\\n\\nMechanism: These genes are all involved in various aspects of DNA repair and transcription regulation, which are essential for maintaining genome stability.\\n\\n] | \n", + "0.92 | \n", + "235 | \n", + "
| 28 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_E2F_TARGETS-0 | \n", + "[Summary: Genes involved in DNA replication, repair, and cell cycle regulation.\\nMechanism: These genes are involved in various stages of DNA replication, repair, and cell cycle regulation, suggesting that they work together to maintain genomic stability and ensure proper cell division.\\n] | \n", + "[Summary: DNA replication and repair\\nMechanism: The genes are involved in DNA replication and repair processes.\\n] | \n", + "0.94 | \n", + "175 | \n", + "
| 29 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_E2F_TARGETS-1 | \n", + "[Summary: DNA replication and repair\\n\\n] | \n", + "[Summary: DNA replication, repair and cell-cycle regulation\\nMechanism: These genes are involved in various aspects of DNA replication, repair and cell-cycle regulation, with some genes directly involved in DNA synthesis and others involved in checkpoint control and regulation of cell division.\\n] | \n", + "0.89 | \n", + "257 | \n", + "
| 30 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[Summary: Extracellular matrix organization and regulation.\\nMechanism: Regulation of extracellular matrix protein expression and function.\\n\\nHypothesis: The enrichment of terms related to extracellular matrix organization and regulation suggests that these genes play a role in maintaining the integrity and function of extracellular matrix components, such as collagen, elastin, and laminin. These proteins provide structure and elasticity to tissues, and the dysregulation of extracellular matrix organization has been linked to a number of pathological conditions, including cancer, cardiovascular disease, and fibrosis. The identified genes likely contribute to the regulation of extracellular matrix protein expression, assembly, and localization, and may represent potential targets for therapeutic intervention in these diseases.] | \n", + "[Summary: Extracellular matrix organization and cell adhesion are the enriched functions of the given gene list.\\nMechanism: Extracellular matrix (ECM) organization, cell adhesion, and related processes are crucial for the development and maintenance of tissue integrity and functionality. These are mediated by interactions between different proteins and cell surface receptors within ECM microenvironments.\\n\\n] | \n", + "0.91 | \n", + "427 | \n", + "
| 31 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[Summary: Extracellular matrix proteins and cytokines are statistically over-represented in these gene functions, as well as proteins involved in collagen binding and actin filament binding.\\n\\nMechanism: These genes may play a role in extracellular matrix organization and remodeling, as well as cell adhesion and migration.\\n\\n] | \n", + "[Summary: Extracellular matrix organization and muscle contraction are enriched functions among these genes.\\nMechanism: These genes are involved in the regulation and maintenance of the extracellular matrix, which is essential for proper tissue and organ function. They also play a role in muscle contraction and cell adhesion.\\n] | \n", + "0.92 | \n", + "3 | \n", + "
| 32 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[Summary: Membrane-associated proteins, enzymes and transcription factors are enriched in the gene list.\\n\\nMechanism: The enriched terms suggest these genes play a role in membrane-associated processes, enzymatic activity, and transcriptional regulation, potentially related to cellular signaling and development.\\n\\n] | \n", + "[Summary: Transport and binding proteins; enzymes; membrane-associated proteins; transcriptional regulators; receptors; cytoskeletal proteins.\\nMechanism: These genes are involved in intracellular transport and binding, metabolism, gene regulation, cellular signaling, and structural support of cells and tissues.\\n\\n] | \n", + "0.90 | \n", + "0 | \n", + "
| 33 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[Summary: Membrane transport and cell signaling.\\nMechanism: These genes are involved in membrane transport and cell signaling pathways. They enable processes such as L-leucine transmembrane transporter activity, sodium/hydrogen exchanger regulatory cofactor, and cytokine and growth factor signaling.\\n\\n] | \n", + "[Summary: Transport and metabolism of fatty acids, regulation of gene expression \\nMechanism: Fatty acid transport and lipid metabolism \\n] | \n", + "0.86 | \n", + "166 | \n", + "
| 34 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[Summary: Membrane-associated proteins, enzymes involved in metabolic processes, and transcriptional regulators are enriched in these gene functions.\\nMechanism: The enriched gene functions suggest a role in cellular metabolism and regulation of gene expression.\\n] | \n", + "[Summary: This list of genes is enriched for terms related to cell signaling, protein binding, and post-translational modifications.\\n\\n\\nHypothesis: These genes are involved in a network of signaling pathways, including protein-protein interactions and post-translational modifications, that regulate cell proliferation, differentiation, and apoptosis. These pathways are likely to involve a wide range of signaling molecules, including kinases, transcription factors, and cytoplasmic regulators. The enrichment of terms related to protein binding and enzyme activity suggests that many of these pathways involve the coordinated action of multiple proteins and their interactions with other regulatory molecules. Further studies will be needed to elucidate the specific pathways that link these genes and their functions.] | \n", + "0.90 | \n", + "558 | \n", + "
| 35 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[Summary: Many of these genes are involved in cellular processes such as protein binding, catalytic activity, and regulation of transcription.\\nMechanism: The enriched terms suggest a role in cellular signaling pathways such as cytokine signaling and regulation of cell growth and differentiation.\\n\\n] | \n", + "[Summary: This list of human genes has commonalities in their involvement in protein and enzyme regulation, as well as cellular transport mechanisms.\\n\\nMechanism: Protein regulation; enzyme regulation; cellular transport mechanisms\\n\\n] | \n", + "0.90 | \n", + "66 | \n", + "
| 36 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[Summary: Genes involved in metabolism and enzyme function are statistically over-represented.\\nMechanism: Enzymes involved in metabolism are crucial for cellular function and maintaining homeostasis. \\n\\n] | \n", + "[Summary: Genes involved in energy metabolism and oxidative stress response.\\n\\nMechanism: These genes are involved in catabolic pathways for the breakdown of fatty acids, amino acids, and carbohydrates to produce energy. They also play a role in the response to oxidative stress, which can result from an imbalance between the production of reactive oxygen species (ROS) and the body's ability to detoxify them.\\n\\n] | \n", + "0.88 | \n", + "210 | \n", + "
| 37 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[Summary: These genes are involved in various metabolic processes, including fatty acid metabolism, oxidation-reduction reactions, and energy production. \\n\\nMechanism: It is hypothesized that these genes are involved in maintaining cellular homeostasis by regulating metabolic processes and energy production.\\n\\n] | \n", + "[Summary: Genes involved in various metabolic processes, including fatty acid metabolism and energy production, are enriched.\\n\\nMechanism: The enrichment of metabolic processes reflects the crucial importance of these genes in maintaining energy balance and metabolic homeostasis in the body.\\n\\n] | \n", + "0.94 | \n", + "17 | \n", + "
| 38 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-0 | \n", + "[Summary: Cell division and DNA repair processes are enriched among the listed genes.\\n\\nMechanism: The genes listed are involved in various aspects of cell division including DNA replication, chromosome segregation, and cytokinesis. \\n\\n] | \n", + "[Summary: Cell cycle regulation and DNA replication are enriched functions among the listed human genes.\\nMechanism: These genes are involved in processes involved in cell division, DNA replication, and DNA repair.\\n] | \n", + "0.94 | \n", + "20 | \n", + "
| 39 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-1 | \n", + "[Summary: Chromosome segregation and DNA replication machinery\\nMechanism: Regulation of cell cycle and DNA replication\\n\\nHypothesis: The enriched terms suggest that these genes play a role in the regulation of the cell cycle, specifically in DNA replication initiation, chromosome segregation, mitotic spindle organization, and cell cycle checkpoint control. The mechanism underlying the common function of these genes could be the assembly of protein-DNA complexes required for the progression of the cell cycle and proper segregation of chromosomes during cell division. Dysfunction in these processes can lead to genomic instability and contribute to the development of cancer.] | \n", + "[Summary: Gene functions are involved in DNA replication, cell cycle regulation, and DNA repair.\\n\\nMechanism: These genes are involved in various stages of cell division, including DNA replication, chromosome segregation, and cytokinesis.\\n\\n] | \n", + "0.91 | \n", + "441 | \n", + "
| 40 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_GLYCOLYSIS-0 | \n", + "[Summary: Enzyme activity involved in carbohydrate metabolism and glycosylation processes.\\n\\nMechanism: Enzymatic reactions involved in the breakdown and synthesis of carbohydrates, as well as the addition of sugar groups to proteins and lipids.\\n\\n\\nHypothesis: The enriched terms suggest that these genes are involved in a wide range of metabolic processes related to carbohydrate and sugar metabolism. This may involve the breakdown of sugars for energy production, as well as the synthesis and modification of sugar molecules for use in various cellular processes. These processes likely involve multiple pathways, including the pentose phosphate pathway, glycolysis, and various UDP-sugar biosynthetic pathways.] | \n", + "[Summary: Glycolysis pathway and carbohydrate metabolism are enriched terms among the listed genes.\\n\\nMechanism: The listed genes are involved in glucose metabolism, glycolysis, and carbohydrate metabolism. They encode enzymes such as phosphoglycerate mutase (PGAM), phosphomannose isomerase (MPI), glucose-6-phosphate dehydrogenase (G6PD), hexokinases (HK2), aldolases (ALDOA, ALDOB), and glycogen debrancher enzyme (AGL).\\n\\n\\nHypothesis: The enriched terms suggest a possible link between the listed genes and the glycolysis pathway, which is a central metabolic pathway in energy production. The genes encode enzymes that are involved in the conversion of glucose into pyruvate, which is further metabolized in the Krebs cycle. Dysfunction in these genes may lead to alterations in glucose metabolism and contribute to metabolic disorders such as diabetes and glycogen storage diseases.] | \n", + "0.93 | \n", + "174 | \n", + "
| 41 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_GLYCOLYSIS-1 | \n", + "[Summary: Glycolysis, carbohydrate metabolism, and signaling pathways are significantly enriched functions in this set of genes.\\nMechanism: These genes are involved in glucose metabolism and signaling pathways, which regulate cellular responses to stress and energy levels.\\n\\nHypothesis: The majority of these genes are associated with glycolysis, carbohydrate metabolism, and signaling pathways, which are central metabolic processes that regulate cellular energy levels and responses to stress. Many of these genes are likely to be involved in glucose transport, which plays an essential role in maintaining cellular energy balance. Additionally, some of these genes are involved in cellular responses to stress, suggesting that altered glucose metabolism could contribute to stress-related disorders.] | \n", + "[Summary: Genes involved in various metabolic processes and enzymatic activity are enriched in this list.\\n\\nMechanism: The enriched terms suggest a commonality in metabolic pathways and enzymatic activity.\\n\\n] | \n", + "0.89 | \n", + "597 | \n", + "
| 42 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[Summary: Neural development and signaling pathway regulation\\nMechanism: These genes are involved in various aspects of neural development and signaling pathways, including axon guidance, cell adhesion, cell communication, and transcriptional regulation.\\n] | \n", + "[Summary: Cell signaling and neuronal development\\nMechanism: Mediation of cell-cell communication and regulation of intracellular signaling pathways\\n\\nHypothesis: The enriched terms suggest that these genes play important roles in the regulation of cell-cell communication and intracellular signaling pathways, particularly those involved in neuronal development and angiogenesis. These processes involve the regulation of cell adhesion, migration, growth cone collapse, and the activation of cytokine receptors. Transcriptional regulation is also likely to play a role in the mediation of these processes.] | \n", + "0.93 | \n", + "351 | \n", + "
| 43 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[Summary: Neuronal development and signaling\\n\\nHypothesis: These genes may be part of a broader signaling pathway that regulates neuronal development and communication, possibly involving other signaling molecules and pathways such as Wnt and Notch signaling. Further investigation into the interactions and regulation of these genes may provide insights into neural disorders and conditions.] | \n", + "[Summary: Cell signaling and adhesion\\nMechanism: Regulation of cell adhesion and signaling pathways\\n] | \n", + "0.83 | \n", + "292 | \n", + "
| 44 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_HEME_METABOLISM-0 | \n", + "[Summary: Several of the enriched terms relate to the regulation of gene expression and protein turnover, as well as ion transport and membrane organization.\\n\\nMechanism: The shared biological mechanism may involve the regulation and modulation of cellular processes through the transport of ions and proteins across membranes, as well as the turnover of proteins and regulation of gene expression.\\n\\n] | \n", + "[Summary: Transport and binding processes\\nMechanism: ATP binding and membrane transport\\n] | \n", + "0.85 | \n", + "311 | \n", + "
| 45 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_HEME_METABOLISM-1 | \n", + "[Summary: Transport; Metabolism; Binding Activity\\nMechanism: Not enough information to form a hypothesis \\n] | \n", + "[Summary: Enriched terms are related to transport, binding activity, and regulation of gene expression.\\nMechanism: These genes likely function in cellular transport and molecular binding, with a potential role in gene expression regulation.\\n\\n] | \n", + "0.84 | \n", + "136 | \n", + "
| 46 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_HYPOXIA-0 | \n", + "[Summary: Glycolysis-related genes are enriched \\n\\nMechanism: Glycolysis regulation\\n\\n] | \n", + "[Summary: Glycolysis, glucose metabolism, protein binding, transcription regulation\\n\\nMechanism: It appears that many of these genes are involved in processes related to glycolysis and glucose metabolism. Additionally, a number of these genes have protein binding functions, which suggests that they may be involved in complex regulatory pathways controlling glucose metabolism and other cellular processes. Finally, several of these genes are involved in transcription regulation, suggesting that they may play a role in modulating the expression of other genes involved in glucose metabolism.\\n\\n\\n] | \n", + "0.91 | \n", + "512 | \n", + "
| 47 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_HYPOXIA-1 | \n", + "[Summary: Genes are involved in glucose metabolism, cell cycle regulation, and transcriptional activities.\\n\\nMechanism: The common mechanism seems to be the regulation of glucose metabolism, possibly through the insulin signaling pathway and its downstream effectors. There may also be an involvement in cell cycle regulation and transcriptional activities.\\n\\n] | \n", + "[Summary: Genes involved in metabolism, cell cycle regulation, and signal transduction are enriched.\\nMechanism: These genes likely contribute to the regulation of cellular processes that involve energy metabolism and promoting cell growth and differentiation.\\n] | \n", + "0.92 | \n", + "98 | \n", + "
| 48 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[Summary: Immune response regulation\\nMechanism: Modulation of cytokine signaling pathways\\n] | \n", + "[Summary: The enriched terms relate to the regulation and signaling of immune system processes and inflammation.\\nMechanism: The genes are involved in the pathways related to immune system response and inflammation, specifically, cytokine signaling, T-cell and B-cell activation, and leukocyte-endothelial interactions.\\n] | \n", + "0.87 | \n", + "229 | \n", + "
| 49 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[Summary: Immune system response and regulation\\n\\n] | \n", + "[Summary: Immune system function, cytokine receptors, and cell surface adhesion molecules are enriched among these genes.\\n\\nMechanism: These genes are involved in the regulation of immune system function, including the response to pathogens and inflammation. Many of the enriched terms involve cytokine receptors and cell surface adhesion molecules, indicating that these genes play a role in cell signaling and communication.\\n\\n] | \n", + "0.84 | \n", + "378 | \n", + "
| 50 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[Summary: Cytokine receptors and signaling pathway genes\\n\\n] | \n", + "[Summary: The enriched terms relate to cytokine signaling, immune response, and cell adhesion and migration.\\n\\nMechanism: The genes are involved in cytokine signaling pathways and immune response, regulating the production and differentiation of various cells, particularly macrophages and lymphocytes.\\n\\n] | \n", + "0.89 | \n", + "245 | \n", + "
| 51 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[Summary: Regulation of immune response and cytokine signaling\\n\\nHypothesis: These genes may contribute to the regulation and promotion of immune response and cytokine signaling, potentially through the binding and activation of cytokine receptors and downstream signaling pathways.] | \n", + "[Summary: Immune response-related genes\\nMechanism: Immune response and cytokine signaling pathway\\n] | \n", + "0.92 | \n", + "184 | \n", + "
| 52 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[Summary: Immune and inflammatory response genes\\nMechanism: Immune activation and inflammation\\n] | \n", + "[Summary: Immune system function\\n\\nHypothesis: These genes are involved in regulating immune system function, specifically in the release and detection of cytokines and chemokines, as well as the migration of leukocytes in response to inflammation. They may be part of a larger pathway involved in coordinating the immune response to invading pathogens.] | \n", + "0.89 | \n", + "258 | \n", + "
| 53 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[Summary: The enriched terms suggest that these genes are involved in immune responses and inflammation, mediated by cytokines, chemokines, and receptors.\\n\\nMechanism: The underlying biological mechanism is likely related to the response of immune cells to infection or injury, leading to the production of cytokines and chemokines that recruit more immune cells to the site.\\n\\n\\nHypothesis: These genes are likely involved in regulating immune responses and inflammation, particularly in response to infection or cellular damage. The cytokines and chemokines produced by these genes may recruit immune cells to the site of infection or injury, amplifying the immune response. The receptors encoded by these genes may play a role in regulating the activation and migration of immune cells. Dysfunction or dysregulation of these genes may contribute to chronic inflammatory diseases] | \n", + "[Summary: Receptor and chemokine-related functions are statistically enriched in this gene list.\\nMechanism: These genes may be involved in immune system regulation and cellular signaling pathways, such as G protein-coupled receptor signaling.\\n] | \n", + "0.92 | \n", + "636 | \n", + "
| 54 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[Summary: The enriched terms suggest that these genes are involved in immune response and antiviral defense. \\n\\nMechanism: These genes likely play a role in the innate immune response to viral infection and may also regulate cell proliferation and differentiation.\\n\\n] | \n", + "[Summary: Immune response and antiviral function\\n] | \n", + "0.88 | \n", + "216 | \n", + "
| 55 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[Summary: The enriched terms suggest that these genes are involved in the immune system response, particularly in the regulation of interferon and cytokine signaling pathways.\\n\\nMechanism: The mechanism underlying the common functions of these genes involves the regulation of the innate and acquired immune responses through the interferon and cytokine signaling pathways, particularly in response to viral infection.\\n\\n] | \n", + "[Summary: Innate immune response and antiviral activity\\n\\nHypothesis: These genes work together to inhibit viral replication and spread by triggering the production and release of interferons, activating innate immune cells, and promoting the degradation of viral components through the proteasome. Through the regulation of cytokine signaling and antigen processing, these genes may also contribute to the adaptive immune response and the development of immunity to viral infection.] | \n", + "0.91 | \n", + "64 | \n", + "
| 56 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[Summary: Immune response regulation\\nMechanism: Up-regulation of interferon signaling pathways\\n] | \n", + "[Summary: Immune response and cytokine signaling pathways are enriched in the list of genes.\\n\\nMechanism: The genes in the list are involved in immune response and cytokine signaling pathways. They play a role in cytokine-mediated signaling pathways, chemokine signaling pathways, and antigen processing and presentation.\\n\\n\\nHypothesis: The genes in the list are primarily involved in regulating the immune response and cytokine signaling pathways. This suggests that they play a key role in the body's ability to recognize and respond to pathogens and other foreign invaders. Dysfunction of these genes may therefore lead to an increased susceptibility to infections and other immune-related disorders.] | \n", + "0.86 | \n", + "607 | \n", + "
| 57 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[Summary: Genes involved in immune response and protein degradation pathways are enriched.\\n\\nMechanism: These genes are involved in regulating the immune response through cytokine signaling and intracellular viral RNA sensing. They also play a role in protein degradation pathways through the proteasome and ubiquitin system.\\n\\n] | \n", + "[Summary: The enriched terms among these genes relate to immune response, specifically innate immune response and antiviral response. \\n\\n\\nHypothesis: These genes are involved in innate immune response and antiviral response, indicating a potential regulatory pathway for immune function in response to viral infection. The enrichment of cytokine activity and regulation of cytokine production suggests that this pathway involves the production of various cytokines involved in immune response, including interferons. The enrichment of positive regulation of type I interferon production and type I interferon signaling pathway further supports this hypothesis.] | \n", + "0.92 | \n", + "334 | \n", + "
| 58 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[Summary: Calcium ion binding\\nMechanism: Calcium signaling pathway\\n\\nHypothesis: Many of the genes listed encode proteins that bind to calcium ions and act in signaling pathways related to calcium. These proteins are involved in various processes such as transmembrane transport, cell adhesion, protein kinase activity, and G protein-coupled receptor signaling. The enrichment of these terms suggests that calcium signaling is a crucial mechanism that regulates diverse cellular processes such as energy metabolism, cell growth and proliferation, and gene expression.] | \n", + "[Summary: Calcium ion binding and transport\\nMechanism: Calcium signaling and regulation\\n\\nHypothesis: These genes are all involved in regulating calcium ion binding and transport, suggesting a potential role in calcium-mediated signaling. This may be related to a variety of biological processes, including muscle contraction, nervous system function, and cellular signaling pathways. The enriched terms suggest that calcium ion binding and transport plays a crucial role in many of these processes, potentially through the regulation of ion channels, transporters, and other calcium-dependent proteins.] | \n", + "0.96 | \n", + "36 | \n", + "
| 59 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[Summary: Many of the genes in this list are involved in various aspects of cell signaling and regulation, including cytokine signaling (IFNG, IL12B), G-protein coupled receptor signaling (ADRA2C, SST4, HTR1B, GPR19), and calcium signaling (CACNG1, STAG3, EFHD1). Additionally, there are several genes related to protein metabolism and processing (CLPS, CPB1, NUDT11, CELSR2, SLC38A3).\\n\\n\\nHypothesis: The common theme among these genes is their involvement in intracellular signaling pathways involved in maintaining cellular homeostasis. These pathways may interact with each other, creating a complex network of interactions that allow cells to adapt and respond to various stimuli. Additionally, the regulation of protein metabolism and processing is likely important for maintaining proper protein function and stability within the cell. Overall, these processes likely contribute to proper cell function and survival.] | \n", + "[Summary: Calcium ion binding activity, cellular response to protein stimulus, negative regulation of apoptotic process.\\nMechanism: Calcium signaling pathway and regulation of apoptosis.\\n] | \n", + "0.83 | \n", + "735 | \n", + "
| 60 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[Summary: Several enriched terms relate to signal transduction and regulation of various cellular processes.\\n\\nMechanism: The genes in this list are involved in various aspects of cellular signaling, including cytokine signaling, receptor activity, and kinase activity. They also play roles in regulating processes such as transcription, protein degradation, and cell migration.\\n\\n] | \n", + "[Summary: Membrane-associated proteins and enzymes involved in various cellular processes.\\nMechanism: Membrane-associated and signaling pathways.\\n] | \n", + "0.87 | \n", + "233 | \n", + "
| 61 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[Summary: Signaling and regulation of various biological processes, including coagulation, cytokine activity, extracellular matrix, and ion channels.\\n\\n] | \n", + "[Summary: Cell signaling and regulation through cytokines, growth factors, and enzymes involved in coagulation and complement activation.\\nMechanism: Activation and regulation of cellular pathways through ligand-receptor interaction and enzymatic activity.\\n\\nHypothesis: These genes are involved in mediating cellular responses to external stimuli, including tissue damage and immune responses. Cytokine and growth factor signaling pathways activate cellular responses such as proliferation, differentiation, and migration. Enzymes involved in coagulation and complement activation play critical roles in host defense and tissue repair. The common mechanism underlying these functions is the activation and regulation of cellular pathways through ligand-receptor interaction and enzymatic activity.] | \n", + "0.90 | \n", + "646 | \n", + "
| 62 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[Summary: These genes are involved in various aspects of cell division, organization of the cytoskeleton, and regulation of protein activity.\\n\\nMechanism: The genes identified likely function in the organization of the cytoskeleton, which is required for proper cell division and cellular organization. They may also contribute to regulation of protein activity during these processes.\\n\\n] | \n", + "[Summary: These genes are involved in various cellular processes including cytoskeletal organization, cell cycle progression, and centrosome function.\\nMechanism: These genes likely interact with each other to regulate cellular processes and maintain proper cellular function.\\n] | \n", + "0.95 | \n", + "110 | \n", + "
| 63 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[Summary: Many of these genes are involved in mitosis, cell division, and microtubule organization.\\nMechanism: These genes likely work together to regulate the organization and division of cells.\\n] | \n", + "[Summary: Microtubule organization and regulation\\nMechanism: Regulation of microtubule dynamics and spindle assembly\\n] | \n", + "0.88 | \n", + "79 | \n", + "
| 64 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-0 | \n", + "[Summary: Enzymatic processes related to metabolism and cellular transport are over-represented in this gene set.\\n\\nMechanism: The genes in this set are involved in various metabolic pathways related to cellular transport and enzymatic processes, including lipid metabolism and glucose homeostasis.\\n\\n] | \n", + "[Summary: Protein synthesis and folding regulation\\nMechanism: The identified genes are involved in processes related to protein synthesis, folding, and degradation. Several of the genes are involved in regulating glucose metabolism, which provides energy for protein synthesis. Others are involved in regulating the structure of microtubules, which help transport proteins within cells.\\n\\n] | \n", + "0.87 | \n", + "89 | \n", + "
| 65 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-1 | \n", + "[Summary: Regulation of protein folding and degradation\\nMechanism: Molecular chaperones and proteasome complexes\\n] | \n", + "[Summary: Many of the genes are involved in metabolic processes, specifically related to nucleotide, lipid, and carbohydrate metabolism. Other common functions include protein folding, protein degradation, and regulation of gene expression.\\n\\nMechanism: The enriched terms suggest a role for these genes in cellular homeostasis and regulation of metabolic processes, likely through coordinated regulation of metabolic pathways and protein turnover.\\n\\n] | \n", + "0.84 | \n", + "336 | \n", + "
| 66 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-0 | \n", + "[Summary: The enriched terms suggest that the genes are involved in protein synthesis, DNA replication, RNA splicing, and nucleotide metabolism.\\n\\nMechanism: These genes are involved in the molecular processes that underlie the maintenance and expression of genetic information. They facilitate the translation of genetic code into functional proteins, the replication and repair of DNA, the processing of RNA molecules, and the regulation of nucleotide metabolism.\\n\\n] | \n", + "[Summary: Ribosome biogenesis and protein translation\\n\\nMechanism: These genes are involved in various aspects of ribosome biogenesis and protein translation, including the assembly and function of the ribosome, mRNA splicing, and regulation of translation initiation.\\n\\n] | \n", + "0.90 | \n", + "197 | \n", + "
| 67 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-1 | \n", + "[Summary: Genes are involved in protein synthesis, including ribosomal proteins, translation factors, and chaperones. \\nMechanism: These genes function in various stages of protein synthesis, including ribosome assembly, translation initiation, elongation, and termination. \\n] | \n", + "[Summary: The enriched terms suggest that the genes in this list are involved in various aspects of protein synthesis, including ribosome biogenesis, translation initiation and elongation, and post-splicing mRNA processing.\\n\\nMechanism: Protein synthesis\\n\\n] | \n", + "0.92 | \n", + "19 | \n", + "
| 68 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-0 | \n", + "[Summary: RNA processing and ribosomal biogenesis are enriched functions among the listed genes.\\n\\nMechanism: The genes in this list are involved in various aspects of RNA processing and ribosomal biogenesis. They encode proteins that are involved in functions such as nucleolar organization, rRNA maturation, and ribosomal protein synthesis.\\n\\n] | \n", + "[Summary: Ribosome biogenesis and nucleolar function are enriched functions among these genes.\\nMechanism: The genes are involved in various steps in ribosome biogenesis and nucleolar function, including RNA processing, assembly of ribosomal subunits, and protein binding to facilitate these processes.\\n] | \n", + "0.96 | \n", + "41 | \n", + "
| 69 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-1 | \n", + "[Summary: Nucleolar ribosomal RNA processing and biogenesis is enriched in these genes, as well as RNA binding and RNA metabolic processes.\\n\\nMechanism: The genes in this list all play a role in the processing and biogenesis of ribosomal RNA, particularly in the nucleolus. They are involved in RNA binding and RNA metabolic processes required for ribosome assembly and regulation.\\n\\n] | \n", + "[Summary: Genes involved in nucleolar and ribosomal function, RNA processing and binding, and cell cycle regulation are statistically enriched.\\n\\nMechanism: These genes likely play a role in ribosome biogenesis and function, as well as in the regulation of RNA processing and binding. They may also be involved in cell cycle regulation.\\n\\n] | \n", + "0.94 | \n", + "45 | \n", + "
| 70 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MYOGENESIS-0 | \n", + "[Summary: Muscle contraction and development\\nMechanism: Actin-myosin interaction regulated by calcium ion concentration\\n] | \n", + "[Summary: These genes are involved in muscle development and function, including muscle contraction, regulation of muscle metabolism, and cytoskeletal organization.\\nMechanism: The enriched terms suggest a common mechanism of regulation and organization of muscle tissue at both the structural and metabolic levels.\\n] | \n", + "0.86 | \n", + "195 | \n", + "
| 71 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_MYOGENESIS-1 | \n", + "[Summary: Muscle contraction and regulation of calcium ion transport\\nMechanism: Activation of troponin-tropomyosin complex\\n] | \n", + "[Summary: Muscle development and function\\nMechanism: Regulation of muscle contraction through troponin-tropomyosin complex and actin-myosin interaction\\n\\nHypothesis: The enriched terms suggest that these genes are involved in muscle development and function, specifically in the regulation of muscle contraction through the troponin-tropomyosin complex and actin-myosin interaction. Troponin complex, actin-binding proteins, and myosin heavy chain are all involved in the regulation of muscle contraction and the formation of sarcomeres, the basic functional units of muscle. This suggests that these genes play a role in muscle development and function, particularly in the regulation of muscle contraction through the troponin-tropomyosin complex and actin-myosin interaction, and calcium ion binding.] | \n", + "0.90 | \n", + "680 | \n", + "
| 72 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-0 | \n", + "[Summary: These genes are involved in cell signaling pathways, including the Notch and Wnt signaling pathways, as well as in ubiquitin-mediated protein degradation. \\nMechanism: These genes collectively form a network of signaling and regulatory pathways involved in cellular differentiation and proliferation.\\n\\nHypothesis: These genes are involved in regulating the balance between cell proliferation and differentiation by modulating the activity of key signaling proteins, such as Notch and Wnt receptors, and regulating the turnover of specific proteins via ubiquitination and proteasomal degradation. Dysregulation of these pathways may contribute to the development of various diseases, including cancer and neurological disorders.] | \n", + "[Summary: Notch signaling and cell fate determination\\nMechanism: The genes are all involved in the Notch signaling pathway, which plays a key role in cell fate determination during embryonic development.\\n] | \n", + "0.90 | \n", + "533 | \n", + "
| 73 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-1 | \n", + "[Summary: Genes involved in Notch signaling pathway and protein ubiquitination.\\nMechanism: Regulation of cell fate decisions and interactions between physically adjacent cells through binding of Notch family receptors to their cognate ligands.\\n] | \n", + "[Summary: Regulation of signaling pathways involved in development and cellular processes.\\nMechanism: Notch signaling pathway and ubiquitination-mediated proteolysis.\\n\\nHypothesis: The enriched terms suggest that the common function of the genes in the list is the regulation of signaling pathways, specifically the Notch signaling pathway and ubiquitination-mediated proteolysis. These genes are involved in the transcriptional regulation of cellular processes, including cell fate determination. The Notch signaling pathway plays a critical role in development and differentiation, while ubiquitination-mediated proteolysis is essential for proper protein degradation and turnover. The various genes in this list work together to coordinate these important cellular processes.] | \n", + "0.93 | \n", + "534 | \n", + "
| 74 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[Summary: Mitochondrial genes involved in oxidative phosphorylation and energy metabolism.\\nMechanism: Mitochondrial function and energy metabolism.\\n\\nHypothesis: These genes are all involved in the process of energy production through oxidative phosphorylation within the mitochondria. The enriched terms indicate the importance of ATP synthesis, electron transport chain, and the mitochondrial respiratory chain. These genes may play a key role in cellular energetics, oxidative stress, and aging.] | \n", + "[Summary: Many of the genes listed are involved in the function of mitochondrial respiratory chain complexes, which are responsible for generating energy in cells. \\n\\nMechanism: Mitochondrial respiratory chain complexes. \\n\\n] | \n", + "0.92 | \n", + "276 | \n", + "
| 75 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[Summary: The enriched terms are related to mitochondrial metabolism, particularly oxidative phosphorylation and the electron transport chain.\\n\\nMechanism: These genes are involved in the function and regulation of complexes I-V in the mitochondrial respiratory chain and oxidative phosphorylation.\\n\\n] | \n", + "[Summary: Mitochondrial respiratory chain function and ATP synthesis are enriched in these genes.\\nMechanism: Electron transport chain and oxidative phosphorylation.\\n] | \n", + "0.94 | \n", + "134 | \n", + "
| 76 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_P53_PATHWAY-0 | \n", + "[Summary: Regulation of gene expression, DNA repair, and cell growth/death pathways.\\nMechanism: These genes are involved in the regulation of cellular processes such as gene expression, DNA repair, and cell growth and death pathways. They are enriched in terms related to DNA repair, regulation of gene expression, and growth factor activity.\\n\\nHypothesis: These genes may be involved in maintaining cellular homeostasis and responding to external signals such as growth factors. The regulation of gene expression and DNA repair pathways are critical for proper cell function and survival. Dysfunction in these processes can result in various diseases, including cancer. The enrichment of growth factor activity terms suggests that these genes may also play a role in regulating cell growth and proliferation.] | \n", + "[Summary: Cell growth regulation and DNA repair\\nMechanism: The genes listed are involved in the regulation of cell growth and cell cycle progression, as well as DNA repair and damage response.\\n] | \n", + "0.93 | \n", + "616 | \n", + "
| 77 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_P53_PATHWAY-1 | \n", + "[Summary: Genes are involved in DNA repair, cell growth regulation, and signal transduction pathways.\\nMechanism: These genes are involved in maintaining the integrity of DNA, controlling cell proliferation, and regulating cellular responses through signaling pathways.\\n] | \n", + "[Summary: Genes involved in various cellular processes, including growth factor activity, transcriptional regulation, apoptosis, and DNA repair.\\nMechanism: These genes are involved in regulating cell growth, survival, and response to stress.\\n] | \n", + "0.94 | \n", + "27 | \n", + "
| 78 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[Summary: Genes involved in glucose and insulin metabolism, as well as pancreatic development and neuroendocrine regulation, are statistically over-represented in this list.\\n\\nMechanism: These enriched genes act in a network that regulates the homeostasis of glucose and insulin in the body, through modulation of pancreatic beta cell development, glucose sensing and stimulation, and insulin production.\\n\\n] | \n", + "[Summary: Glucose metabolism and insulin regulation\\nMechanism: Glycolysis; Gluconeogenesis; Insulin secretion; Pancreas development and differentiation\\n\\n] | \n", + "0.89 | \n", + "252 | \n", + "
| 79 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[Summary: Genes in this list are involved in glucose and insulin metabolism, as well as in pancreatic islet development and neuroendocrine differentiation. They also play a role in motor neuron generation, synaptic plasticity, and neurotransmitter release. Enriched terms include \"glucose metabolism,\" \"pancreatic islet development,\" \"neuroendocrine differentiation,\" \"neurotransmitter release,\" and \"synaptic plasticity.\"\\n\\nMechanism: The common mechanism underlying these functions is likely the regulation of gene expression through transcription factors and signaling pathways involved in glucose and insulin metabolism, as well as in neuroendocrine differentiation and synaptic plasticity.\\n\\n] | \n", + "[Summary: Genes involved in glucose and insulin metabolism, as well as pancreatic islet development and neuroendocrine differentiation show enrichment in this list.\\n\\nMechanism: These genes likely play a role in the regulation of glucose homeostasis, insulin secretion, and pancreatic islet development.\\n\\n] | \n", + "0.96 | \n", + "391 | \n", + "
| 80 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PEROXISOME-0 | \n", + "[Summary: The common function of these genes is involvement in metabolic processes including transport, binding, and enzymatic activities of lipids, hormones, and other molecules. \\n\\nMechanism: These genes are part of the cellular machinery involved in lipid transport and metabolism. \\n\\n] | \n", + "[Summary: Transport of various molecules across extra- and intra-cellular membranes is enriched.\\nMechanism: ABC transporters are involved in the transport of a wide range of molecules and play a critical role in maintaining cellular homeostasis.\\n] | \n", + "0.85 | \n", + "40 | \n", + "
| 81 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PEROXISOME-1 | \n", + "[Summary: Peroxisomal membrane proteins & enzymes, fatty acid beta-oxidation pathway, and antioxidant enzymes are enriched functions among the given genes.\\n\\nMechanism: Peroxisomes play a crucial role in fatty acid metabolism. Some of the enriched functions are involved in either fatty acid import, beta-oxidation, or metabolism of by-products of beta-oxidation such as acetyl-CoA. Also, some genes code for peroxisomal membrane proteins that facilitate peroxisomal proliferation or matrix protein import.\\n\\n\\nHypothesis: The enriched functions might suggest a link between fatty acid metabolism, oxidative stress, and peroxisomal proliferation. In oxidative stress conditions, the cell may require to degrade excess fatty acids via peroxisomal beta-oxidation to reduce ROS generation. This acts as a feedback inhibition mechanism to prevent ROS accumulation in the mitochondria. Peroxisomal membrane proteins regulate peroxisomal proliferation to respond to cellular stress.] | \n", + "[Summary: Peroxisomal functions, fatty acid metabolism, and antioxidant defense mechanisms are enriched in this gene list.\\nMechanism: The genes in this list are involved in facilitating fundamental metabolic pathways, such as fatty acid metabolism and peroxisomal functions that involve beta-oxidation, as well as antioxidant defense mechanisms that include the degradation of reactive oxygen species.\\n] | \n", + "0.93 | \n", + "572 | \n", + "
| 82 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[Summary: Genes are involved in intracellular signaling, enzymatic activity, and cytoskeletal regulation.\\nMechanism: These genes play a role in various cellular pathways and contribute to cellular growth, differentiation, and regulation of cellular processes.\\n] | \n", + "[Summary: Intracellular signaling, protein kinase activity, and regulation of cellular processes are enriched functions among these genes.\\n\\nMechanism: These genes are involved in various aspects of intracellular signaling, such as activation or inhibition of protein kinase activity and regulation of cellular processes.\\n\\n] | \n", + "0.94 | \n", + "62 | \n", + "
| 83 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[Summary: Protein phosphorylation and signal transduction pathways are enriched functions among the provided human genes.\\nMechanism: Many of the genes in this list encode for serine/threonine kinases or components of signaling pathways. These pathways are involved in transmitting information from the cell surface (either extracellular signals or internal signals) to the nucleus, resulting in changes in gene expression or other cellular processes. Protein phosphorylation is a key mechanism in these pathways, regulating protein activity and localization.\\n\\n] | \n", + "[Summary: Protein kinases and signaling pathways.\\nMechanism: Genes encode for proteins involved in the phosphorylation of other proteins, leading to activation or inhibition of various signaling pathways.\\n] | \n", + "0.94 | \n", + "355 | \n", + "
| 84 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-0 | \n", + "[Summary: The enriched terms for these genes are related to intracellular trafficking, specifically vesicle transport, Golgi apparatus, and lysosome.\\n\\nMechanism: These genes encode a variety of proteins involved in vesicle trafficking and intracellular transport pathways, specifically related to the Golgi apparatus and lysosome.\\n\\n] | \n", + "[Summary: Intracellular vesicular transport and trafficking\\nMechanism: Adaptor protein complexes and small GTPases regulate vesicle formation, sorting, and fusion with target membranes.\\n] | \n", + "0.88 | \n", + "146 | \n", + "
| 85 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-1 | \n", + "[Summary: Vesicular transport and protein sorting in the Golgi apparatus are enriched functions among the listed genes. \\n\\nMechanism: These genes encode proteins involved in membrane trafficking, protein sorting, vesicle fusion, and transport between different membrane-bound compartments. \\n\\n] | \n", + "[Summary: Membrane trafficking and vesicular transport \\nMechanism: Genes involved in membrane trafficking and vesicular transport function together to regulate the movement of proteins and lipids between organelles in the cell. They do so by promoting the budding, fusion, and sorting of transport vesicles. \\n] | \n", + "0.93 | \n", + "18 | \n", + "
| 86 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[Summary: Genes involved in antioxidant defense and oxidative stress response are enriched.\\n\\nMechanism: The enriched genes have significant functions in oxidoreductase activity, antioxidant activity, and glutathione metabolic processes. \\n\\n\\nHypothesis: The enriched genes suggest the importance of maintaining a balance between oxidative stress and antioxidant defense to combat cellular damage. The glutathione metabolic process plays a crucial role in regulating the redox status of the cell and possibly maintaining proper protein folding. These genes may be involved in cellular responses to oxidative stress and the regulation of redox signaling pathways.] | \n", + "[Summary: Genes involved in antioxidant defense and redox regulation.\\n\\n] | \n", + "0.92 | \n", + "589 | \n", + "
| 87 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[Summary: Redox homeostasis and antioxidant defense mechanisms. \\nMechanism: Multiple genes involved in redox balance and antioxidant defense mechanisms. \\n\\nHypothesis: The enriched terms suggest that the commonality among the gene functions is the regulation of redox homeostasis and maintenance of antioxidant defense mechanisms. The gene products are involved in the reduction of reactive oxygen species (ROS) and oxidative stress to maintain cellular function and survival. The proteins may act as antioxidants, reducing ROS such as hydrogen peroxide and organic hydroperoxides, or they may function in redox regulation, playing key roles in redox signaling pathways and the maintenance of redox balance. Overall, these genes are important in protecting cellular integrity and maintaining homeostasis.] | \n", + "[Summary: Anti-oxidative stress response pathway\\nMechanism: Enzymatic reduction of oxidative stress\\n\\nHypothesis: The commonality in function among these genes is their involvement in the anti-oxidative stress response pathway. These genes encode enzymes that are responsible for reducing oxidative stress, regulating reactive oxygen species and superoxide anion radicals, and participating in antioxidative defense mechanisms. The pathway involves the regulation of glutathione metabolism, peroxiredoxin-mediated detoxification, and other mechanisms that help to mitigate the effects of oxidative stress.] | \n", + "0.93 | \n", + "199 | \n", + "
| 88 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-0 | \n", + "[Summary: Cell cycle regulation and DNA binding\\nMechanism: These genes are involved in regulating cell cycle progression and DNA interactions, with many of them being DNA or RNA binding proteins.\\n\\n] | \n", + "[Summary: Reproductive development, specifically sperm function and testis differentiation, is enriched in these genes.\\n\\n\\nHypothesis: These genes all have roles in either male reproductive development or sperm function, which suggests they may share a common pathway or mechanism in regulating these processes. One hypothesis is that these genes may be involved in the regulation of gene expression during spermatogenesis, as many of them are specifically expressed in the testes and have been linked to sperm motility and acrosome reaction.] | \n", + "0.83 | \n", + "345 | \n", + "
| 89 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-1 | \n", + "[Summary: Cellular processes involved in protein binding, enzymatic activity, and ion transport are enriched in this list of human genes.\\n\\nMechanism: The proteins encoded by these genes may form complexes involved in signal transduction pathways, protein degradation, and ion channel regulation.\\n\\n] | \n", + "[Summary: These genes are involved in various cellular and molecular functions, including but not limited to ion transport, protein phosphorylation, ubiquitination, spermatogenesis, and receptor signaling.\\nMechanism: The genes are involved in diverse biological pathways or mechanisms, reflecting the complexity of cellular and molecular biology.\\n] | \n", + "0.92 | \n", + "50 | \n", + "
| 90 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[Summary: Signaling and regulation of growth and differentiation processes.\\nMechanism: TGF-beta superfamily signaling pathways.\\n] | \n", + "[Summary: Genes involved in regulating transforming growth factor-beta (TGF-beta) superfamily signaling and transcriptional regulation.\\nMechanism: Regulation of TGF-beta signaling pathway and transcriptional regulation.\\n\\nHypothesis: These genes are involved in the regulation of the TGF-beta signaling pathway, which controls a variety of cellular processes including cell growth, differentiation, and apoptosis. They also play a role in transcriptional regulation, which may contribute to their regulatory functions in the TGF-beta pathway. These findings suggest a potential mechanism for how these genes may interact and contribute to the regulation of TGF-beta signaling.] | \n", + "0.91 | \n", + "548 | \n", + "
| 91 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[Summary: Members of this group of genes are involved in transforming growth factor-beta (TGF-beta) superfamily signaling, cell growth and differentiation, transcriptional regulation, ubiquitination, and phosphorylation. \\nMechanism: TGF-beta signaling pathway\\n] | \n", + "[Summary: Signaling pathways involving transforming growth factor-beta (TGF-beta) and bone morphogenetic proteins (BMPs)\\nMechanism: Regulation of gene expression through transcription factor binding and signal transduction\\n] | \n", + "0.93 | \n", + "37 | \n", + "
| 92 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[Summary: Genes involved in immune response, cytokine signaling, and transcription regulation.\\n\\n] | \n", + "[Summary: Immune system-related genes that regulate inflammation and cytokine signaling.\\n\\nMechanism: These genes are involved in regulating the immune response by controlling inflammation and cytokine signaling pathways.\\n\\n] | \n", + "0.93 | \n", + "126 | \n", + "
| 93 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[Summary: Genes are involved in immune response, cytokine signaling, and transcription regulation.\\n\\nMechanism: These genes have a role in modulating the immune response, with some genes involved in cytokine signaling and others in transcription regulation.\\n\\n] | \n", + "[Summary: Cytokine signaling and immune response\\nMechanism: Genes are involved in cytokine production and response pathways, specifically in the interleukin and chemokine families.\\n] | \n", + "0.93 | \n", + "77 | \n", + "
| 94 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[Summary: These genes are involved in protein folding, stress response, and RNA metabolism.\\n\\nMechanism: These genes likely function in the regulation of protein folding and quality control, as well as the response to cellular stress and the maintenance of RNA stability.\\n\\n] | \n", + "[Summary: Genes involved in protein folding, stress response, and RNA processing are enriched.\\nMechanism: These genes likely function in maintaining proper protein folding and preventing protein misfolding, as well as responding to stress and modulating RNA processing.\\n] | \n", + "0.95 | \n", + "2 | \n", + "
| 95 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[Summary: Genes involved in protein folding and regulation of RNA processing and translation.\\nMechanism: These genes play a role in maintaining cellular homeostasis by regulating the synthesis and folding of proteins, and the processing and translation of RNA. \\n\\nHypothesis: These genes likely work together to promote proper protein conformation and prevent improper folding and aggregation. They may also play a role in regulating cellular responses to stress, such as the unfolded protein response. In addition, they may be involved in controlling translation rates and ensuring proper ribosome function.] | \n", + "[Summary: Protein folding, transport, and translation regulation \\nMechanism: Endoplasmic reticulum-associated protein degradation (ERAD) and unfolded protein response (UPR) pathways \\n] | \n", + "0.87 | \n", + "425 | \n", + "
| 96 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-0 | \n", + "[Summary: These genes are enriched for terms related to intracellular signaling and regulation, specifically in regards to calcium ion transport and cytoskeletal organization.\\n\\nMechanism: The identified genes are involved in intracellular signaling pathways that regulate cellular processes through calcium ion transport and cytoskeletal organization.\\n\\n] | \n", + "[Summary: Extracellular matrix, cell signaling, protein kinase activity, ion transport, transcription regulation, and growth factor receptor activity are the common functions of the listed genes.\\n\\nMechanism: An underlying biological mechanism for the enriched terms is the regulation of cell growth and differentiation by extracellular matrix signaling pathways, which involve ion transport, protein kinase activity, and transcriptional regulation.\\n\\n] | \n", + "0.92 | \n", + "97 | \n", + "
| 97 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-1 | \n", + "[Summary: Extracellular matrix organization, cellular signaling, and ion transport are enriched functions in this list of genes.\\n\\nMechanism: These genes likely play a role in the formation and maintenance of the extracellular matrix, cellular communication and signaling pathways, and ion transport.\\n\\n] | \n", + "[Summary: Extracellular matrix organization, cell adhesion, signaling and protein phosphorylation are enriched functions in these genes.\\n\\nMechanism: These genes are involved in biological processes related to cell adhesion, extracellular matrix organization, signaling pathway activity and protein phosphorylation.\\n\\n] | \n", + "0.94 | \n", + "15 | \n", + "
| 98 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-0 | \n", + "[Summary: Transport, catalysis, and regulation of cellular processes are the enriched functions of these genes.\\nMechanism: ABC transporters, enzymes, and transcription factors are involved in these processes.\\n\\n] | \n", + "[Summary: Transport and metabolism of small molecules\\nMechanism: ABC transporters; Enzymatic metabolism\\n] | \n", + "0.87 | \n", + "106 | \n", + "
| 99 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-1 | \n", + "[Summary: This set of human genes is involved in various biological processes, including metabolism, nucleotide and protein biosynthesis, and signaling pathways.\\n\\n] | \n", + "[Summary: Nucleic acid binding and metabolism\\nMechanism: RNA and DNA processing\\n] | \n", + "0.86 | \n", + "83 | \n", + "
| 100 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[Summary: Genes involved in Wnt signaling pathway regulation.\\nMechanism: Negatively regulating Wnt pathway through inhibition of beta-catenin stabilization and/or transcriptional activation.\\n\\nHypothesis: The genes listed above are all involved in negative regulation of the Wnt signaling pathway, either through inhibiting beta-catenin stabilization or transcriptional activation. This results in downstream effects on processes such as transcriptional and cell cycle regulation.] | \n", + "[Summary: Genes involved in signaling pathways related to Wnt signaling, cell cycle progression, and transcriptional regulation.\\n\\nMechanism: Wnt signaling pathway regulates cell fate determination, cell proliferation, and differentiation through binding of specific receptors to Wnt proteins.\\n\\n] | \n", + "0.92 | \n", + "186 | \n", + "
| 101 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[Summary: Genes involved in the Wnt signaling pathway and transcription regulation are enriched in this gene list.\\nMechanism: These genes play a role in the regulation of the Wnt signaling pathway and transcriptional regulation.\\n] | \n", + "[Summary: Genes involved in the Wnt signaling pathway, regulation of cell cycle, and transcriptional regulation are statistically over-represented.\\n\\nMechanism: These genes play a role in various cellular processes, including cell fate determination, embryonic development, and tumorigenesis.\\n\\n] | \n", + "0.94 | \n", + "64 | \n", + "
| 102 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "T cell proliferation-0 | \n", + "[Summary: Immune response and signal transduction genes are enriched in this list.\\n\\nMechanism: These genes function in various aspects of immune response, including immune signaling, cytokine production, and cell proliferation and differentiation.\\n\\n\\nHypothesis: These genes may be involved in the regulation of immune responses by modulating cytokine production and signaling, controlling cell proliferation and differentiation, and regulating apoptosis. Further investigation could lead to a better understanding of the complex interplay between these genes and their role in maintaining a healthy immune system.] | \n", + "[Summary: Immune response and signal transduction\\nMechanism: C-type lectin receptors and cytokine signaling pathways\\n] | \n", + "0.87 | \n", + "497 | \n", + "
| 103 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "T cell proliferation-1 | \n", + "[Summary: Immune response and cytokine signaling\\nMechanism: Regulation of immune response and cytokine signaling\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of the immune response and cytokine signaling. Specifically, these genes are implicated in the signaling pathways that are activated in response to immune system activation and in the subsequent regulation of T cell function. The overall biological mechanism is the regulation of immune defense against foreign pathogens and tumor cells.] | \n", + "[Summary: Immune response and cell signaling\\nMechanism: These genes are involved in immune response and cell signaling pathways, such as the TNF-receptor superfamily and cytokine signaling.\\n] | \n", + "0.93 | \n", + "349 | \n", + "
| 104 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "Yamanaka-TFs-0 | \n", + "[Summary: These genes are involved in embryonic development, stem cell pluripotency, and tumorigenesis. They encode transcription factors that regulate gene expression and control cell cycle progression.\\nMechanism: Transcriptional regulation\\n\\nHypothesis: These genes may function together in a signaling pathway involved in the maintenance of stem cell pluripotency and/or regulation of cell differentiation during embryonic development. Dysregulation of this pathway could contribute to tumorigenesis. The transcription factors encoded by these genes may also interact with other proteins involved in DNA damage response and repair.] | \n", + "[Summary: These genes share a role in the regulation of embryonic development, cell fate determination, and cell cycle progression.\\nMechanism: These genes encode transcription factors that regulate gene expression and are important for stem cell pluripotency and cell differentiation.\\n] | \n", + "0.96 | \n", + "349 | \n", + "
| 105 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "Yamanaka-TFs-1 | \n", + "[Summary: Genes involved in transcription factor activity and regulation of development.\\nMechanism: Transcriptional regulation of development.\\n\\nHypothesis: These genes play a crucial role in the transcriptional regulation of embryonic development and stem cell maintenance. They are likely involved in the regulation of gene expression during critical periods of development, and abnormalities in their function may contribute to developmental disorders and tumorigenesis. Further research is needed to fully elucidate the molecular mechanisms by which these genes act and their interactions within regulatory pathways.] | \n", + "[Summary: Embryonic development and stem cell pluripotency\\nMechanism: Transcriptional regulation\\n\\n] | \n", + "0.91 | \n", + "522 | \n", + "
| 106 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "amigo-example-0 | \n", + "[Summary: Extracellular matrix and cell signaling related genes are enriched.\\n\\nMechanism: Extracellular matrix formation and remodeling, as well as cell migration and signaling pathways are likely involved.\\n\\n] | \n", + "[Summary: Extracellular matrix and cell adhesion-related genes.\\nMechanism: Extracellular matrix remodeling and cell adhesion.\\n] | \n", + "0.94 | \n", + "82 | \n", + "
| 107 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "amigo-example-1 | \n", + "[Summary: Extracellular matrix organization and cell adhesion.\\nMechanism: Regulation of cell attachment and migration via extracellular matrix interactions.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of cell attachment and migration via interactions with the extracellular matrix. Specifically, these genes play a role in extracellular matrix organization and cell adhesion, as well as proteoglycan and keratan sulfate metabolic processes. The integrin-mediated signaling pathway is also likely involved in these processes, as integrins are transmembrane receptors that mediate cell adhesion to the extracellular matrix. Finally, platelet activation may be involved, as some of these genes are associated with platelet-derived growth factors and other factors that regulate platelet activation and adhesion. Overall, these genes likely play a key role in regulating cell behavior in response to changes in the extracellular matrix, and may be involved in a variety of physiological and pathological processes, including wound healing, tissue development and maintenance, and cancer progression.] | \n", + "[Summary: Extracellular matrix (ECM) organization and regulation, cell adhesion and migration, tissue development and regeneration, signaling pathways, and platelet function are enriched in these gene functions.\\n\\nMechanism: ECM proteins, such as SPP1, COL5A2, and LUM, are involved in tissue organization and regulation. Cell adhesion and migration are mediated by proteins such as VCAN, ITGAV, and VTN. Tissue development and regeneration involve proteins like POSTN, MSX1, and JAG1. Signaling pathways are regulated by genes such as JAG2, NRP1, and TNFRSF21. Platelet function is affected by genes such as PF4, PDGFA, and PRG2.\\n\\n] | \n", + "0.94 | \n", + "509 | \n", + "
| 108 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_0-0 | \n", + "[Summary: Membrane transport and binding activity\\nMechanism: ABC Transporter Signaling Pathway\\n] | \n", + "[Summary: Several of the genes are involved in transcription regulation and protein binding.\\n\\nHypothesis: These genes may be involved in regulating cellular processes through the regulation of gene expression and protein interactions, with zinc fingers and calcium ion binding domains playing important roles in protein-protein interactions and regulatory functions. The membrane proteins may mediate these interactions and functions at the cellular membrane.] | \n", + "0.80 | \n", + "365 | \n", + "
| 109 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_0-1 | \n", + "[Summary: Genes are involved in various cellular processes, including RNA binding, calcium signaling, protein binding, transcription factor activity, and membrane transport. \\n\\n] | \n", + "[Summary: Calcium-binding proteins, receptor proteins, and transcription factors are over-represented in this list of human genes.\\n\\nMechanism: These genes are involved in diverse biological processes but share common molecular functions, such as calcium binding, transcriptional regulation, receptor activity, and protein binding.\\n\\n] | \n", + "0.89 | \n", + "156 | \n", + "
| 110 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_1002-0 | \n", + "[Summary: Muscle contraction and regulation\\nMechanism: Gene products involved in the structure, organization, and regulation of the contractile machinery in striated muscle.\\n\\nHypothesis: The enriched terms indicate that the gene products listed are all involved in the structure, organization, and regulation of the contractile machinery in striated muscle. More specifically, these gene products contribute to the organization of actin filaments via actin binding, tropomyosin binding, and muscle filament sliding speed regulation, as well as the regulation of muscle contraction through calcium ion binding to the troponin complex and myosin binding. There are specific enriched terms, such as regulation of muscle filament sliding speed, which suggest that these gene products may play distinct roles within the muscle contractile machinery, but this remains to be fully elucidated.] | \n", + "[Summary: These genes are primarily involved in muscle contraction and regulation, with some playing a role in ion channel activity, protein binding, and phosphorylation.\\nMechanism: These genes are involved in the regulation of muscle development, contraction, and calcium signaling pathways.\\n] | \n", + "0.90 | \n", + "593 | \n", + "
| 111 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_1002-1 | \n", + "[Summary: Genes are involved in muscle contraction, regulation, and structure.\\n\\n\\nHypothesis: The muscle structure and function depend on the proper regulation of actin-myosin interaction, calcium ion flux, and energy metabolism. Dysfunctions in these pathways lead to the development of various muscle disorders. Therefore, the enriched terms represent the key biological processes and molecular functions that underlie muscle structure, function, and dysfunction.] | \n", + "[Summary: Genes involved in muscle contraction, regulation of calcium ions in muscle, and energy homeostasis.\\nMechanism: These genes contribute to the structure and function of striated muscle fibers, allowing for efficient and regulated contraction and relaxation.\\n] | \n", + "0.92 | \n", + "199 | \n", + "
| 112 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "endocytosis-0 | \n", + "[Summary: Many of the genes in this list are involved in endocytosis, intracellular trafficking, and cytoskeleton reorganization.\\n\\nMechanism: These genes likely play a role in the regulation and maintenance of cellular processes by contributing to the turnover and recycling of molecules within the cell.\\n\\n] | \n", + "[Summary: Genes in this list are involved in various cellular processes, including endocytosis, cytoskeletal reorganization, and signal transduction. They are also involved in lipid homeostasis and bone and brain development.\\n\\nMechanism: These genes are involved in intracellular transport, regulation of membrane dynamics, and signaling pathways. \\n\\n] | \n", + "0.96 | \n", + "44 | \n", + "
| 113 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "endocytosis-1 | \n", + "[Summary: Genes involved in endocytosis, vesicle trafficking, and intracellular signaling.\\nMechanism: These genes function in various aspects of intracellular trafficking, particularly endocytosis and vesicle trafficking.\\n\\n] | \n", + "[Summary: The enriched terms are involved in intracellular trafficking, endocytosis, and cytoskeletal reorganization.\\nMechanism: These genes function in regulating cellular processes involving endocytic recycling and protein degradation.\\n\\n] | \n", + "0.92 | \n", + "16 | \n", + "
| 114 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "glycolysis-gocam-0 | \n", + "[Summary: The genes in this list are involved in glucose metabolism and glycolysis, which is the breakdown of glucose to provide energy for cellular processes.\\n\\n\\nHypothesis: The common function of these genes in glucose metabolism and glycolysis suggests a role in regulating energy production in cells. Dysfunction in these genes may lead to diseases related] | \n", + "[Summary: These genes are involved in various stages of glucose metabolism and glycolysis.\\n\\nMechanism: The enriched terms suggest that these genes are involved in energy metabolism, specifically glycolysis and the conversion of glucose to ATP.\\n\\n] | \n", + "0.93 | \n", + "115 | \n", + "
| 115 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "glycolysis-gocam-1 | \n", + "[Summary: Enzymes involved in glycolysis and related metabolic pathways.\\nMechanism: Metabolism of glucose to produce energy.\\n] | \n", + "[Summary: These genes are involved in various steps of glycolysis, a central metabolic pathway for the conversion of glucose into pyruvate, with the production of energy-rich ATP molecules.\\n\\nMechanism: Glycolysis is a multi-step process consisting of various enzymes that catalyze the conversion of glucose to pyruvate. This process occurs in the cytoplasm of cells and is an important pathway for the production of ATP.\\n\\n\\nHypothesis: These genes are involved in the regulation of energy metabolism and play a crucial role in providing cells with energy in the form of ATP. Dysfunction of these pathways can lead to various metabolic disorders, including glycogen storage diseases, hemolytic anemia, and cancer. The enrichment of terms related to glucose and fructose metabolism suggests that these pathways are particularly important for the function of these genes.] | \n", + "0.92 | \n", + "743 | \n", + "
| 116 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "go-postsynapse-calcium-transmembrane-0 | \n", + "[Summary: Calcium signaling regulation and ion channels\\nMechanism: Calcium homeostasis and neuronal signaling \\n\\nHypothesis: The gene function common to this list is the regulation of calcium signaling and ion channels in neurons. These genes are involved in the transport and binding of calcium ions in the intracellular space and the regulation of ion channel activity in the plasma membrane, particularly in the postsynaptic density of neurons. Calcium transport is vital for regulating neuronal signaling and synaptic plasticity, which underlie many physiological processes, including learning and memory. The ionotropic glutamate receptor activity is also enriched, which is involved in fast neurotransmission in the synapses. Overall, this suggests that these genes contribute to the regulation of calcium signaling essential for proper neuron function and synaptic plasticity.] | \n", + "[Summary: Calcium regulation and signaling\\nMechanism: Calcium ion transport and homeostasis\\n\\nHypothesis: The list of genes all play a critical role in calcium ion transport and homeostasis. They are involved in regulating intracellular calcium concentrations through ion transport across cell membranes. Specifically, many of the genes encode for ionotropic glutamate receptors that mediate synaptic plasticity in the central nervous system, which is believed to underlie memory and learning. The NMDA receptor subunits are key components of these receptors and are involved in calcium signaling. Additionally, several genes encode for sodium/calcium exchanger proteins that are responsible for regulating calcium ion homeostasis in a wide variety of cell types. The TRP ion channel family plays a role in transducing painful stimuli such as capsaicin and thermal stimuli. Overall, these genes are involved in multiple processes that ultimately impact calcium regulation and signaling.] | \n", + "0.96 | \n", + "103 | \n", + "
| 117 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "go-postsynapse-calcium-transmembrane-1 | \n", + "[Summary: Ion channels and receptors\\nMechanism: Regulation of cellular calcium levels\\n\\nHypothesis: The enriched terms suggest a mechanism by which these genes regulate cellular calcium levels, likely through ion channels and receptors. This regulation is crucial for synaptic transmission and neurotransmitter receptor activity. Dysfunction of these genes could lead to disruptions in calcium homeostasis, potentially contributing to neurological disorders.] | \n", + "[Summary: All listed genes are involved in ion channel activity, particularly calcium channels and receptors. \\n\\nMechanism: Calcium signaling \\n\\n] | \n", + "0.91 | \n", + "315 | \n", + "
| 118 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "go-reg-autophagy-pkra-0 | \n", + "[COULD NOT PARSE] | \n", + "[Summary: Regulation of cell growth and survival through various signaling pathways is a common function of the listed genes.\\n\\nMechanism: The genes listed are involved in various signaling pathways that regulate cellular growth and survival, including the PI3K/AKT/mTOR pathway, TORC1 signaling, and the NF-kappaB pathway.\\n\\n] | \n", + "0.68 | \n", + "308 | \n", + "
| 119 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "go-reg-autophagy-pkra-1 | \n", + "[Summary: Genes are involved in cell signaling, regulation of apoptosis, immune response, and protein kinase activity.\\nMechanism: These genes regulate various cellular processes such as cell division, survival, and metabolism through protein signaling and kinase activity pathways.\\n] | \n", + "[Summary: Genes involved in cell growth, signaling, and immune response are enriched.\\n\\nMechanism: These genes converge on signaling pathways that control cell growth and immune response through regulation of protein kinases such as AKT, TOR, and CDK5, and activation of transcription factors such as NF-kappaB.\\n\\n] | \n", + "0.92 | \n", + "30 | \n", + "
| 120 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[Summary: These genes are involved in the degradation of glycosaminoglycans, glycogen, and glycolipids, as well as the hydrolysis of glycosidic bonds in carbohydrates. \\n\\n\\nHypothesis: The enriched terms point to a common mechanism of lysosomal degradation of carbohydrate molecules, with specific enzymes targeting different types of molecules (e.g. glycosaminoglycans, glycogen, glycolipids). This process is important for maintaining cellular homeostasis and energy metabolism.] | \n", + "[Summary: Genes involved in the hydrolysis of carbohydrates and degradation of glycosaminoglycans, along with those involved in the turnover of hyaluronan and chitin, are enriched. \\nMechanism: Carbohydrate and glycosaminoglycan metabolism. \\n] | \n", + "0.93 | \n", + "237 | \n", + "
| 121 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[Summary: Enzymes involved in carbohydrate metabolism, specifically in the breakdown of complex sugars like glycosaminoglycans and polysaccharides.\\n\\nMechanism: Carbohydrate metabolism\\n\\n] | \n", + "[Summary: Enzymes involved in glycosaminoglycan degradation and processing are enriched in this gene set.\\n\\nMechanism: Glycosaminoglycans are long chains of complex carbohydrates that are integral components of the extracellular matrix and play a role in cell signaling and tissue development. These enzymes are involved in the degradation and processing of glycosaminoglycans, specifically the cleavage of terminal carbohydrate residues.\\n\\n] | \n", + "0.91 | \n", + "254 | \n", + "
| 122 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "ig-receptor-binding-2022-0 | \n", + "[Summary: The enriched terms are related to immunoglobulin receptor binding activity and immune response. \\nMechanism: The genes listed all code for proteins involved in the function of immunoglobulins, which are the key molecules of adaptive immunity (the portion of the immune system that learns to recognize and remember specific pathogens). \\n] | \n", + "[Summary: The enriched terms suggest that these genes are involved in the immune response and specifically in the function of immunoglobulins (Ig) and immunoglobulin receptors.\\n\\nMechanism: The genes function in the immune response and interaction with antigens.\\n\\n] | \n", + "0.96 | \n", + "82 | \n", + "
| 123 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "ig-receptor-binding-2022-1 | \n", + "[Summary: Genes are involved in adaptive immune response and immune system processes, likely through antigen binding activity and immunoglobulin receptor binding activity. \\n\\n] | \n", + "[Summary: Genes related to immunoglobulin receptor binding activity and activation of immune response.\\nMechanism: Adaptive immune response\\n] | \n", + "0.93 | \n", + "35 | \n", + "
| 124 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "meiosis I-0 | \n", + "[Summary: These genes are primarily involved in meiotic recombination, double-strand break repair, and chromosomal segregation during meiosis. They all play a role in some aspect of the meiotic cell cycle process.\\n\\n\\nHypothesis: The underlying biological mechanism for these genes is the regulation and coordination of meiotic recombination and double-strand break repair via homologous recombination, as well as the proper segregation of chromosomes during meiosis. Dysfunction in any of these genes may result in chromosomal abnormalities and infertility in individuals.] | \n", + "[Summary: Meiotic recombination and DNA repair are enriched functions among the listed genes.\\nMechanism: The genes listed play a role in DNA repair and recombination during meiosis, particularly in the resolution of double-stranded DNA breaks. \\n] | \n", + "0.92 | \n", + "327 | \n", + "
| 125 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "meiosis I-1 | \n", + "[Summary: Genes involved in meiotic recombination and DNA break repair are enriched.\\n\\nMechanism: These genes play a crucial role in meiotic recombination and repair of DNA double-strand breaks. During meiosis, DNA breaks are introduced, repaired, and exchanged between chromosomes to generate genetic diversity.\\n\\n] | \n", + "[Summary: These genes are involved in various aspects of meiotic recombination, DNA repair, and chromosome segregation.\\nMechanism: Meiosis\\n\\n\\nHypothesis: These genes are involved in various aspects of meiotic recombination. They likely function in the repair of double-strand DNA breaks, the resolution of Holliday junctions, and the proper segregation of homologous chromosomes during meiosis. They may also play a role in the formation and maintenance of the synaptonemal complex, which helps to ensure accurate chromosome pairing and recombination. Overall, these genes are critical for the proper functioning of meiosis and the generation of viable gametes.] | \n", + "0.94 | \n", + "348 | \n", + "
| 126 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "molecular sequestering-0 | \n", + "[Summary: Cellular processes involved in protein binding and regulation, immune response, and intracellular transport are enriched in the given list of genes.\\n\\n\\nHypothesis: The enriched terms suggest that the genes in this list are involved in several overlapping pathways related to protein binding and regulation, immune response, and intracellular transport. Specifically, these genes may play a role in regulating protein-protein interactions, immune system signaling and response, and the movement of molecules and particles within cells. These pathways may be key to cellular development, maintenance, and response to stressors and damage. Further investigation into the relationships and interactions between these genes may lead to a better understanding of how these processes are regulated and coordinated in human cells.] | \n", + "[Summary: Regulation of cellular processes, including immunity, apoptosis, and signal transduction.\\nMechanism: These genes are involved in a range of biological pathways, including immune response, cell cycle regulation, and intracellular transport.\\n\\n] | \n", + "0.90 | \n", + "581 | \n", + "
| 127 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "molecular sequestering-1 | \n", + "[Summary: Transport functions, regulation of cell growth and survival, inhibition of apoptosis, and regulation of gene expression are enriched in this set of genes.\\nMechanism: These genes likely function in a variety of cellular processes, including transport and signaling pathways, cell cycle regulation, and gene expression regulation.\\n\\n] | \n", + "[Summary: Regulation of cellular processes, including immune response and cell cycle progression.\\nMechanism: Not specified.\\n] | \n", + "0.86 | \n", + "216 | \n", + "
| 128 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "mtorc1-0 | \n", + "[Summary: Enzymatic processes related to metabolism and cellular transport are over-represented in this gene set.\\n\\nMechanism: The genes in this set are involved in various metabolic pathways related to cellular transport and enzymatic processes, including lipid metabolism and glucose homeostasis.\\n\\n] | \n", + "[Summary: Protein synthesis and folding regulation\\nMechanism: The identified genes are involved in processes related to protein synthesis, folding, and degradation. Several of the genes are involved in regulating glucose metabolism, which provides energy for protein synthesis. Others are involved in regulating the structure of microtubules, which help transport proteins within cells.\\n\\n] | \n", + "0.87 | \n", + "89 | \n", + "
| 129 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "mtorc1-1 | \n", + "[Summary: These genes are involved in various cellular processes, but a common theme is their involvement in protein degradation. \\n\\nMechanism: The 26S proteasome is a multicatalytic proteinase complex that plays a critical role in the degradation of intracellular proteins that are damaged, misfolded, or no longer needed. \\n\\n] | \n", + "[Summary: These genes are involved in various cellular processes such as protein degradation, glucose transport, nucleic acid metabolism, and energy metabolism.\\n\\nMechanism: The biological mechanism underlying the common function of these genes may relate to their involvement in cellular metabolism and maintenance.\\n\\n] | \n", + "0.89 | \n", + "8 | \n", + "
| 130 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "peroxisome-0 | \n", + "[Summary: Genes involved in peroxisome biogenesis and protein import.\\nMechanism: Peroxisome biogenesis and maturation pathway.\\n\\n\\nHypothesis: These genes are involved in the peroxisome biogenesis and maturation pathway, which is responsible for the assembly of functional peroxisomes. This pathway involves the formation of membrane vesicles by PEX3, followed by translocation of matrix proteins via PEX5 and PEX7. Mutations in these genes lead to peroxisome biogenesis disorders, which are characterized by multiple defects in peroxisome function, including import of matrix proteins. Therefore, these genes are involved in the import of peroxisomal matrix proteins and the maturation of peroxisomes. The commonalities in their function are related to their roles in peroxisome biogenesis and protein import.] | \n", + "[Summary: Genes involved in peroxisome biogenesis and protein import\\nMechanism: Peroxisome assembly and maintenance pathway\\n\\nHypothesis: These genes are all involved in the same pathway for peroxisome assembly and maintenance, specifically in the import of peroxisomal matrix proteins. Mutations in these genes lead to various peroxisomal biogenesis disorders, including neonatal adrenoleukodystrophy, Zellweger syndrome, and infantile Refsum disease. Defects in PEX7 specifically have been associated with a wider range of disorders, including RCDP1 and Refsum disease. Overall, these genes play critical roles in the proper function of peroxisomes and their associated metabolic processes.] | \n", + "0.96 | \n", + "117 | \n", + "
| 131 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "peroxisome-1 | \n", + "[Summary: Genes involved in peroxisome biogenesis disorders\\nMechanism: Peroxisome assembly and matrix protein import\\n] | \n", + "[Summary: Peroxisome biogenesis genes are enriched for terms related to peroxisome assembly and function.\\n\\nMechanism: Peroxisomes are important organelles responsible for numerous metabolic functions, including the degradation of fatty acids and the synthesis of cholesterol. The genes listed here are involved in the assembly and maintenance of peroxisomes, as well as the import of proteins into the organelle.\\n\\n\\nHypothesis: The AAA family of ATPases plays a central role in peroxisome biogenesis by providing energy for protein translocation and membrane remodeling. Mutations in these genes disrupt the normal assembly and function of peroxisomes, leading to a range of disorders collectively known as peroxisome biogenesis disorders.] | \n", + "0.92 | \n", + "622 | \n", + "
| 132 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "progeria-0 | \n", + "[Summary: Genes involved in nuclear structure and function \\nMechanism: Proteolytic processing of prelamin A to mature lamin A, maintenance of genome stability \\n] | \n", + "[Summary: Genes involved in nuclear structure and maintenance.\\nMechanism: These genes encode proteins that are involved in maintaining the structure and function of the nucleus. They are involved in processes such as DNA repair, replication, and chromatin organization.\\n] | \n", + "0.91 | \n", + "110 | \n", + "
| 133 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "progeria-1 | \n", + "[Summary: Genes LMNA, WRN, and BANF1 are all involved in nuclear functions and stability.\\nMechanism: These genes are involved in maintaining the stability of the genome by regulating chromatin structure, repairing DNA, and facilitating nuclear reassembly.\\n] | \n", + "[Summary: Genes involved in nuclear organization and stability.\\nMechanism: These genes play important roles in maintaining nuclear stability and integrity by organizing chromatin structure and gene expression, repairing DNA damage, and promoting nuclear reassembly.\\n] | \n", + "0.90 | \n", + "10 | \n", + "
| 134 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "regulation of presynaptic membrane potential-0 | \n", + "[Summary: Genes involved in neurotransmission through ion channels, specifically GABA and glutamate receptors, as well as voltage-gated potassium and sodium channels, are over-represented in this list.\\n\\nMechanism: These genes encode proteins involved in the regulation of ion flow in neuronal membranes, allowing for the transmission of electrical signals and control of neuronal excitability.\\n\\n] | \n", + "[Summary: Genes involved in ion channels and neurotransmission through GABA and glutamate receptors. \\nMechanism: Regulation of neuronal excitability and synaptic transmission. \\n] | \n", + "0.94 | \n", + "218 | \n", + "
| 135 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "regulation of presynaptic membrane potential-1 | \n", + "[Summary: These genes are involved in the regulation of ion channels in the central nervous system.\\nMechanism: Regulation of ion channels\\n] | \n", + "[Summary: The enriched terms are related to ion channels in the central nervous system, particularly potassium and chloride channels. \\n\\nMechanism: Ion channels play critical roles in regulating the electrical properties of cells, including neurons. Potassium channels are important for regulating action potential firing and synaptic transmission, while chloride channels are involved in inhibitory neurotransmission mediated by GABA. \\n\\n] | \n", + "0.89 | \n", + "299 | \n", + "
| 136 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "sensory ataxia-0 | \n", + "[Summary: Myelin upkeep and neurological diseases\\n\\nHypothesis: Dysregulation of the myelin upkeep pathways can lead to mitochondrial dysfunction, accumulations of toxic metabolites, and impaired protein processing, which contribute to the development of neurological diseases. Dysfunction of the transporter proteins and nuclear membrane transporters can further exacerbate cell dysfunction and death. Treatment strategies aimed at restoring mitochondrial function and enhancing myelin synthesis and repair may alleviate symptoms of these diseases.] | \n", + "[Summary: Peripheral nervous system myelination and neurodegenerative diseases are enriched in this set of genes. \\nMechanism: Maintenance of peripheral nervous system myelin structure and function through regulation of protein import, DNA replication, and degradation pathways in the endoplasmic reticulum and mitochondria. \\n] | \n", + "0.90 | \n", + "224 | \n", + "
| 137 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "sensory ataxia-1 | \n", + "[Summary: Peripheral nerve myelin upkeep and related disease mechanisms\\nMechanism: The genes are involved in maintaining and degrading myelin sheaths in peripheral nerve cells.\\n\\nHypothesis: The enrichment of genes involved in peripheral nerve myelin upkeep suggests a common underlying biological mechanism of maintaining appropriate myelin structure, which can be disrupted by various genetic causes leading to different neuropathic diseases. These genes play crucial roles in ensuring proper nervous system and myelin development, and focus on various biological processes that regulate these mechanisms. Ultimately, disruptions in these genes can lead to peripheral neuropathies and degeneration.] | \n", + "[Summary: Genes involved in various peripheral nervous system disorders are enriched for terms related to myelin formation and maintenance, as well as protein transport and degradation in the ER.\\n\\n\\nHypothesis: These genes likely contribute to proper formation and maintenance of myelin in the peripheral nervous system. Dysfunctions in protein transport and degradation pathways in the ER may also contribute to disease pathogenesis.] | \n", + "0.93 | \n", + "266 | \n", + "
| 138 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "term-GO:0007212-0 | \n", + "[Summary: Signaling via G protein-coupled receptors and cyclic AMP (cAMP) signaling pathway are enriched biological processes in the list of genes.\\n\\nMechanism: The enriched terms suggest that these genes are involved in the regulation of downstream signaling pathways activated by G protein-coupled receptors (GPCRs) and their ligands, leading to the generation of cAMP, a key second messenger in many intracellular signaling pathways.\\n\\n\\nHypothesis: The majority of the genes in the list encode proteins involved in the regulation of GPCR-stimulated cAMP signaling pathways. Signaling through these pathways plays a crucial role in cell proliferation, differentiation, development, synaptic plasticity, and behavior. Dysfunction in cAMP signaling pathways has been implicated in numerous pathophysiological conditions, including psychiatric disorders and cancer.] | \n", + "[Summary: Regulation of signal transduction pathways through G-protein-coupled receptors and neurotransmitter activity.\\nMechanism: G proteins play a central role in signal transduction by coupling receptors to downstream effectors.\\n] | \n", + "0.89 | \n", + "631 | \n", + "
| 139 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "term-GO:0007212-1 | \n", + "[Summary: These genes are involved in signaling pathways mediated by G proteins and second messenger systems, including the dopamine receptor signaling pathway.\\n\\nMechanism: Activation of G protein-coupled receptors results in the dissociation of the G protein alpha subunit from the beta-gamma subunit, leading to the activation of downstream effectors such as adenylyl cyclase and phospholipase C. This results in the production of second messenger molecules such as cyclic AMP and inositol triphosphate, which then activate downstream signaling pathways.\\n\\n] | \n", + "[Summary: These genes are involved in various aspects of cell signaling pathways including G-protein signaling, neurotransmitter receptors, and intracellular signaling.\\n\\nMechanism: These genes are involved in the regulation of cellular responses to extracellular signals, such as neurotransmitter and hormone signals, through G-protein-coupled receptors, resulting in activation of intracellular signaling pathways.\\n\\n] | \n", + "0.93 | \n", + "141 | \n", + "
| 140 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "tf-downreg-colorectal-0 | \n", + "[Summary: Transcriptional regulation and chromatin remodeling are enriched functions in the given set of genes.\\n\\n] | \n", + "[Summary: Transcriptional regulation and chromatin remodeling.\\nMechanism: These genes encode transcription factors and chromatin-associated proteins involved in the regulation of gene expression and chromatin structure.\\n] | \n", + "0.94 | \n", + "107 | \n", + "
| 141 | \n", + "gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "tf-downreg-colorectal-1 | \n", + "[Summary: DNA binding transcription factors involved in regulation of gene transcription and cell development.\\nMechanism: These genes encode for proteins that bind to DNA and regulate gene expression.\\n] | \n", + "[Summary: Transcription regulation\\n\\nHypothesis: These genes are likely to be involved in a common pathway or biological process related to the regulation of gene expression. They may play a role in coordinating the expression of multiple genes, such as those involved in cell differentiation or development. The proteins encoded by these genes may also function together within a larger protein complex involved in regulating transcription.] | \n", + "0.91 | \n", + "240 | \n", + "
| 142 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "EDS-0 | \n", + "[Summary: The common function of the genes is related to extracellular matrix (ECM) organization, collagen synthesis, and glycosaminoglycan (GAG) biosynthesis.\\n\\nMechanism: The enriched terms suggest that these genes play a significant role in extracellular matrix organization and collagen synthesis. The genes involved in glycosaminoglycan biosynthesis are also enriched, indicating their role in stabilizing the extracellular matrix.\\n\\n\\nHypothesis: The extracellular matrix is a complex network of proteins and carbohydrates that provides structural support to tissues. The genes identified in this enrichment are involved in collagen synthesis and extracellular matrix organization. The stabilization of the extracellular matrix is facilitated by the biosynthesis of GAGs. These processes are essential for tissue repair and homeostasis and altered expression of these genes may lead to several connective tissue disorders.] | \n", + "[Summary: Extracellular matrix organization and connective tissue structure are enriched in the given genes.\\nMechanism: Extracellular matrix (ECM) maintenance and remodeling\\n\\nHypothesis: The enriched terms suggest that the given genes are involved in ECM maintenance and remodeling, particularly in collagen fibril organization, protein glycosylation, and peptidase activity. TNXB, COL12A1, ADAMTS2, COL1A2, COL3A1, COL5A1, and COL5A2 are all involved in collagen fibril organization, which is critical for maintaining connective tissue strength and elasticity. B3GALT6, B4GALT7, and CHST14 participate in protein glycosylation, important for the formation of collagens and proteoglycans, while DSE is involved in dermatan sulfate biosynthesis. SLC39A13 regulates zinc ion transport, which is important for ECM structure and stability. FKBP14 and PRDM5 play a role in collagen fiber generation and remodeling. Lastly, C1] | \n", + "0.94 | \n", + "5 | \n", + "
| 143 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "EDS-1 | \n", + "[Summary: Genes are primarily related to extracellular matrix (ECM) organization and collagen biosynthesis.\\nMechanism: The biosynthesis, processing, and assembly of collagen and other ECM components.\\n\\nHypothesis: The listed genes are mostly involved in the organization and biosynthesis of collagens and other components of the extracellular matrix (ECM). The majority of the genes belong to the Category of ECM and Collagen Synthesis in Gene Ontology (GO) hierarchy. The enriched terms include \"Collagen fibril organization,\" \"Extracellular matrix organization,\" and \"Collagen biosynthesis.\" These genes may interact through different pathways to affect ECM composition, remodeling, and cell-ECM interactions. Dysregulation of these genes can lead to various diseases, such as connective tissue disorders and cancer.] | \n", + "[Summary: Genes are enriched for extracellular matrix organization and collagen metabolic process.\\nMechanism: The genes are involved in collagen biosynthesis and extracellular matrix (ECM) remodeling.\\n\\nHypothesis: These genes are involved in extracellular matrix remodeling by encoding proteins involved in collagen biosynthesis and likely play a role in maintaining tissue structure and elasticity.] | \n", + "0.97 | \n", + "418 | \n", + "
| 144 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "FA-0 | \n", + "[Summary: Genes are enriched for DNA repair mechanisms. \\nMechanism: DNA Repair \\n\\nHypothesis: The enriched terms point towards the involvement of these genes in repairing DNA double-strand breaks. These genes are involved in repairing DNA damage and maintaining genome stability, which is critical in preventing cancer development. This suggests that mutations in these genes may increase the risk of cancer due to DNA damage accumulation.] | \n", + "[Summary: Genes are mostly involved in DNA repair and maintenance.\\nMechanism: DNA repair and maintenance pathway\\n] | \n", + "0.91 | \n", + "326 | \n", + "
| 145 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "FA-1 | \n", + "[Summary: These genes are involved in DNA damage repair and cell-cycle checkpoint control.\\nMechanism: Homologous recombination repair pathway\\n\\nHypothesis: These genes are all involved in the homologous recombination repair pathway, which repairs double-strand breaks in DNA. They also contribute to mitotic cell-cycle checkpoint control and the DNA damage response. Dysfunction in these genes can lead to defects in DNA repair and increased risk of cancer development.] | \n", + "[Summary: The genes listed are involved in DNA repair and share functions related to the Fanconi anemia pathway, homologous recombination, and double-strand break repair.\\n\\nMechanism: The genes identified in this list are associated with DNA damage response and repair pathways. Specifically, they are enriched in the Fanconi anemia (FA) pathway, which is a network of proteins involved in the detection and repair of DNA interstrand crosslinks (ICLs). The FA pathway activates a cascade of events that lead to the repair of damaged DNA, including the recruitment of nucleases, helicases, and recombinases to the site of the ICL.\\n\\n] | \n", + "0.92 | \n", + "161 | \n", + "
| 146 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ADIPOGENESIS-0 | \n", + "[Summary: Energy metabolism and lipid transport pathways are enriched in the list of human genes.\\nMechanism: These genes are involved in the regulation and transport of lipids, fatty acids, and energy in the body.\\n\\n] | \n", + "[Summary: Metabolism and energy production are the common themes among the listed genes. Numerous processes and pathways related to energy metabolism, including lipid metabolism, fatty acid oxidation, and mitochondrial function, are enriched.\\n\\nMechanism: The overlapping functions of these genes suggest that they are involved in various metabolic processes important for energy production in cells, including lipid and mitochondrial metabolism.\\n\\n] | \n", + "0.93 | \n", + "232 | \n", + "
| 147 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ADIPOGENESIS-1 | \n", + "[Summary: Several enriched terms relate to energy metabolism and lipid transport/storage, as well as protein folding and stress response mechanisms.\\nMechanism: Possible biological mechanisms include mitochondrial function and fatty acid metabolism.\\n\\n] | \n", + "[Summary: Mitochondrial function and lipid metabolism are enriched functions among the given genes.\\nMechanism: The genes are involved in processes related to mitochondrial function and lipid metabolism. \\n\\n] | \n", + "0.90 | \n", + "45 | \n", + "
| 148 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[Summary: Immune system response and regulation.\\nMechanism: Immune response pathways are activated and regulated by these genes, which contribute to various stages of immune cell development, differentiation, activation, and signaling.\\n] | \n", + "[Summary: Immune response and signaling pathway genes are statistically over-represented in this gene set.\\nMechanism: These genes are involved in regulating different stages of immune response, including the activation and differentiation of immune cells, cytokine signaling, and antigen presentation to T cells.\\n\\n] | \n", + "0.93 | \n", + "78 | \n", + "
| 149 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[Summary: Immune response and inflammation genes are over-represented in the list.\\nMechanism: Immune system activation and response\\n] | \n", + "[Summary: Immune-related functions are enriched in the list of genes.\\nMechanism: Multiple genes involved in various aspects of the immune response.\\n\\n\\nHypothesis: The enrichment of immune-related functions in the list of genes indicates their importance in the immune response. Many of these genes are involved in T cell activation, cytokine signaling, antigen processing and presentation, and leukocyte migration, which are all critical processes in mounting an effective immune response against pathogens or foreign invaders. The enrichment of genes involved in B cell differentiation also suggests a role in the adaptive immune response. Additionally, the significant enrichment of chemokine signaling and interferon signaling genes could indicate a broader regulatory mechanism that influences the immune response.] | \n", + "0.89 | \n", + "686 | \n", + "
| 150 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[Summary: Regulation of transcription, metabolism, and protein degradation are enriched processes among the listed genes.\\nMechanism: The mechanism underlying the enriched processes is likely through the interaction between the genes and transcription factors.\\n] | \n", + "[Summary: Several terms related to transcriptional regulation and protein degradation are enriched in the list of human genes provided.\\n\\nMechanism: The enriched terms suggest that the genes in the list are involved in regulating gene expression, protein stability, and turnover. The specific biological mechanisms underlying these functions likely involve cellular pathways such as ubiquitin-proteasome system, protein degradation, and transcriptional regulation.\\n\\n] | \n", + "0.93 | \n", + "205 | \n", + "
| 151 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[Summary: Genes are involved in various biological processes such as signal transduction, metabolism, and transcriptional regulation.\\nMechanism: None identified.\\n] | \n", + "[Summary: Regulation of transcriptional activity, cell signaling, and metabolism are enriched functions among these genes.\\nMechanism: These genes may be involved in cancer development and progression, as well as other cellular processes.\\n] | \n", + "0.90 | \n", + "76 | \n", + "
| 152 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ANGIOGENESIS-0 | \n", + "[Summary: Extracellular matrix organization and regulation of signaling pathways are enriched functions in the list of genes.\\nMechanism: Extracellular matrix is a complex network of proteins and carbohydrates that provides structural support to cells and tissues, regulates cell behavior, and modulates signaling pathways involved in various physiological and pathological processes.\\n\\nHypothesis: The extracellular matrix is a key regulator of cell behavior and signaling, and its dysfunction is associated with various diseases, including cancer, cardiovascular disease, and connective tissue disorders. These genes are involved in various aspects of extracellular matrix organization and dynamics, such as collagen synthesis and assembly, proteoglycan biosynthesis, adhesion molecules, and extracellular matrix remodeling enzymes. They also regulate key signaling pathways, such as MAP kinase and PI3 kinase pathways, involved in cell proliferation, survival, and migration. Dysfunction of these genes can disrupt extracellular matrix homeostasis and alter cell behavior, leading to various pathological conditions.] | \n", + "[Summary: Genes associated with extracellular matrix and growth factor regulation are enriched.\\nMechanism: Extracellular matrix remodeling and growth factor signaling pathways.\\n\\nHypothesis: The enriched genes are all involved in the regulation and maintenance of the extracellular matrix (ECM), suggesting a significant role in ECM organization and remodeling. The genes are also involved in growth factor signaling, suggesting a role in cell proliferation, differentiation, and wound healing. The findings indicate the importance of ECM organization and growth factor signaling in developmental processes and diseases such as osteogenesis imperfecta, Marfan syndrome, and atherosclerosis.] | \n", + "0.93 | \n", + "428 | \n", + "
| 153 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ANGIOGENESIS-1 | \n", + "[Summary: Extracellular matrix organization and angiogenesis\\nMechanism: Regulation of signaling pathways involving TGF-beta and VEGF\\n\\nHypothesis: The enriched terms suggest that these genes are involved in extracellular matrix organization and angiogenesis. These processes are tightly regulated by signaling pathways involving TGF-beta and VEGF. The list of genes is enriched for those involved in positive regulation of cell migration, endothelial cell proliferation, and cell adhesion, which are all necessary for angiogenesis. Dysregulation of these genes might contribute to pathological conditions such as cancer and cardiovascular diseases.] | \n", + "[Summary: Extracellular matrix organization and angiogenesis\\nMechanism: Integrin signaling\\n\\nHypothesis: The genes in this list are enriched for those involved in the extracellular matrix organization and angiogenesis. These genes are related to integrin signaling which is important for mediating cell adhesion and signaling between the cell and extracellular matrix. The upregulation of these genes indicates an increased demand for extracellular matrix remodeling and angiogenesis in certain contexts, such as tissue regeneration or wound healing.\\n\\nThe enriched terms in this gene list suggest that the genes are involved in extracellular matrix organization, angiogenesis, and cell adhesion. These processes are important for tissue growth and repair and are likely regulated by integrin signaling. This suggests that the genes in this list may be involved in mediating these processes during tissue development or in response to injury.] | \n", + "0.96 | \n", + "293 | \n", + "
| 154 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-0 | \n", + "[Summary: Cell-Cell adhesion and Extracellular matrix organization are statistically enriched functions of the genes.\\n\\nMechanism: These genes are commonly involved in the formation and maintenance of cell-cell adhesion and extracellular matrix (ECM) interactions which play an important role in developmental processes, tissue morphogenesis, and homeostasis.\\n\\n] | \n", + "[Summary: Cell adhesion and cytoskeleton organization processes are enriched in the given list of genes.\\nMechanism: Cell adhesion and cytoskeleton organization are key processes in cell signaling and migration. \\n\\n] | \n", + "0.91 | \n", + "147 | \n", + "
| 155 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-1 | \n", + "[Summary: Cell adhesion and communication, with a focus on tight junctions and claudins\\nMechanism: Signaling pathways involved in regulating tight junctions, such as the MAPK and PI3K-Akt pathways\\n\\nHypothesis: The genes listed are primarily involved in regulating tight junctions, which are structures that serve to tightly regulate the permeability of cells and contribute to the formation of physical barriers between various tissues and organs. The enrichment of terms related to cell adhesion, communication, and cytoskeletal organization suggest that these genes help to coordinate signaling between cells and the actin cytoskeleton, which is necessary for tight junction formation and maintenance. The specific signaling pathways involved likely include the MAPK and PI3K-Akt pathways, as these have been shown to modulate the activity of various tight junction proteins, including claudins. Additionally, several of the genes listed are involved in endothelial cell migration and angiogenesis] | \n", + "[Summary: Cell adhesion and migration\\n] | \n", + "0.86 | \n", + "962 | \n", + "
| 156 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_SURFACE-0 | \n", + "[Summary: Cell adhesion and signaling pathways appear to be the most enriched functions across these genes.\\nMechanism: These genes may be involved in regulating cell signaling pathways and adhesion through their various functions, such as receptor binding, protein interaction, and membrane transport.\\n\\n\\nHypothesis: These genes may play a role in modulating cell signaling and adhesion events that are critical for cellular communication and tissue development. Dysregulation of these pathways may result in various diseases, such as cancer and metabolic disorders.] | \n", + "[Summary: Genes are enriched in terms related to cell adhesion, signaling and transport.\\nMechanism: These genes are involved in pathways that regulate cell adhesion and communication, as well as transport of molecules across cellular membranes.\\n\\n] | \n", + "0.94 | \n", + "320 | \n", + "
| 157 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_SURFACE-1 | \n", + "[Summary: Cell adhesion, migration, and signaling are enriched functions among the listed genes.\\nMechanism: The genes are involved in regulating the activity of various receptor tyrosine kinases, membrane channels, and enzymes involved in intracellular signaling pathways.\\n\\n] | \n", + "[Summary: Genes are enriched for functions related to cell adhesion, signal transduction, and regulation of metabolism.\\nMechanism: These genes may be involved in coordinating cellular processes and responses to environmental signals.\\n\\n\\nHypothesis: The enriched terms suggest that these genes may be involved in regulating cellular processes related to adhesion, signaling, and metabolism. Specifically, they] | \n", + "0.91 | \n", + "134 | \n", + "
| 158 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_APOPTOSIS-0 | \n", + "[Summary: Apoptosis-related and immune response genes are statistically over-represented in the given list of genes.\\nMechanism: The enrichment of these genes suggests the involvement of apoptosis and immune response-related pathways in the biological processes of these genes.\\n] | \n", + "[Summary: Cell death regulation\\n\\nHypothesis: The genes on this list may interact with each other to form signaling pathways that regulate the balance between cell survival and death. Dysregulation of these pathways can lead to pathological conditions such as cancer. Further studies are needed to elucidate the specific mechanisms and interactions among these genes in the context of cell death regulation.] | \n", + "0.87 | \n", + "130 | \n", + "
| 159 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_APOPTOSIS-1 | \n", + "[Summary: Genes are enriched in cellular stress and apoptosis pathways.\\nMechanism: Cellular stress and apoptosis pathways are activated to maintain cellular survival and function.\\n] | \n", + "[Summary: Genes in this list are enriched for functions related to apoptosis, immune response, and cancer.\\nMechanism: These genes play a role in regulating cell death, inflammatory response, and tumor development.\\n\\n] | \n", + "0.90 | \n", + "35 | \n", + "
| 160 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[Summary: Genes are involved in lipid metabolism, specifically in bile acid biosynthesis, cholesterol synthesis and transport, and peroxisome biogenesis.\\nMechanism: Lipid metabolism\\n\\nHypothesis: These genes are enriched for lipid metabolism, specifically in bile acid biosynthesis, cholesterol synthesis and transport, and peroxisome biogenesis. This suggests that these genes are involved in maintaining a healthy balance of lipids in the body and may play a role in the development of lipid-related diseases.] | \n", + "[Summary: Genes are involved in lipid and sterol metabolism, as well as peroxisome biogenesis and function.\\n] | \n", + "0.94 | \n", + "403 | \n", + "
| 161 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[Summary: Genes are enriched for lipid metabolism and transport, as well as peroxisomal and mitochondrial functions.\\nMechanism: Peroxisomes and mitochondria are both involved in various aspects of lipid metabolism and transport, and the enrichment of peroxisomal genes may suggest a role for peroxisomes in these processes.\\n] | \n", + "[Summary: The enriched terms are related to lipid metabolism, transport and catabolism, as well as cellular organelle biogenesis and function.\\nMechanism: These genes are involved in pathways related to cholesterol and bile acid biosynthesis, peroxisomal biogenesis and function, and fatty acid metabolism and transport.\\n\\n] | \n", + "0.94 | \n", + "3 | \n", + "
| 162 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[Summary: Processes related to sterol biosynthesis, lipid metabolism, and cholesterol homeostasis are overrepresented in this gene set.\\nMechanism: Cholesterol homeostasis\\n\\nHypothesis: This gene set is enriched for genes involved in cholesterol homeostasis, reflecting the importance of cholesterol regulation in human biology. Specifically, processes related to sterol biosynthesis, lipid metabolism, and cholesterol transport are overrepresented. Cholesterol is a critical component of cell membranes and is involved in many important cellular processes. Dysregulation of cholesterol metabolism has been linked to a number of human diseases, including cardiovascular disease and neurological disorders. Further research into the genes in this set and their interactions may provide insights into the regulation of cholesterol homeostasis and potential therapeutic targets.] | \n", + "[Summary: Lipid metabolism and cholesterol biosynthesis are significantly enriched in the list of genes provided.\\nMechanism: The enriched terms suggest a pathway leading to the synthesis and transport of lipids and cholesterol within cells.\\n\\n] | \n", + "0.92 | \n", + "632 | \n", + "
| 163 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[Summary: Genes are enriched for lipid metabolism and cholesterol biosynthesis.\\nMechanism: Lipid metabolism and cholesterol biosynthesis pathways.\\n\\nHypothesis: The enriched terms suggest that the listed genes are involved in the biosynthesis, regulation, and metabolism of cholesterol and other lipids, likely through the mevalonate pathway. This pathway generates isoprenoids, which are essential for cholesterol synthesis and other cellular functions. Dysregulation of these genes may contribute to metabolic disorders such as hypercholesterolemia.] | \n", + "[Summary: Lipid metabolism, cholesterol biosynthesis, and steroid biosynthesis are enriched functions among the given genes.\\nMechanism: The enriched functions suggest that these genes play a role in cholesterol and lipid metabolism pathways.\\n\\n] | \n", + "0.95 | \n", + "308 | \n", + "
| 164 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_COAGULATION-0 | \n", + "[Summary: Blood coagulation and complement pathways are enriched in the list of genes.\\nMechanism: The enriched genes are involved in the regulation and activation of the blood coagulation and complement pathways.\\n\\nHypothesis: The enrichment of genes involved in blood coagulation and complement pathways suggests that this list may be specifically relevant to the regulation and activation of these pathways. This may indicate potential involvement in diseases related to these pathways, such as thrombosis, hemophilia, and acute inflammation.] | \n", + "[Summary: Extracellular matrix organization and coagulation cascade regulation are statistically overrepresented functions among the listed genes.\\nMechanism: Many of the genes in the list are involved in regulating extracellular matrix composition and integrity, which is important for tissue structure and homeostasis. This process involves the interaction of various proteases and inhibitors, as well as proteins involved in coagulation cascade regulation. \\n] | \n", + "0.89 | \n", + "84 | \n", + "
| 165 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_COAGULATION-1 | \n", + "[Summary: Extracellular matrix organization, blood coagulation and fibrinolysis, immune defense, and proteolysis are enriched functions shared by the human genes in the list.\\n\\nMechanism: The genes are involved in the formation and maintenance of the extracellular matrix, blood coagulation and fibrinolysis pathways, immune response, and proteolytic processes.\\n\\n] | \n", + "[Summary: Blood coagulation and immune response-related functions are over-represented in the list of genes provided.\\nMechanism: The genes are involved in producing factors required for blood clotting and regulating immune responses.\\n\\n] | \n", + "0.91 | \n", + "127 | \n", + "
| 166 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_COMPLEMENT-0 | \n", + "[Summary: Immune response and inflammation-related functions are enriched in the list of genes.\\nMechanism: Immune response and inflammation-related pathways are activated.\\n\\nHypothesis: The genes in this list play a role in immune response and inflammation. The enriched terms suggest that these genes are involved in complement activation, regulation of proteolysis, and apoptotic signaling. The activation of these pathways may modulate the host immune response to infectious agents and tissue damage. Some of the genes may also play a role in regulating endopeptidase activity, which could be involved in immune response regulation.] | \n", + "[Summary: Immune system regulation and thrombosis prevention\\n\\nHypothesis: The genes in this set are involved in immune system surveillance and regulation, as well as the prevention of thrombosis by maintaining the delicate balance between hemostasis and clotting. These functions are critical in preventing pathological infections and clots, and their dysregulation could lead to autoimmune conditions or thrombotic events.] | \n", + "0.88 | \n", + "211 | \n", + "
| 167 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_COMPLEMENT-1 | \n", + "[Summary: Immune function, coagulation, and protein turnover pathways are enriched based on the list of human genes provided.\\nMechanism: These genes are involved in various biological pathways related to immune response, hemostasis, and regulation of protein turnover.\\n\\n\\nHypothesis: The enrichment of immune response and blood coagulation terms suggests that these genes may be involved in the inflammatory response and contribute to the maintenance of the immune system. The enrichment of protein turnover terms suggests that these genes may be involved in the regulation of protein stability and degradation, which could be important for cellular function and homeostasis. Overall, these genes likely play key roles in a variety of biological processes and pathways that are critical for normal physiological function in humans.] | \n", + "[Summary: Immune system response and blood coagulation are the most statistically over-represented functions in the list of human genes provided.\\nMechanism: The genes in this list are mostly involved in regulating the immune response and blood coagulation pathways. \\n\\n] | \n", + "0.93 | \n", + "563 | \n", + "
| 168 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_DNA_REPAIR-0 | \n", + "[Summary: DNA replication and repair, transcription, mRNA processing, and purine metabolism are over-represented in the set of human genes.\\nMechanism: These genes are mainly involved in maintaining genome integrity, providing the necessary machinery for DNA replication and repair, and regulating gene expression.\\n\\n] | \n", + "[Summary: DNA replication and repair\\nMechanism: DNA replication and repair\\n] | \n", + "0.86 | \n", + "240 | \n", + "
| 169 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_DNA_REPAIR-1 | \n", + "[Summary: RNA transcription and DNA repair are enriched functions among the given genes.\\nMechanism: These genes encode for proteins involved in DNA transcription and repair processes.\\n\\nHypothesis: The enriched functions suggest that these genes are involved in the regulation of RNA transcription and DNA repair processes. The RNA polymerase activity and DNA binding terms demonstrate their role in the initial transcription process, while the mRNA processing and DNA repair terms represent their involvement in the post-transcriptional regulation and repair of DNA damage, respectively. Overall, these genes likely play a crucial role in maintaining genetic stability and proper gene expression.] | \n", + "[Summary: Genes in the list are involved in DNA replication, repair, and transcription.\\nMechanism: DNA maintenance\\n] | \n", + "0.89 | \n", + "582 | \n", + "
| 170 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_E2F_TARGETS-0 | \n", + "[Summary: DNA replication and cell cycle regulation\\nMechanism: Genes are involved in DNA replication and mitotic cell cycle regulation\\n] | \n", + "[Summary: DNA replication, cell division and chromosome segregation\\nMechanism: DNA replication and mitosis\\n\\nHypothesis: This list of genes is heavily enriched for genes involved in DNA replication, mitosis and chromosome segregation, suggesting that these are the major underlying biological mechanisms. Many of these genes are part of regulatory pathways that control these processes, such as the cell cycle and DNA damage response pathways. The enrichment of nucleosome assembly genes in this list suggests that this is a critical step in the DNA replication process, as nucleosomes must be efficiently assembled and disassembled to enable the progression of the replication fork. Additionally, genes involved in DNA repair are also enriched, indicating that these processes are tightly coordinated with DNA replication and mitosis to ensure genome stability.] | \n", + "0.91 | \n", + "727 | \n", + "
| 171 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_E2F_TARGETS-1 | \n", + "[Summary: DNA replication and repair are enriched functions of the given genes.\\nMechanism: These genes are predominantly involved in the control and regulation of DNA replication and repair. Specific functions include DNA unwinding, strand break repair, DNA synthesis, and checkpoint signaling.\\n] | \n", + "[Summary: DNA replication and repair, cell cycle regulation, and chromosome segregation are enriched terms among the given genes.\\nMechanism: These genes are involved in the regulation of DNA replication, repair mechanisms, proper chromosome segregation during mitosis, and inactivation of the cell cycle checkpoints.\\n] | \n", + "0.93 | \n", + "22 | \n", + "
| 172 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[Summary: Extracellular matrix (ECM) organization and regulation of cell signaling are significantly enriched functions for the given set of genes.\\nMechanism: The enriched terms suggest that these genes are involved in maintaining tissue integrity and regulating cellular activity in response to the extracellular environment.\\n\\n\\nHypothesis: The genes in this list are involved in maintaining tissue integrity and regulating cellular activity in response to the extracellular environment. The ECM is critical in regulating cell behavior and signaling, and therefore the ECM organization is necessary for cellular homeostasis. The enriched terms suggest that the set of genes play a role in cell adhesion and integrin-mediated signaling pathways, which are important] | \n", + "[Summary: Extracellular matrix organization and regulation of growth factor signaling pathways\\nMechanism: The genes in this list are enriched for functions involved in extracellular matrix organization and regulation of signaling pathways for growth factors. These processes are critical for tissue development, maintenance, and repair.\\n\\n] | \n", + "0.93 | \n", + "427 | \n", + "
| 173 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[Summary: Extracellular matrix organization and cell adhesion.\\nMechanism: ECM remodeling and tissue development during embryogenesis, wound healing and cancer progression.\\n] | \n", + "[Summary: Extracellular matrix organization and regulation of cell adhesion are enriched functions common among the listed genes.\\n\\nMechanism: The genes identified are involved in the maintenance of extracellular matrix homeostasis and cell adhesion. They are part of a complex network that controls the behavior and function of cells in various tissues.\\n\\n\\nHypothesis: The identified genes are involved in the regulation of a variety of cellular processes that are required for proper tissue development and homeostasis. Dysregulation of these genes may contribute to various pathological conditions, such as fibrosis, cancer, and developmental disorders.] | \n", + "0.89 | \n", + "483 | \n", + "
| 174 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[Summary: Transport and cellular metabolic processes are overrepresented in these genes.\\nMechanism: Many of these genes are involved in transport and metabolic processes of cells. These pathways play a crucial role in the functioning of cells.\\n] | \n", + "[Summary: Calcium ion binding and metabolism\\nMechanism: Calcium ions modulate a wide range of biological processes, including intracellular signaling, protein function, and gene expression.\\n] | \n", + "0.81 | \n", + "54 | \n", + "
| 175 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[Summary: Genes are enriched for functions involved in lipid metabolism and transport, signal transduction, and transcriptional regulation.\\nMechanism: The over-representation of lipid metabolism and transport genes likely reflects the importance of efficient lipid processing and transport in cell growth and homeostasis. The signal transduction and transcriptional regulation pathways may be involved in modulating lipid metabolism and transport in response to changing cellular or environmental conditions.\\n] | \n", + "[Summary: The common function among the provided genes is related to various cellular and biological processes such as metabolism, transport, signaling, and regulation.\\n\\nMechanism: No specific mechanism can be inferred without further analysis.\\n\\n] | \n", + "0.91 | \n", + "263 | \n", + "
| 176 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[Summary: Genes are enriched in multiple biological processes and pathways.\\nMechanism: Multiple mechanisms and pathways are involved in the functions of these genes.\\n] | \n", + "[Summary: Calcium ion binding and transport, regulation of cell division, and inhibition of apoptosis are enriched functions among the given genes.\\nMechanism: Calcium signaling and regulation of cellular processes through calcium ions.\\n] | \n", + "0.83 | \n", + "70 | \n", + "
| 177 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[Summary: The enriched terms describe genes involved in various biological processes such as metabolism, signal transduction, development, and immune response.\\nMechanism: No specific mechanism was identified given the broad range of enriched terms.\\n] | \n", + "[Summary: Cell cycle regulation and cancer-related functions are enriched in the gene set.\\nMechanism: The genes are mostly involved in regulating cell division and proliferation, with some genes also implicated in cancer progression.\\n] | \n", + "0.84 | \n", + "15 | \n", + "
| 178 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[Summary: Genes involved in metabolism and oxidative stress response are enriched.\\nMechanism: These genes are involved in the metabolism of lipids, amino acids, and carbohydrates, as well as in the detoxification of harmful substances and protection against oxidative stress.\\n\\n\\nHypothesis: These genes work together in maintaining cellular metabolism and homeostasis, including the production and utilization of energy, regulation of nutrient balance, and protection against external and internal stressors. This involves the breakdown and synthesis of biomolecules, generation of reducing equivalents for energy production, and removal of toxic compounds and reactive oxygen species. The enriched pathways suggest that these genes are involved in oxidative phosphorylation and other mitochondrial processes, lipid and glucose metabolism, and ion transport. Dysfunction of these genes may] | \n", + "[Summary: Beta-oxidation of fatty acids, metabolic processes, and energy production pathways are enriched in the list of genes.\\n\\nMechanism: The list of genes is involved in the pathway of β-oxidation of fatty acids and energy production, promoting various metabolic processes.\\n\\n] | \n", + "0.90 | \n", + "611 | \n", + "
| 179 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[Summary: Genes are involved in lipid metabolism, energy production, and oxidative stress response.\\nMechanism: These genes function in pathways related to maintaining cellular homeostasis through the production and utilization of energy, the breakdown and metabolism of lipids, and the response to oxidative stress.\\n] | \n", + "[Summary: These genes are involved in various metabolic processes, including lipid metabolism and energy production. \\nMechanism: The common underlying mechanism appears to be mitochondrial function and metabolism.\\n] | \n", + "0.94 | \n", + "102 | \n", + "
| 180 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-0 | \n", + "[Summary: Chromosomal segregation and cell cycle progression\\nMechanism: Regulation of the cell cycle and mitosis\\n\\nHypothesis: \\nThe enrichment of terms related to cell cycle progression and chromosomal segregation suggests that the genes on this list primarily play a role in regulating the progression of cells through the cell cycle and ensuring proper chromosome segregation during mitosis. These genes likely encode various proteins involved in DNA replication, mitotic spindle organization, microtubule cytoskeleton dynamics, and the regulation of cell cycle checkpoints, all of which are critical for the proper progression of cells through the cell cycle and the maintenance of genomic stability. The diverse range of gene functions represented on this list is likely indicative of the complex and tightly regulated nature of the cell cycle and mitotic processes.] | \n", + "[Summary: Cell cycle regulation and chromosome segregation\\nMechanism: The genes are enriched for functions involved in cell cycle regulation, specifically in the G2/M phase transition and chromosome segregation.\\n\\n] | \n", + "0.93 | \n", + "656 | \n", + "
| 181 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-1 | \n", + "[Summary: DNA replication and cell cycle regulation.\\nMechanism: The genes enriched for this analysis are mainly involved in the regulation of DNA replication and cell cycle progression.\\n] | \n", + "[Summary: Cell cycle regulation and DNA replication are enriched functions in the given list of genes.\\n\\nMechanism: The enriched functions of cell cycle regulation and DNA replication suggest that the genes in the list play a role in regulating the overall cell division process. Specifically, the genes are involved in DNA synthesis, repair, and proper chromosomal segregation, ensuring genomic stability and accurate transmission of genetic information.\\n\\n] | \n", + "0.95 | \n", + "270 | \n", + "
| 182 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_GLYCOLYSIS-0 | \n", + "[Summary: Glycosylation and Metabolism\\nMechanism: Glycosylation is a common function enriched in these genes, and many are involved in metabolic pathways such as glycolysis and the pentose phosphate pathway.\\n\\n] | \n", + "[Summary: Energy metabolism and glycosylation pathways are significantly enriched.\\nMechanism: These genes are involved in energy metabolism, specifically in glycolysis and glycogen biosynthesis pathways. Additionally, they are involved in glycosylation pathways, which play a role in post-translational modifications.\\n] | \n", + "0.95 | \n", + "109 | \n", + "
| 183 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_GLYCOLYSIS-1 | \n", + "[Summary: Cellular metabolism and energy production\\nMechanism: Glycolysis and related pathways\\n] | \n", + "[Summary: Genes are involved in cellular metabolism and signaling pathways.\\nMechanism: This set of genes appears to be involved in the regulation of metabolic pathways in cells and are involved in various signaling pathways affecting cellular functions.\\n] | \n", + "0.87 | \n", + "159 | \n", + "
| 184 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[Summary: Neuronal development and axon guidance-related terms are significantly enriched in the list of genes.\\nMechanism: Neuronal development and axon guidance.\\n\\nHypothesis: The genes in the list are involved in the development and guidance of neuronal cells. Several enriched terms denote processes that are crucial for the proper formation and function of the nervous system, such as neuron differentiation, axon guidance, and cell migration. This suggests that the identified genes play a role in the establishment and maintenance of neural connections. The common functional theme may be mediated by signaling pathways that regulate cell adhesion, migration, and proliferation, which are critical for neural development and the formation of axonal connections. The enriched terms suggest that the proteins encoded by these genes might be involved in the modulation of cytoskeletal dynamics, cell signaling, and adhesion processes that regulate neurite outgrowth and synapse formation. Some genes listed here have been shown to play a role in neurodevelopmental disorders such as autism and epilepsy.] | \n", + "[Summary: Genes are enriched in terms related to nervous system development, signaling and angiogenesis.\\nMechanism: Signaling pathways related to neural development and angiogenesis.\\n\\nHypothesis: This set of genes is involved in the signaling pathways related to neural development and angiogenesis. The enriched terms, including nervous system development, neuron differentiation, embryonic morphogenesis, and regulation of angiogenesis, suggest that these genes are involved in complex processes related to neural network formation and elaboration, as well as vascular patterning and growth. Additionally, the genes in this list seem to be involved in positive regulation of signaling, which may play a role in the tight regulation of the complex developmental processes involved.] | \n", + "0.93 | \n", + "323 | \n", + "
| 185 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[Summary: Genes are primarily involved in nervous system development, signal transduction, and cell adhesion.\\nMechanism: Not specified.\\n] | \n", + "[Summary: Genes are mainly involved in neural development and signaling pathways.\\nMechanism: Regulation of neural development and signaling pathways.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the development and maintenance of the nervous system. Many of the genes are associated with axon guidance and are involved in regulating the development of neuronal projections. The regulation of nervous system development and cell-cell signaling pathways may also play a role in coordinating the development of different types of neurons and neural circuits.] | \n", + "0.93 | \n", + "448 | \n", + "
| 186 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_HEME_METABOLISM-0 | \n", + "[Summary: Transport, binding, and metabolism processes are enriched in these human genes.\\nMechanism: These genes are involved in various cellular pathways such as ion transport, protein binding, and metabolic processes.\\n\\n] | \n", + "[Summary: Transport and binding process for heme and iron-sulfur clusters, as well as [2Fe-2S] clusters, are enriched among the listed genes.\\nMechanism: Iron-containing proteins involved in biological processes require a tightly regulated system of transport and binding, which is facilitated by these enriched gene functions.\\n\\n] | \n", + "0.89 | \n", + "107 | \n", + "
| 187 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_HEME_METABOLISM-1 | \n", + "[Summary: Hemoglobin production and erythropoiesis are over-represented in the list of genes.\\nMechanism: Regulation of hemoglobin synthesis through erythropoietin signaling pathway.\\n\\n] | \n", + "[Summary: This set of genes is enriched for terms related to gene expression regulation, metabolism, and transport.\\n\\n] | \n", + "0.83 | \n", + "66 | \n", + "
| 188 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_HYPOXIA-0 | \n", + "[Summary: Cellular metabolism and response to stress-related stimuli are enriched in the gene list.\\nMechanism: Metabolic pathways and cellular stress response pathways may be dysregulated in diseases associated with these genes.\\n\\n] | \n", + "[Summary: Cell metabolism, growth, and development are the most enriched functions among the given list of genes.\\nMechanism: These genes are predominantly associated with the regulation of glucose and energy homeostasis, cell proliferation, and extracellular matrix formation.\\n\\nHypothesis: The common biological mechanisms that underlie the functions of these genes involve the regulation of glucose and energy metabolism, which is essential for cell growth and development. They also regulate the formation of the extracellular matrix, which is crucial for the organization and maintenance of tissues and organs. These genes might be involved in signaling cascades that regulate cell proliferation, differentiation, and migration in response to changes in the microenvironment.] | \n", + "0.89 | \n", + "549 | \n", + "
| 189 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_HYPOXIA-1 | \n", + "[Summary: Energy metabolism\\n\\nHypothesis: The genes listed display over-represented functions involved in energy metabolism, leading to the hypothesis that they may be involved in maintaining energy homeostasis in the body. The shared functions related to glucose uptake and metabolism may be regulated by a common pathway, such as the insulin signaling pathway, that coordinates the activity of these genes. Additionally, the functions related to ATP production may be affected by mitochondrial activity and oxidative phosphorylation. Further studies are needed to elucidate the exact mechanisms and pathways involved in the regulation of these genes.] | \n", + "[Summary: Carbohydrate metabolism and glycolysis are statistically over-represented in the list of genes.\\nMechanism: The genes involved in carbohydrate metabolism and glycolysis play a key role in energy production and cell signaling.\\n] | \n", + "0.91 | \n", + "417 | \n", + "
| 190 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[Summary: Immune system and inflammation-related functions are enriched in this gene list.\\nMechanism: These genes may be involved in regulating the immune response and inflammatory processes.\\n\\n] | \n", + "[Summary: Immune system functions are enriched in these genes, particularly those related to cytokine signaling, cell activation, and regulation.\\n\\nMechanism: The genes on this list are primarily involved in regulating the immune system. Many are involved in cytokine signaling, cell activation, and regulation. This suggests that the enriched terms are related to immune response and function.\\n\\n] | \n", + "0.93 | \n", + "202 | \n", + "
| 191 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[Summary: Signaling pathways related to immune response, cytokine signaling, and inflammation are enriched in the list of human genes.\\n\\nMechanism: These genes likely play a role in coordinating the immune system's response to pathogens or damage signals.\\n\\n] | \n", + "[Summary: Cell signaling and immune response\\nMechanism: Pathways involving cytokines, chemokines, and growth factors\\n\\nHypothesis: The genes in the list are involved in cell signaling and immune response. They play critical roles in the regulation of immune cell function, inflammation, and chemotaxis. The enriched terms, including immune response, cytokine activity, and chemokine activity, suggest that the genes are involved in cytokine signaling pathways, which mediate cellular responses to pathogens and other external stimuli. The genes may also be involved in growth factor signaling, which regulates cell proliferation and differentiation during development and tissue repair. Overall, the genes in the list likely form a complex regulatory network that is essential for the proper functioning of the immune system.] | \n", + "0.94 | \n", + "569 | \n", + "
| 192 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[Summary: Immune response and cytokine signaling pathway are enriched functions among the listed human genes.\\nMechanism: These genes seem to be involved in regulation and activation of immune cells and cytokine signaling pathways.\\n\\nHypothesis: These genes are potentially involved in the immune response to infections and inflammation. They may also play a role in the regulation of cytokine production and signaling, which can influence the development and progression of inflammatory and autoimmune diseases.] | \n", + "[Summary: Immune response and signaling\\nMechanism: Cytokine signaling and immune response activation \\n\\n] | \n", + "0.89 | \n", + "408 | \n", + "
| 193 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[Summary: Immune system response\\nMechanism: Cytokine signaling pathway\\n] | \n", + "[Summary: Cytokine signaling and inflammation are the common functions enriched in these genes.\\nMechanism: These genes are involved in modulating the immune system's response to infection, injury, or stress.\\n\\nHypothesis: These genes are involved in regulating the inflammatory response through cytokine signaling. They are responsible for activating immune cells, triggering inflammation, and recruiting immune cells to sites of infection or injury. The JAK-STAT and Toll-like receptor signaling pathways play important roles in this process. Dysregulation of these genes can lead to chronic inflammation and autoimmune diseases.] | \n", + "0.87 | \n", + "559 | \n", + "
| 194 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[Summary: Immune response and signal transduction\\nMechanism: Immune regulation and inflammation\\n] | \n", + "[Summary: Immune response, inflammation, and cytokine signaling-related functionality is enriched in the given list of genes.\\nMechanism: These genes are involved in the activation, regulation, and resolution of immune response and inflammation.\\n] | \n", + "0.88 | \n", + "149 | \n", + "
| 195 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[Summary: Immune response and inflammation processes.\\nMechanism: Signaling pathways involved in immune response and inflammation.\\n\\nHypothesis: The enriched terms suggest that the genes in the list may be involved in immune response and inflammation. Immune cells recruit cytokines and chemokines to elicit an immune response. The genes could be involved in signaling pathways that regulate leukocyte migration and inflammation. Additionally, they may play a role in mediating adaptive and innate immune responses.] | \n", + "[Summary: These human genes are enriched in immune system-related functions.\\nMechanism: These genes are involved in immune response and immunoregulation pathways.\\n\\n] | \n", + "0.90 | \n", + "350 | \n", + "
| 196 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[Summary: Genes are involved in interferon signaling, immune response, and antiviral defense mechanisms.\\nMechanism: These genes are involved in the innate immune response to viral infection and defense against other pathogens.\\n\\nHypothesis: These genes are likely involved in the interferon signaling pathway, which triggers an innate immune response against viral infections and activates antiviral defense mechanisms. The enriched terms suggest that the genes are involved in various stages of the immune response, including detection of viral RNA and DNA (DDX60, DHX58, IFIH1, etc.), induction of interferon production (IRF7, IRF9, etc.), and downstream signaling and immune activation (STAT2, TRAFD1, TRIM25, etc.). Additionally, some genes (ISG15, MX1, OAS1, etc.) directly inhibit viral replication and promote viral clearance. Overall, these genes are critical for the body's defense against viral infections and likely interact with other immune response pathways to maintain homeostasis.] | \n", + "[Summary: These genes are involved in the antiviral response and immune system regulation.\\nMechanism: These genes are part of the Type I interferon response pathway, which is activated by viral infection.\\n\\n] | \n", + "0.95 | \n", + "790 | \n", + "
| 197 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[Summary: Immune response and antiviral pathways are enriched functions in the given gene list.\\nMechanism: The genes are involved in various pathways that contribute to the antiviral defense mechanism of the human body.\\n\\n\\nHypothesis: The enriched terms suggest that the given genes function in the activation of innate and adaptive immune responses against viral infections through the interferon signaling pathway. The genes act as key regulators of viral replication and transcription, and contribute to the antiviral defense mechanism of the human body.] | \n", + "[Summary: Genes associated with antiviral response, immune system processes, and interferon signaling pathways.\\n\\nMechanism: These genes are involved in the activation of the antiviral response and immune system processes, particularly through the interferon signaling pathway.\\n\\n] | \n", + "0.93 | \n", + "279 | \n", + "
| 198 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[Summary: This list of genes includes those involved in antiviral and immunological responses, as well as genes involved in regulating cellular processes such as cellular growth and metabolism. \\n\\nMechanism: These genes are involved in the immune response to viral infections and in regulating cellular processes such as growth and metabolism.\\n\\n\\nHypothesis: The enriched terms suggest that the common function of these genes is the regulation of antiviral and immunological responses in addition to the regulation of cellular processes such as metabolism and growth. It is likely that these genes work together to promote cellular immunity against viral infections and regulate cellular processes that support antiviral responses.] | \n", + "[Summary: Type I interferon signaling pathway activation, immune response, antigen processing and presentation \\n\\n] | \n", + "0.83 | \n", + "617 | \n", + "
| 199 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[Summary: Immune response and antiviral pathways are enriched.\\n\\nMechanism: The genes in the list have a common function in response to viral infection through various pathways including interferon signaling, antigen processing and presentation, and immune cell activation.\\n\\n] | \n", + "[Summary: Genes involved in immune response and inflammation are enriched.\\n\\nMechanism: These genes are all involved in the immune response and inflammation. They play a role in antigen processing and presentation, interferon response, cytokine production, and activation of inflammatory pathways.\\n\\n] | \n", + "0.92 | \n", + "24 | \n", + "
| 200 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[Summary: Calcium ion binding and regulation of muscle contraction \\nMechanism: Calcium signaling \\n] | \n", + "[Summary: Calcium ion binding and membrane transport are the most enriched functions in these genes.\\nMechanism: The majority of enriched terms are related to the transport of calcium ions across cell membranes, as well as regulation of intracellular calcium concentration.\\n\\n] | \n", + "0.86 | \n", + "176 | \n", + "
| 201 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[Summary: This list of human genes is enriched for terms related to ion binding, signaling, and regulation of metabolic and cellular processes.\\nMechanism: These functions are likely involved in maintaining homeostasis and cell function through various signaling pathways.\\n\\n] | \n", + "[Summary: Genes are enriched for terms related to ion transport, neurological signaling, and tissue development.\\n\\nHypothesis: These genes are potentially involved in regulating ion transport, such as calcium, sodium, and potassium, which are critical for neuronal signaling and tissue morphogenesis. Many of these genes are expressed in a variety of tissues and organs, including the brain, heart, and endocrine glands, suggesting they may have widespread physiological roles. The function of these genes may overlap in the regulation of cellular calcium balance, neural transmission, and developmental processes, which could contribute to human disease when disrupted.] | \n", + "0.92 | \n", + "397 | \n", + "
| 202 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[Summary: Regulation of immune response and cell signaling \\nMechanism: Not enough information to make a hypothesis \\n] | \n", + "[Summary: Regulation of immune response, cellular signaling, and angiogenesis.\\nMechanism: The enriched terms suggest that these genes are involved in the regulation of immune response and cellular signaling pathways, as well as angiogenesis.\\n] | \n", + "0.87 | \n", + "126 | \n", + "
| 203 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[Summary: Immune response and inflammation-related functions are enriched in the list of genes.\\nMechanism: The genes are involved in regulating the immune system and its response to pathogens, as well as controlling inflammation pathways.\\n\\n\\nHypothesis: The enriched functions suggest that the genes play a role in regulating the immune system response to pathogens and inflammation. The genes may be involved in controlling signaling pathways for cytokines, chemokines, and interleukins, as well as regulating leukocyte activation and complement activation. Additionally, the genes may be involved in eicosanoid synthesis pathways and platelet activation and aggregation. Overall, the enrichment of these functions suggests that the genes play a role in immune system surveillance and response to infections and other stimuli.] | \n", + "[Summary: Immune response and inflammation, coagulation, cell adhesion, and signal transduction are enriched functions among the genes.\\n\\n] | \n", + "0.93 | \n", + "690 | \n", + "
| 204 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[Summary: Genes are enriched for microtubule-based processes and cellular division.\\nMechanism: The genes listed are involved in microtubule-based processes and cellular division. The enriched terms highlight the specific aspects of these processes that these genes are involved in. \\n\\n] | \n", + "[Summary: Cell division and cytoskeleton organization are the commonly enriched functions among the given genes.\\nMechanism: The enrichment of these terms suggests that these genes play an important role in regulating mitotic spindle formation and organization of actin filaments.\\n\\n] | \n", + "0.92 | \n", + "3 | \n", + "
| 205 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[Summary: Microtubule formation and spindle assembly during cell division.\\nMechanism: The genes are involved in microtubule formation and spindle assembly during cell division. These genes are related to the structural integrity and mediator of spindle formation and the cleavage furrow during cytokinesis.\\n] | \n", + "[Summary: Mitotic spindle organization and chromosome segregation\\nMechanism: Mitotic spindle assembly checkpoint\\n\\nHypothesis: The enrichment of terms related to the mitotic spindle organization, chromosome segregation, and spindle assembly checkpoint suggests that these genes play a critical role in mitosis and cell division. These genes likely regulate microtubule dynamics, centrosome function, and kinetochore-microtubule interactions to ensure the proper alignment, segregation, and separation of chromosomes during mitosis. Dysfunction of these genes may lead to chromosomal instability, aneuploidy, and tumorigenesis.] | \n", + "0.90 | \n", + "319 | \n", + "
| 206 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-0 | \n", + "[Summary: The enriched terms shared among these genes are related to protein folding, metabolism, and immune response pathways.\\n\\nMechanism: These genes appear to share a connection through signaling pathways that regulate protein folding, metabolism, and immune response.\\n\\n] | \n", + "[Summary: Cellular metabolism\\n] | \n", + "0.81 | \n", + "243 | \n", + "
| 207 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-1 | \n", + "[Summary: Genes identified have functions predominantly involved in cellular metabolism and protein handling, including regulation of transcription and translation. There is also enrichment in genes associated with response to stress and DNA repair.\\n\\n\\nHypothesis: The identified genes are likely involved in cellular processes that are essential for growth and survival, including the maintenance of cellular metabolism, response to stress, and DNA repair. Dysregulation of these pathways may lead to disease states such as cancer or neurodegeneration. Further analysis and studies of these genes and their pathways could inform novel therapies for these conditions.] | \n", + "[Summary: Protein folding and metabolism are enriched functions among these human genes.\\nMechanism: These genes may play a key role in maintaining protein homeostasis and regulating metabolic pathways.\\n] | \n", + "0.90 | \n", + "465 | \n", + "
| 208 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-0 | \n", + "[Summary: Genes associated with protein synthesis, processing, and folding are overrepresented in the list.\\n\\nHypothesis: These genes work together in a network to facilitate protein synthesis, processing, and folding. They may also play a role in RNA splicing through their association with the U4/U6.U5 tri-snRNP complex. Dysfunction of this network may lead to disrupted protein synthesis and processing, resulting in diseases such as neurodegeneration and cancer.] | \n", + "[Summary: RNA processing and translation initiation\\nMechanism: Regulation of ribosome assembly and function\\n] | \n", + "0.84 | \n", + "359 | \n", + "
| 209 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-1 | \n", + "[Summary: RNA processing and translation \\nMechanism: The enriched terms suggest that the genes are involved in various aspects of RNA processing and translation.\\n\\n] | \n", + "[Summary: RNA processing and translation are enriched functions in the given gene list.\\nMechanism: The genes are involved in regulating RNA processing and translation, necessary for cellular growth and proliferation.\\n\\n] | \n", + "0.94 | \n", + "55 | \n", + "
| 210 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-0 | \n", + "[Summary: RNA processing and ribosome biogenesis\\nMechanism: These genes are involved in RNA processing and ribosome biogenesis, specifically in various stages of transcription, modifying RNA, ribosomal assembly, and transport.\\n] | \n", + "[Summary: The common function among the genes is related to RNA processing and ribosome biogenesis. \\nMechanism: The genes are involved in various steps of transcription, splicing, and translation of RNA.\\n\\nHypothesis: The enriched terms suggest that the genes are primarily involved in the regulation of ribosome biogenesis and RNA processing. This may be due to their role in the maintenance of cellular homeostasis by controlling protein synthesis and turnover. Dysfunction of these genes may lead to defects in ribosome biogenesis, causing impaired protein synthesis and contributing to various diseases, including cancer and neurodegenerative disorders.] | \n", + "0.93 | \n", + "430 | \n", + "
| 211 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-1 | \n", + "[Summary: The common function of the genes is related to RNA processing and transcription regulation. \\nMechanism: The genes are involved in regulating different steps in the transcription and processing of RNA. \\n\\nHypothesis: The genes in this list are all involved in different aspects of RNA processing and transcription regulation. These processes are essential for the production of functional RNAs, which are required for gene expression and cellular communication. It is likely that the proteins encoded by these genes interact with each other and with other factors to form complexes that facilitate RNA processing and transcription. Dysfunction of these processes has been associated with a range of human diseases, including cancer and developmental disorders.] | \n", + "[Summary: Genes in the list are functionally enriched in processes related to ribosome biogenesis and RNA metabolism.\\nMechanism: The genes in the list are all involved in the formation and functioning of ribosomes, which are essential cellular machinery for protein synthesis. They are also involved in RNA metabolism, which includes transcription, splicing, ribonucleoprotein assembly, and RNA transport.\\n\\n] | \n", + "0.91 | \n", + "362 | \n", + "
| 212 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MYOGENESIS-0 | \n", + "[Summary: Muscle structure and function, including contraction and calcium handling, are enriched functions among the listed genes.\\nMechanism: Muscle contraction and calcium handling.\\n\\nHypothesis: The enriched genes are largely involved in the structure and function of skeletal and cardiac muscle tissue, contributing to processes such as contraction and calcium handling. The Z-disc, sarcomere, and thin filaments are important structural components of muscle, and genes involved in their assembly and maintenance are among the enriched terms. Calcium ion transport is also an important function in muscle cells, and genes involved in this process, as well as those involved in the assembly and regulation of the troponin-tropomyosin complex that regulates calcium-dependent muscle contraction, are also enriched.] | \n", + "[Summary: Muscle contraction and development\\n\\nHypothesis: The significant enrichment of genes involved in muscle contraction and sarcomere development suggests that there may be shared pathways and mechanisms governing these processes. One potential pathway may involve the regulation of actin and myosin filaments, which are crucial components of the sarcomere and fundamental to muscle contraction. Another potential pathway may involve the coordination of signaling cascades that promote muscle growth and differentiation. Further research in these areas could lead to a better understanding of muscle function and the treatment of muscle-related diseases.] | \n", + "0.90 | \n", + "156 | \n", + "
| 213 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_MYOGENESIS-1 | \n", + "[Summary: Muscle structure and function\\nMechanism: Muscle contraction and maintenance\\n\\nHypothesis: These genes are mainly involved in muscle structure and function. They function in muscle contraction and maintenance through various mechanisms, including regulation of muscle filaments, myosin activity, and actin dynamics. The statistically over-represented terms are related to muscle structure and function, such as muscle, myosin, actin, troponin, and filament. These genes likely interact to control muscle contraction and maintenance, and may be involved in various muscle disorders and diseases.] | \n", + "[Summary: Muscle structure and contraction.\\nMechanism: Actin-myosin interaction and sarcomere formation.\\n] | \n", + "0.88 | \n", + "498 | \n", + "
| 214 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-0 | \n", + "[Summary: Genes are enriched for functions involved in Notch signaling and Wnt signaling pathways.\\nMechanism: Notch and Wnt signaling pathways are major signaling pathways that regulate cell fate determination and differentiation during development.\\n\\n] | \n", + "[Summary: Genes are primarily involved in Notch pathway signaling and Wnt pathway signaling.\\nMechanism: The Notch pathway and Wnt pathway signaling are two important mechanisms for cell signaling and development.\\n\\nHypothesis: The genes listed are involved in regulating cell signaling and differentiation pathways such as the Notch and Wnt pathways. These pathways are responsible for the development of various tissues and organs in the body. Dysregulation of these genes and pathways can lead to developmental abnormalities and diseases.] | \n", + "0.96 | \n", + "289 | \n", + "
| 215 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-1 | \n", + "[Summary: These genes are involved in the Notch signaling pathway and cell proliferation regulation.\\nMechanism: The Notch signaling pathway is involved in cell fate specification and differentiation during development and in adult tissues.\\n] | \n", + "[Summary: Genes are mostly involved in the development and regulation of the Notch signaling pathway.\\nMechanism: The Notch signaling pathway is involved in cell-to-cell communication, controlling cell fate decisions and differentiation during development.\\n] | \n", + "0.95 | \n", + "16 | \n", + "
| 216 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[Summary: Mitochondrial respiration\\n\\nHypothesis: Dysregulation of these genes may result in impaired mitochondrial function, decreased ATP production, and cellular metabolic dysfunction, leading to a variety of diseases including neurodegenerative disorders and metabolic disorders.] | \n", + "[Summary: Mitochondrial function and energy production pathways are enriched in the list of genes.\\n\\nMechanism: The genes in the list are involved in various aspects of mitochondrial oxidative phosphorylation and energy production pathways.\\n\\n] | \n", + "0.88 | \n", + "42 | \n", + "
| 217 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[Summary: These genes are involved in mitochondrial function and energy metabolism.\\nMechanism: Mitochondrial electron transport chain and oxidative phosphorylation.\\n\\n] | \n", + "[Summary: Mitochondrial respiratory chain function\\nMechanism: Oxidative Phosphorylation\\n\\nHypothesis: These genes are primarily involved in mitochondrial respiratory chain function, specifically in oxidative phosphorylation through NADH dehydrogenase activity and electron transport chain. They contribute to the assembly of respiratory chain complexes I, II, III, IV, V, VI, which are located in the mitochondrial inner membrane. Additionally, these genes are involved in the organization and biogenesis of mitochondria, as well as in ubiquinone and fatty acid metabolism. Mutations in these genes can cause various mitochondrial disorders affecting energy production and cell function.] | \n", + "0.94 | \n", + "521 | \n", + "
| 218 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_P53_PATHWAY-0 | \n", + "[Summary: DNA damage response and cell cycle regulation pathways are enriched among the listed genes.\\nMechanism: The genes are involved in processes that regulate cell growth and proliferation, as well as response to DNA damage.\\n] | \n", + "[Summary: Regulation of cell cycle and cell death. \\n\\nHypothesis: The enriched terms suggest that these genes play a crucial role in normal cellular processes, and their dysregulation may result in abnormal growth and proliferation of cells. The underlying biological mechanism may involve activation of DNA damage response pathways and regulation of the p53 tumor suppressor protein, leading to cell cycle arrest and apoptosis.] | \n", + "0.92 | \n", + "199 | \n", + "
| 219 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_P53_PATHWAY-1 | \n", + "[Summary: Cell cycle regulation and DNA damage response.\\nMechanism: Transcriptional regulation and DNA repair.\\n\\nHypothesis: \\nThe list of genes is enriched for functions related to cell cycle regulation and DNA damage response. Many of these genes are involved in processes such as cell cycle arrest, DNA repair, and transcriptional regulation, indicating a potential role in maintaining genome stability. Some of these genes, such as TP53, are known to play a central role in the DNA damage response and are involved in regulating the expression of genes involved in DNA repair and cell cycle arrest. Other enriched terms, such as the G1/S transition of mitotic cell cycle, suggest that these genes may also play a role in controlling the progression of the cell cycle and cell proliferation. Overall, the enrichment of these functions suggests that the genes in this list are involved in maintaining genomic integrity and proper cell cycle progression.] | \n", + "[Summary: DNA damage response and cell cycle regulation\\nMechanism: Activation of p53 pathway and downstream effector genes\\n] | \n", + "0.89 | \n", + "830 | \n", + "
| 220 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[Summary: Genes involved in pancreatic beta cell development and function\\nMechanism: Beta cell differentiation and insulin secretion\\n] | \n", + "[Summary: These genes are associated with pancreatic beta cell development and function.\\nMechanism: Beta cell development and function\\n\\nHypothesis: These genes are involved in the development and function of pancreatic beta cells, which produce and secrete insulin and play a critical role in glucose homeostasis. The enriched terms suggest that these genes are important for the differentiation, development, and function of pancreatic beta cells as well as overall pancreatic islet cell development. This suggests that disruptions in these genes could lead to impaired beta cell function and contribute to the development of diabetes.] | \n", + "0.94 | \n", + "504 | \n", + "
| 221 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[Summary: Genes are enriched for functions related to pancreatic beta cell development and insulin secretion.\\nMechanism: Beta cells in the pancreas produce and secrete insulin, and defects in this process can lead to diabetes.\\n] | \n", + "[Summary: The genes in this list are enriched for terms related to pancreatic beta cell development and function.\\nMechanism: Pancreatic beta cells are responsible for insulin secretion, which regulates glucose levels in the body. Dysfunction of these cells can lead to diabetes.\\n] | \n", + "0.96 | \n", + "52 | \n", + "
| 222 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PEROXISOME-0 | \n", + "[Summary: Transport and metabolism of lipids, hormones, and xenobiotics are enriched gene functions.\\nMechanism: Lipid and xenobiotic metabolism pathways are activated.\\n\\nHypothesis: The enriched gene functions are consistent with the liver's role in detoxification and energy metabolism. These genes may play a role in maintaining liver homeostasis and responding to environmental toxins and hormonal changes.] | \n", + "[Summary: Genes involved in lipid metabolism, transport, and signaling are significantly over-represented in this list.\\n\\nMechanism: Lipid metabolism and transport\\n\\n\\nHypothesis: The genes in this list are involved in the metabolism, transport, and signaling of lipids. ABC transporters are responsible for the transport of lipids across membranes. Fatty acid metabolism and cholesterol biosynthesis are crucial in lipid homeostasis. PPAR signaling pathway regulates the expression of genes involved in lipid metabolism. Peroxisomes play an important role in the breakdown of fatty acids.] | \n", + "0.90 | \n", + "178 | \n", + "
| 223 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PEROXISOME-1 | \n", + "[Summary: Enriched terms include fatty acid metabolism, bile acid transport, peroxisome organization, and DNA repair.\\nMechanism: These genes are involved in various metabolic pathways and cellular processes, including fatty acid metabolism, bile acid transport, peroxisome organization, and DNA repair.\\n\\n] | \n", + "[Summary: Genes involved in lipid metabolism and transport are enriched.\\nMechanism: Lipid metabolism and transport pathways are affected by the genes in the list.\\n\\n] | \n", + "0.91 | \n", + "140 | \n", + "
| 224 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[Summary: Signal transduction and regulation of cell cycle and apoptosis\\n\\nHypothesis: The listed genes are involved in different stages of signal transduction pathways that ultimately converge on either the MAPK cascade or PI3K-Akt signaling pathway, which regulate cellular proliferation, differentiation, and apoptosis. The genes identified under enriched term \"regulation of cell proliferation\" might work as positive or negative regulators of cell growth and death signals. Altered functions or dysregulation of these genes could lead to abnormal growth or development, contributing] | \n", + "[Summary: Signaling and regulation\\n\\nHypothesis: These genes could be involved in regulating cellular responses to extracellular stimuli, including growth factors and cytokines. They could also play a role in tumor growth and progression.] | \n", + "0.91 | \n", + "349 | \n", + "
| 225 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[Summary: Signaling pathways and cellular responses are enriched in these genes.\\nMechanism: The genes seem to be involved in multiple pathways and cellular responses.\\n] | \n", + "[Summary: Signaling and metabolism pathways are significantly enriched among the given genes.\\n\\nMechanism: These genes are involved in cellular signaling pathways, including the MAPK and PI3K pathways, which play a role in cell growth, proliferation, and survival. Many of the genes are also involved in metabolic processes, such as glucose metabolism.\\n\\n] | \n", + "0.93 | \n", + "186 | \n", + "
| 226 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-0 | \n", + "[Summary: Membrane trafficking and vesicle transport\\nMechanism: The genes in this list are all involved in various processes of membrane trafficking and vesicle transport.\\n] | \n", + "[Summary: Vesicular trafficking and membrane transport are enriched functions in the given list of genes.\\nMechanism: Membrane transport and trafficking between various cellular compartments, such as the endoplasmic reticulum (ER), Golgi, lysosome, and plasma membrane, involve the trafficking of cargoes in vesicles. The formation, budding, tethering, and fusion of these vesicles are tightly regulated by various membrane-bound proteins and adaptors. \\n\\n] | \n", + "0.94 | \n", + "282 | \n", + "
| 227 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-1 | \n", + "[Summary: Membrane transport and vesicle-mediated transport\\nMechanism: Membrane trafficking and vesicle formation and fusion\\n\\nHypothesis: The enrichment of terms related to membrane transport and vesicle-mediated transport suggests that the genes on this list are involved in the processes of vesicle formation, membrane trafficking, and vesicle fusion. Multiple genes on this list are involved in the transport of proteins to the Golgi, endosomes, and lysosomes, suggesting a potential role in intracellular protein transport and protein sorting. Additionally, the enrichment of terms related to ion transport and regulation of membrane potential may indicate a role in cellular signaling or homeostasis. Overall, these genes are likely involved in various aspects of membrane trafficking and vesicle-mediated transport within the cell.] | \n", + "[Summary: Transport and trafficking of proteins and molecules within cells.\\nMechanism: These genes play a role in vesicular transport, protein sorting, and trafficking within the cell. The enriched terms provide insight into the specific pathways and compartments involved in this process.\\n\\n\\nHypothesis: These genes are involved in the coordinated transport of proteins and molecules between different intracellular compartments, such as the endoplasmic reticulum, Golgi apparatus, and lysosomes. They likely form part of a complex network of regulatory pathways ensuring the efficient and accurate sorting of cargo to their appropriate destinations. The enrichment of terms related to clathrin-mediated endocytosis suggests that this process is also important in regulating protein trafficking within the cell.] | \n", + "0.95 | \n", + "26 | \n", + "
| 228 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[Summary: Genes are involved in oxidative stress response and redox regulation.\\nMechanism: Gene products involved in antioxidant response and maintenance of redox balance.\\n\\nHypothesis: The majority of the genes in the list are involved in the response to oxidative stress. They act through different but interconnected mechanisms to maintain redox balance in cells. These include direct antioxidant activity, such as the scavenging of reactive oxygen species (ROS), and the regulation of antioxidant enzyme activity and cellular levels of ROS. The results of the enrichment test suggest that these processes are statistically over-represented in the list of genes. Specifically, the list is enriched with genes involved in peroxiredoxin activity, catalysing the reduction of H2O2 and other ROS. Additionally, genes involved in glutathione metabolism, which provides an important reducing environment in cells, are also enriched. Overall, these genes act in concert to maintain cellular redox balance and protect against oxidative damage.] | \n", + "[Summary: Genes involved in antioxidant defense and redox regulation are enriched.\\n\\nMechanism: Antioxidant defense and redox regulation are essential for maintaining cellular homeostasis and preventing oxidative stress-induced damage.\\n\\n\\nHypothesis: These genes likely play important roles in maintaining proper cellular redox balance, which is critical for preventing oxidative damage to cellular components such as DNA, proteins, and lipids. Additionally, they may contribute to the detoxification of harmful reactive oxygen species produced during normal cellular metabolism or in response to various stressors such as environmental toxins and pathogens.] | \n", + "0.96 | \n", + "381 | \n", + "
| 229 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[Summary: Redox regulation \\nMechanism: The genes in this list are involved in maintaining redox homeostasis through processes such as antioxidant defense, regulation of protein function through thiol-based modifications, iron regulation, and DNA repair.\\n\\n] | \n", + "[Summary: Oxidative stress response and redox regulation\\nMechanism: These genes are involved in regulation of redox balance and response to oxidative stress.\\n] | \n", + "0.92 | \n", + "97 | \n", + "
| 230 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-0 | \n", + "[Summary: Enrichment analysis identified terms related to spermatogenesis and meiosis as over-represented in the list of genes.\\n\\nMechanism: The identified genes are likely involved in the regulation of various processes related to spermatogenesis and meiosis, including DNA replication, chromosome segregation, and cell division.\\n\\n] | \n", + "[Summary: Enriched terms suggest that the listed genes may function primarily in the process of spermatogenesis and meiosis.\\nMechanism: Spermatogenesis and meiosis.\\n\\nHypothesis: The enriched terms suggest that these genes function primarily in the process of spermatogenesis and meiosis. These genes may play roles in meiotic recombination, chromosome segregation, and overall gamete formation. Many of the genes are involved in regulating cell division, which is necessary for proper gamete formation. Additionally, some genes are involved in regulating hormone secretion, which is important for the development and maturation of male reproductive organs.] | \n", + "0.95 | \n", + "326 | \n", + "
| 231 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-1 | \n", + "[Summary: Genes are enriched for regulation of mitotic cell cycle processes.\\nMechanism: The genes are involved in the regulation of mitosis and cell cycle.\\n] | \n", + "[Summary: Cell cycle regulation and chromosome organization \\nMechanism: Mitotic checkpoint and spindle assembly \\n\\nHypothesis: The enrichment of terms related to mitotic spindle organization and chromosome segregation suggests that these genes may play a role in regulating the cell cycle. Specifically, many of these genes are involved in mitotic checkpoint signaling pathways that help ensure proper chromosome alignment and segregation during cell division. Additionally, some of these genes may play a role in organizing the microtubules and proteins that make up the mitotic spindle. Overall, these genes likely play critical roles in maintaining genomic stability and preventing the development of cancer and other genetic diseases.] | \n", + "0.91 | \n", + "582 | \n", + "
| 232 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[Summary: Genes are involved in TGF-beta signaling pathway\\nMechanism: TGF-beta signaling pathway\\n\\nHypothesis: The enriched terms suggest that the genes are involved in the TGF-beta signaling pathway, as well as the regulation of BMP signaling pathway. TGF-beta signaling pathway plays a crucial role in cell growth, differentiation, and apoptosis. The interaction between TGF-beta and BMP signaling pathways has a significant influence on organ development and tissue regeneration. These genes may regulate cellular responses to growth factors and transcription, which are the downstream processes of the TGF-beta signaling pathway.] | \n", + "[Summary: Genes are involved in the TGF-beta signaling pathway.\\nMechanism: The TGF-beta signaling pathway plays a key role in cell growth, differentiation, and development.\\n] | \n", + "0.95 | \n", + "460 | \n", + "
| 233 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[Summary: The genes are enriched in terms related to transforming growth factor-beta (TGF-beta) signaling pathway and extracellular matrix (ECM) regulation.\\nMechanism: TGF-beta signaling pathway and ECM regulation.\\n\\n] | \n", + "[Summary: Genes associated with regulation of transforming growth factor-beta (TGF-beta) signaling pathway.\\nMechanism: TGF-beta signaling pathway regulation\\n\\n] | \n", + "0.93 | \n", + "58 | \n", + "
| 234 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[Summary: Genes involved in inflammation and immune response are enriched.\\nMechanism: These genes are likely involved in regulating the inflammatory response and immune system signaling.\\n\\n] | \n", + "[Summary: Immune response and inflammation-related gene functions are statistically over-represented in this list of genes.\\nMechanism: These genes are involved in the regulation of immune response and inflammation pathways.\\n\\n] | \n", + "0.93 | \n", + "37 | \n", + "
| 235 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[Summary: Genes involved in immune response and inflammation pathways are enriched, specifically those related to cytokine signaling, transcription factor regulation, and stress response.\\nMechanism: These genes likely play a role in regulating the immune response and inflammation in various tissues, as well as responding to cellular stress.\\n] | \n", + "[Summary: Immune response and inflammation-related gene functions are enriched in the given list of genes.\\n\\nHypothesis: The enriched terms suggest that these genes play an important role in regulating the immune system response and controlling inflammation. This includes controlling cytokine and TNF production, which are important factors in regulating inflammation. The negative regulation of the NF-kappaB transcription factor activity may play a role in preventing inflammation and maintaining immune system homeostasis. These findings may have implications for understanding a range of inflammatory conditions and immune system disorders.] | \n", + "0.93 | \n", + "302 | \n", + "
| 236 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[Summary: Protein folding and degradation pathways are enriched.\\nMechanism: The genes are involved in regulation of protein synthesis and processing, particularly related to endoplasmic reticulum-associated degradation (ERAD) and the unfolded protein response (UPR).\\n] | \n", + "[Summary: The genes in the list are enriched for functions related to protein folding and sorting, as well as response to stress and cellular damage. \\n\\nMechanism: The enriched terms suggest that these genes are involved in regulating protein quality control in the cell, ensuring that misfolded or damaged proteins are properly degraded or refolded.\\n\\n\\nHypothesis: The genes in this list are enriched for functions related to the quality control of cellular proteins, ensuring that only properly folded and functional proteins are allowed to move through the various stages of processing and trafficking. This involves a highly coordinated series of regulatory and surveillance pathways, including chaperone-mediated folding, ubiquitin-mediated proteolysis, and mRNA processing and splicing. Dysfunction in any one of these pathways can result in accumulation of misfolded proteins, leading to cellular damage and disease.] | \n", + "0.91 | \n", + "655 | \n", + "
| 237 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[Summary: The enriched terms for these genes relate to protein processing and regulation, RNA metabolism, and stress response.\\nMechanism: These genes are involved in the regulation of protein synthesis and folding, as well as RNA metabolism, which could contribute to cellular stress response and adaptation.\\n\\n] | \n", + "[Summary: Genes enriched in protein folding-related functions \\n\\nMechanism: These genes are involved in regulation of protein homeostasis, such as protein folding, chaperone-mediated protein processing, and protein transport.\\n\\n] | \n", + "0.91 | \n", + "84 | \n", + "
| 238 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-0 | \n", + "[Summary: Genes in this list are mostly involved in signal transduction, cell adhesion, and extracellular matrix organization, with a significant enrichment in the TGF-beta signaling pathway.\\nMechanism: TGF-beta signaling pathway plays a significant role in regulating various cellular processes, including cell proliferation, differentiation, and apoptosis.\\n\\n] | \n", + "[Summary: Regulation of gene expression and signal transduction\\nMechanism: Kinase signaling pathways and transcription regulation\\n\\n\\nHypothesis: The genes in this list are involved in regulating gene expression and signal transduction. Many of these genes are involved in kinase signaling pathways and transcription regulation, which are essential for proper cellular growth and differentiation. This suggests that the underlying biological mechanisms may involve a complex interplay between various signaling pathways governing gene expression and cellular processes. Additionally, many of these genes are involved in regulation of protein phosphorylation and intracellular transport, suggesting that they play important roles in cellular communication and the regulation of downstream signaling events.] | \n", + "0.89 | \n", + "444 | \n", + "
| 239 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-1 | \n", + "[Summary: Extracellular matrix and cytoskeletal organization\\nMechanism: Cell adhesion and migration \\n\\n\\nHypothesis: The enriched terms suggest that these genes play roles in extracellular matrix and cytoskeletal organization for cellular adhesion and migration. They are likely involved in pathways that regulate cytoskeletal dynamics and cell adhesion to the extracellular matrix through integrin signaling, as well as the regulation of migratory behavior in various cell types.] | \n", + "[Summary: Genes are involved in extracellular matrix organization, signal transduction, and neural development.\\nMechanism: Regulation of cell signaling pathways.\\n\\n\\nHypothesis: These genes are involved in regulating cell signaling pathways and controlling neural development by modulating extracellular matrix organization. The enriched terms suggest that these genes are involved in growth factor activity and neurogenesis, indicating that they play a critical role in regulating cell proliferation and differentiation during neural development. Dysfunction of these genes could lead to abnormalities in neural development and function, possibly leading to neurological disorders.] | \n", + "0.92 | \n", + "202 | \n", + "
| 240 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-0 | \n", + "[Summary: Genes are involved in regulation of transcription, cellular metabolism, and signaling pathways.\\nMechanism: Biological pathways involved in gene regulation, metabolic pathways, and signaling pathways.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of transcription, cellular metabolism, and signaling pathways. These pathways are involved in the regulation of gene expression, cellular homeostasis, and response to external stimuli. The mechanism involves complex networks of interactions between proteins and other molecules that mediate these pathways.] | \n", + "[Summary: The common function of the genes in the list is related to regulation of cellular processes and response to stimuli.\\n\\nMechanism: The genes in the list are involved in cellular processes such as metabolism, transport, and signaling. They also play a role in response to stimuli such as stress, inflammation, and DNA damage.\\n\\n] | \n", + "0.90 | \n", + "271 | \n", + "
| 241 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-1 | \n", + "[Summary: Genes are involved in diverse biological processes, with some enrichment in immune response, cell cycle regulation, and protein localization.\\nMechanism: No specific mechanism could be elucidated, as the genes are involved in diverse functions.\\n] | \n", + "[Summary: Gene Ontology (GO) term enrichment analysis was performed on a list of human genes to identify common functional themes.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in cellular responses to different kinds of stressors. The mechanism may involve signal transduction pathways that lead to activation of transcription factors, changes in protein localization, and alterations in cell cycle progression and apoptosis in response to stress stimuli, such as DNA damage, oxidative stress, and hypoxia. These genes may also contribute to the maintenance of cellular homeostasis under conditions of stress.] | \n", + "0.88 | \n", + "381 | \n", + "
| 242 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[Summary: The enriched terms suggest that these genes are involved in the regulation of cellular signaling pathways and gene expression, particularly the Wnt signaling pathway and the Notch signaling pathway.\\nMechanism: The Wnt and Notch signaling pathways are essential for embryonic development, tissue homeostasis, and cell fate determination in adult tissues. These pathways are tightly regulated and involve a complex network of ligands, receptors, and downstream effectors.\\n\\n] | \n", + "[Summary: Genes involved in the Wnt signaling pathway and Notch signaling pathway\\nMechanism: Interaction between Wnt and Notch signaling pathways\\n] | \n", + "0.92 | \n", + "335 | \n", + "
| 243 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[Summary: Regulation of Notch signaling pathway\\nMechanism: Notch pathway activation\\n\\nHypothesis: These genes are involved in the regulation of the Notch signaling pathway, which plays a critical role in cell fate commitment during development and tissue homeostasis. They are implicated in the activation, positive regulation, and negative regulation of the Notch pathway, suggesting a complex regulatory mechanism that ensures proper cell differentiation and tissue patterning. These genes may act on different levels of the pathway, including ligands, receptors, and downstream effectors, and may participate in multiple developmental processes, such as neurogenesis, angiogenesis, and epithelial-mesenchymal transition. Dysfunction of these genes may lead to developmental disorders and cancers, highlighting their importance as therapeutic targets.] | \n", + "[Summary: Genes are involved in the Wnt signaling pathway and Notch signaling pathway.\\nMechanism: Signaling pathways\\n\\nHypothesis: The enrichment of Wnt and Notch signaling pathways and protein and transcription factor binding suggests that these genes function in regulating gene expression and cell proliferation during development and homeostasis. Specifically, Wnt pathway plays essential roles during embryonic development, tissue homeostasis, and wound healing. The Notch pathway has a crucial role in cellular differentiation, proliferation, and apoptosis. Protein and transcription factor binding may regulate Wnt and Notch signaling or downstream gene expression changes.] | \n", + "0.94 | \n", + "173 | \n", + "
| 244 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "T cell proliferation-0 | \n", + "[Summary: Immune response regulation \\nMechanism: Regulation of T cell receptor signaling\\n] | \n", + "[Summary: Immune system regulation and response is over-represented in these genes.\\nMechanism: These genes function in the activation and regulation of immune cells and signaling pathways.\\n\\n] | \n", + "0.89 | \n", + "101 | \n", + "
| 245 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "T cell proliferation-1 | \n", + "[Summary: Genes are enriched in immune system and cell signaling functions.\\nMechanism: These genes are involved in a variety of processes, including immune system regulation and various signaling pathways.\\n] | \n", + "[Summary: Immune system function\\n\\nHypothesis: These genes may be involved in the overall function of the immune system, particularly in the regulation and activation of T cells in response to pathogens or cancer cells. They may also play a role in autoimmune disorders, in which the immune system mistakenly targets and attacks the body's own cells. Further research into the specific mechanisms of these genes in immune function could lead to better treatment and prevention strategies for immune-related disorders.] | \n", + "0.92 | \n", + "311 | \n", + "
| 246 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "Yamanaka-TFs-0 | \n", + "[Summary: The common function shared by POU5F1, SOX2, KLF4, and MYC is transcriptional regulation and cell differentiation.\\nMechanism: The genes are involved in maintaining pluripotency and promoting cell proliferation and differentiation in embryonic and somatic cells.\\n\\nHypothesis: These genes play a crucial role in regulating pluripotency and inducing distinct cell types during embryonic development. They may act through various pathways, such as the NANOG, WNT, and BMP pathways, to promote stem cell maintenance and differentiation. Dysregulation of these genes may lead to developmental disorders or cancer.] | \n", + "[Summary: Genes POU5F1, SOX2, KLF4, and MYC are all involved in regulating gene expression and cellular growth, with a focus on stem cells.\\nMechanism: These genes are part of the transcriptional regulatory network that controls stem cell self-renewal, proliferation, and differentiation.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of transcriptional activity by binding directly to DNA and controlling the expression of genes involved in stem cell differentiation. The transcriptional regulatory network formed by these genes may play a role in maintaining the balance between self-renewal and differentiation of stem cells, which is critical for tissue repair and regeneration.] | \n", + "0.95 | \n", + "107 | \n", + "
| 247 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "Yamanaka-TFs-1 | \n", + "[Summary: These three genes are involved in the regulation of pluripotency and differentiation in stem cells. \\nMechanism: Together, KLF4, POU5F1, and SOX2 activate the expression of genes that maintain stem cell identity and prevent differentiation, while also repressing genes that promote differentiation. \\n\\nHypothesis: The mechanism involving these genes is likely to be part of a larger regulatory network, involving other transcription factors and signaling pathways, that is necessary for the proper development and maintenance of stem cells in various tissues and organs. These genes may also play a role in cancer progression, by promoting or suppressing the self-renewal and differentiation of cancer stem cells.] | \n", + "[Summary: These genes are all involved in transcriptional regulation and have been identified as key players in the maintenance of pluripotency and self-renewal in stem cells.\\nMechanism: Transcriptional regulation\\n\\nHypothesis: These genes play a crucial role in the regulation of stem cell differentiation by maintaining the pluripotency and self-renewal capacity of stem cells through their transcriptional regulation. The enriched terms suggest that these genes have a specific role in regulating stem cell differentiation and fate determination.] | \n", + "0.94 | \n", + "173 | \n", + "
| 248 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "amigo-example-0 | \n", + "[Summary: Extracellular matrix organization and angiogenesis are over-represented functions among the listed human genes.\\nMechanism: The identified genes are involved in the regulation of extracellular matrix composition and organization, as well as angiogenesis which suggests a potential role in developmental processes.\\n\\n] | \n", + "[Summary: Extracellular matrix organization and angiogenesis\\nMechanism: Signaling pathways through FGFR1 and integrin ITGAV\\n] | \n", + "0.89 | \n", + "200 | \n", + "
| 249 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "amigo-example-1 | \n", + "[Summary: Genes are enriched in extracellular matrix organization and regulation of cell adhesion.\\nMechanism: Extracellular matrix remodeling \\n\\nHypothesis: The enrichment of terms related to extracellular matrix organization and regulation of cell adhesion suggests that these genes play a role in extracellular matrix remodeling, which is important for cellular activities such as migration and proliferation. The extracellular matrix can influence cell behavior by providing mechanical support and signaling cues, and regulating cell adhesion is crucial for the maintenance of tissue integrity and embryonic development. Dysfunction of these processes has been implicated in several diseases, including cancer, cardiovascular disorders, and developmental abnormalities.] | \n", + "[Summary: Several of the genes are involved in extracellular matrix organization, cell adhesion, and angiogenesis.\\nMechanism: Extracellular matrix (ECM) organization and remodeling, cell adhesion, and angiogenesis are essential processes in tissue development, maintenance, and repair. Dysregulation of these processes can lead to pathological conditions such as cancer and fibrosis.\\n\\n\\nHypothesis: These genes are likely involved in a common biological pathway that regulates ECM organization, cell adhesion, and angiogenesis. One possible mechanism is the activation of MAPK signaling, which plays a central role in cell migration, proliferation, and survival, and is often dysregulated in cancer and other diseases. Further studies are needed to elucidate the precise biological mechanisms underlying these enriched terms.] | \n", + "0.95 | \n", + "53 | \n", + "
| 250 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_0-0 | \n", + "[Summary: The common function among the listed genes is related to nervous system development and signal transduction, with enrichment in terms related to calcium ion binding, synapse organization, and transcriptional regulation.\\n\\nMechanism: These genes may be involved in regulating signal transduction pathways in the nervous system, particularly related to calcium signaling and synapse formation and function. They may also play a role in transcriptional regulation during nervous system development.\\n\\n] | \n", + "[Summary: Genes are enriched in terms related to neuronal development and signaling, transcriptional regulation, and ion transport.\\nMechanism: These genes are likely involved in a variety of biological mechanisms, including brain development, synaptic transmission, and the regulation of gene expression.\\n\\n] | \n", + "0.93 | \n", + "200 | \n", + "
| 251 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_0-1 | \n", + "[Summary: Several genes are involved in signal transduction, cellular communication, and regulation of gene expression.\\n\\nMechanism: The enriched terms suggest that these genes are involved in various cellular functions such as signal transduction, cell communication, and gene expression regulation.\\n\\n] | \n", + "[Summary: The enriched terms are related to the function of transcription and RNA processing.\\nMechanism: These genes may regulate gene expression and transcriptional processes.\\n] | \n", + "0.90 | \n", + "124 | \n", + "
| 252 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_1002-0 | \n", + "[Summary: Muscle contraction and regulation of muscle fiber type are the significantly enriched biological mechanisms shared among the given human genes.\\nMechanism: Muscle contraction and regulation of muscle fiber type\\n] | \n", + "[Summary: Genes are involved in muscle contraction and regulation.\\n\\nMechanism: The genes in this list are mainly expressed in muscle tissues and play a critical role in the contraction and regulation of various muscle types.\\n\\n] | \n", + "0.91 | \n", + "6 | \n", + "
| 253 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_1002-1 | \n", + "[Summary: Genes are involved in muscle contraction and development.\\nMechanism: Muscle development and regulation.\\n\\nHypothesis: The common function of these genes is in the regulation of muscle development and contraction. Many of these genes are involved in myofibril assembly and muscle fiber development, suggesting that they play critical roles in the formation and function of skeletal muscle tissue. The identification of these enriched terms supports the idea that the genes are involved in muscle contraction and development. Further study may reveal new insights into the specific mechanisms by which these genes influence muscle function, potentially leading to new therapies for muscle-related disorders.] | \n", + "[Summary: Muscle protein regulation and contractility\\nMechanism: Myofilament formation and calcium signaling\\n] | \n", + "0.86 | \n", + "606 | \n", + "
| 254 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "endocytosis-0 | \n", + "[Summary: The common function of the given genes is related to intracellular trafficking, particularly of endocytosis and lysosomal degradation.\\nMechanism: The genes are involved in regulating the pathways of endocytosis, vesicular trafficking, and lysosomal degradation, contributing to protein degradation and cellular homeostasis.\\n\\nHypothesis: The genes identified in the term enrichment analysis suggest that they may be associated with intracellular trafficking processes, particularly endocytosis and lysosomal degradation. The endocytic pathway is responsible for a variety of functions, including extracellular nutrient uptake, synaptic transmission, and maintenance of plasma membrane composition. The lysosomal degradation pathway is responsible for breakdown and degradation of intracellular materials, including misfolded/unfolded proteins. These pathways are essential to prevent accumulation of toxic waste in the cell and maintain cellular homeostasis. The enriched gene set may play a role in regulating the balance between endocytosis, vesicular trafficking, and lysosomal degradation, contributing to protein and cellular homeostasis.] | \n", + "[Summary: The common function among the given human genes is related to lipid and cholesterol processing and transport, as well as endosomal trafficking and protein degradation.\\nMechanism: The genes are involved in regulating intracellular vesicle trafficking and endosome maturation, as well as lipid and cholesterol metabolism.\\n\\nHypothesis: It is likely that the genes are involved in regulating the endocytic pathway and in processing and transporting lipids and cholesterol. The genes play critical roles in maintaining cellular homeostasis by regulating protein degradation and recycling, as well as lipid and cholesterol storage and utilization. Dysfunction in these genes may lead to the development of metabolic disorders, such as dyslipidemia or atherosclerosis.] | \n", + "0.94 | \n", + "381 | \n", + "
| 255 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "endocytosis-1 | \n", + "[Summary: The list of human genes is enriched for terms related to endocytosis and receptor signaling.\\n\\nMechanism: The majority of genes in the list are involved in endocytosis, the cellular process of internalizing molecules from the extracellular environment via vesicles. Many of the enriched terms are related to the trafficking, sorting, and recycling of receptors that are involved in cell signaling pathways.\\n\\n\\nHypothesis: The genes listed are involved in the regulation of endocytosis and receptor signaling, which play critical roles in cell signaling and communication. Dysregulation of these processes can contribute to a variety of diseases, including cancer, neurodegenerative disorders, and metabolic diseases. Further investigation of the specific roles of these genes in endocytic and receptor signaling pathways may offer insights into novel therapeutic targets for these diseases.] | \n", + "[Summary: Endocytosis and Vesicular Trafficking\\nMechanism: These genes are involved in endocytosis and vesicular trafficking pathway which involves the internalization of extracellular molecules, membrane proteins and lipids. This pathway plays a crucial role in the regulation of cell signaling, nutrient uptake, and receptor desensitization.\\n] | \n", + "0.92 | \n", + "555 | \n", + "
| 256 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "glycolysis-gocam-0 | \n", + "[Summary: These genes are mostly involved in glycolysis, with a focus on catalyzing the conversion of glucose to pyruvate. \\n\\nMechanism: Glycolysis is the metabolic pathway that breaks down glucose into pyruvate, which can then be used to produce ATP or other metabolic intermediates. \\n\\n] | \n", + "[Summary: The list of human genes is enriched for terms related to glycolysis and glucose metabolism.\\nMechanism: The genes in this list are all involved in the initial steps of glycolysis, converting glucose to pyruvate.\\n\\nHypothesis: The enriched terms suggest that the genes in this list are all involved in the process of converting glucose to pyruvate via glycolysis. This process is a central metabolic pathway in almost all organisms, providing energy for cellular processes and serving as a carbon source for biosynthesis. The presence of these specific genes in this list implies that they may be particularly important for the regulation and successful execution of the glycolytic process.] | \n", + "0.91 | \n", + "412 | \n", + "
| 257 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "glycolysis-gocam-1 | \n", + "[Summary: The common function shared by the given human genes is glycolytic process.\\nMechanism: Glycolysis is a metabolic pathway that breaks down glucose into pyruvate.\\n] | \n", + "[Summary: Enzymes involved in glycolysis.\\nMechanism: Glycolysis pathway.\\n\\nHypothesis: These genes are all involved in the glycolysis pathway, a metabolic pathway that converts glucose into pyruvate and produces ATP. The over-representation of terms related to carbohydrate and glucose metabolic processes suggests that these genes play a key role in the breakdown of glucose and the production of ATP, which is essential for cellular energy metabolism.] | \n", + "0.87 | \n", + "283 | \n", + "
| 258 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "go-postsynapse-calcium-transmembrane-0 | \n", + "[Summary: Calcium ion signaling pathways are enriched amongst the list of human genes provided.\\nMechanism: Calcium ion signaling pathways play a crucial role in various physiological processes, including neurotransmitter release, muscle contraction, and gene expression regulation. The genes in this list contribute to the activity of different types of calcium channels, transporters, and receptors, as well as other proteins that modulate calcium signaling.\\n\\n] | \n", + "[Summary: Calcium signaling and neurotransmission-related functions are enriched in the given genes.\\nMechanism: These genes are involved in the regulation of ion channels and neurotransmitter receptors, affecting calcium influx and signaling in neurons.\\n] | \n", + "0.95 | \n", + "207 | \n", + "
| 259 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "go-postsynapse-calcium-transmembrane-1 | \n", + "[Summary: Calcium signaling and neurotransmission-related functions appear to be enriched in the list of genes.\\n\\nMechanism: Calcium signaling plays a key role in neurotransmission, regulating the release of neurotransmitters from presynaptic terminals and the activation of postsynaptic receptors.\\n\\n] | \n", + "[Summary: \\nThese human genes are involved in ion channel activity and neurotransmitter signaling. \\n\\nMechanism: \\nThe enriched terms suggest that these genes are involved in the regulation of synaptic transmission.\\n\\n\\nHypothesis: \\nThe high number of ion channel and neurotransmitter signaling related genes in this list suggests that they may play a crucial role in the regulation of synaptic transmission. Specifically, these genes may contribute to the modulation of calcium ion flux at synapses, which is necessary for proper neurotransmitter release and subsequent neuronal signaling. Dysregulation of this pathway may lead to various neurological disorders.] | \n", + "0.91 | \n", + "361 | \n", + "
| 260 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "go-reg-autophagy-pkra-0 | \n", + "[Summary: Many of these genes are related to cellular stress response, signaling pathways, and regulation of autophagy.\\nMechanism: The genes may be involved in a complex network of responses to cellular stress that involve the regulation of signaling pathways and autophagy.\\n] | \n", + "[Summary: Genes are enriched in terms related to cellular stress response and apoptotic processes.\\nMechanism: Activation of stress response pathways leading to apoptosis.\\n\\nHypothesis: These genes may be involved in regulating cellular response to stress through activation of NF-kappaB and JNK signaling pathways, leading to apoptosis. The enriched terms suggest that they may function together in regulating the activation or inhibition of these pathways in response to cellular stressors.] | \n", + "0.91 | \n", + "216 | \n", + "
| 261 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "go-reg-autophagy-pkra-1 | \n", + "[Summary: The common function of the genes is associated with regulation of apoptotic signaling pathways, cellular metabolism, and protein processing.\\nMechanism: The genes are involved in the PI3K-Akt signaling pathway, which regulates cell growth, proliferation, and survival.\\n\\nHypothesis: The PI3K-Akt pathway plays an important role in regulating cell survival and metabolism, therefore mutations or dysregulation in the genes could contribute to the development of cancer or other diseases involving abnormal cell growth and metabolism.] | \n", + "[Summary: The functions of the given genes are enriched in regulation of autophagy, cellular response to stress, and apoptotic process.\\nMechanism: Autophagy regulation and cellular response to stress pathways are overrepresented in the given genes.\\n\\nHypothesis: It is possible that the genes listed are involved in the regulation of autophagy and cellular response to stress. The over-representation of apoptotic process may reflect the role of these genes in cellular homeostasis, survival, and death. The genes may be involved in the mTOR signaling pathway or PI3K/AKT pathway which regulate autophagy, as they include genes such as PIK3CA, AKT1, RPTOR, MLST8, which play a vital role in these pathways. Alternatively, the genes may be related to the JNK signaling pathway, which modulates cellular response to stress and can activate apoptosis. Further experimentation is required to determine the exact mechanism and pathway of these genes.] | \n", + "0.91 | \n", + "404 | \n", + "
| 262 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[Summary: Glycosidase activity and carbohydrate metabolism\\nMechanism: These genes are involved in the hydrolysis of glycoside bonds in carbohydrates, specifically the breakdown of glycoproteins, glycolipids, and oligosaccharides. \\n\\nHypothesis: These genes are primarily involved in the breakdown of complex carbohydrates, specifically in lysosomes and the endoplasmic reticulum. Dysfunction in these genes can lead to lysosomal storage disorders, such as mucopolysaccharidosis, where complex carbohydrates accumulate in the cell and cause systemic disease.] | \n", + "[Summary: Enzyme activity and carbohydrate metabolism are over-represented functions in the given list of genes.\\nMechanism: These genes may primarily be involved in lysosomal function and the digestion of complex carbohydrates and glycoproteins.\\n\\n] | \n", + "0.92 | \n", + "310 | \n", + "
| 263 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[Summary: Glycoside hydrolases and related genes involved in carbohydrate metabolism\\nMechanism: These genes are involved in the catabolism and processing of complex carbohydrates into simple sugars.\\n\\n\\nHypothesis: These genes are all involved in the breakdown of complex carbohydrates including glycosphingolipids, oligosaccharides, and sialic acids. This catabolism likely takes place in lysosomes, where these complex carbohydrates are transported to be broken down into simple sugars. The mechanism by which these genes function is likely a combination of enzymatic activity and transport function. Dysfunction of these genes could lead to lysosomal storage diseases where the catabolism of complex carbohydrates is impaired, leading to a buildup of these molecules in lysosomes and subsequent pathology.] | \n", + "[Summary: The genes in this list are involved in carbohydrate metabolism, glycosylation, and degradation processes.\\nMechanism: These genes all play a role in various stages of carbohydrate processing, from synthesis to degradation.\\n\\nHypothesis: These genes are involved in the processing, modification, and breakdown of carbohydrates in the body. This includes glycosylation of proteins for proper folding and function, as well as the breakdown of complex carbohydrates for energy production. The enrichment of terms related to hydrolase activity suggests a particular focus on breaking down O-glycosyl compounds. The variety of specific enzyme activities present in these genes likely reflects the diverse range of carbohydrates and glycoproteins that are present in the body.] | \n", + "0.96 | \n", + "29 | \n", + "
| 264 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "ig-receptor-binding-2022-0 | \n", + "[Summary: The common function of these genes is related to immunoglobulin and T cell receptor production and signaling.\\nMechanism: These genes are involved in the development and function of B cells and T cells.\\n] | \n", + "[Summary: Genes related to immunoglobulins and T- and B-cell receptor chains.\\n\\nHypothesis: \\nThese genes are mostly related to immunoglobulin and T- and B-cell receptor chains. The enriched terms suggest that they are involved in various aspects of the immune response, such as recognizing and binding to foreign antigens and activating B and T cells. These genes are crucial for proper functioning of the adaptive immune system which plays a vital role in protecting the body against pathogens.] | \n", + "0.92 | \n", + "283 | \n", + "
| 265 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "ig-receptor-binding-2022-1 | \n", + "[Summary: Enriched terms include immune response, lymphocyte activation, and lymphocyte differentiation.\\nMechanism: These genes are involved in various aspects of the immune system, particularly in the activation and differentiation of lymphocytes.\\n] | \n", + "[Summary: Immune system function\\nMecanism: Antibody-mediated immunity\\n\\nHypothesis: The list of genes are all involved in the immune system function, specifically in the production and activation of immunoglobulins. They are all related to B cells and play a crucial role in the antibody-mediated immune response.] | \n", + "0.87 | \n", + "64 | \n", + "
| 266 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "meiosis I-0 | \n", + "[Summary: Enriched terms suggest these genes are primarily involved in meiosis and DNA repair processes. \\nMechanism: Meiotic recombination and crossover formation, DNA damage response and repair.\\n\\nHypothesis: The enriched terms suggest that these genes are involved in meiotic recombination and crossover formation enabling the accurate pairing, exchange of genetic information, and separation of chromosomes during cell division. They may also be involved in DNA damage response and repair pathways important for maintaining genomic integrity during these processes.] | \n", + "[Summary: Genes are mainly involved in DNA repair, recombination, and chromosome segregation during meiosis.\\nMechanism: Meiosis and DNA repair\\n] | \n", + "0.90 | \n", + "425 | \n", + "
| 267 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "meiosis I-1 | \n", + "[Summary: These genes are enriched in terms related to meiotic recombination and chromosome segregation.\\nMechanism: Meiosis\\n\\n\\nHypothesis: These genes are involved in the regulation and maintenance of meiotic recombination during meiosis, and the proper segregation of chromosomes during cell division. Meiosis is a specialized cell division process that generates haploid gametes with genetic diversity. This process involves several steps, including DNA replication, chromosome recombination, synapsis, and segregation. The enriched terms suggest that these genes are involved in the regulation of these processes, which are critical for proper meiotic cell division and genetic diversity.] | \n", + "[Summary: Genes involved in meiosis and DNA repair.\\nMechanism: Meiotic recombination and chromosome segregation.\\n\\n] | \n", + "0.92 | \n", + "577 | \n", + "
| 268 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "molecular sequestering-0 | \n", + "[Summary: The genes in the list are enriched for terms related to immune response and regulation, protein folding and metabolism, cellular transport and localization, and gene expression regulation.\\nMechanism: The enriched terms suggest that these genes are involved in cell survival and response to stress, likely through regulation of various signaling pathways.\\n\\n] | \n", + "[Summary: The common function among the given genes is related to cellular response to stress and regulation of cell growth.\\n\\nMechanism: These genes are involved in multiple pathways that control cell growth and homeostasis, including the NF-κB and STAT3 signaling pathways. They also play a role in cellular response to stress, particularly oxidative stress. \\n\\n] | \n", + "0.89 | \n", + "4 | \n", + "
| 269 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "molecular sequestering-1 | \n", + "[Summary: Regulation of cellular processes and response to stress\\nMechanism: Regulation of transcription and protein turnover\\n\\nHypothesis: The commonalities in the function of these genes suggest a regulatory mechanism whereby the cells respond to stress by upregulating protective mechanisms. The enriched terms suggest that these protective mechanisms involve regulation of oxidative stress response, protein turnover and iron homeostasis. The negative regulation of NF-kappaB transcription factor activity implies that this pathway is activated downstream of these protective mechanisms, leading to an overall inhibition of pro-inflammatory signaling. Finally, the negative regulation of apoptotic process could suggest an additional component of these protective mechanisms that involves inhibiting programmed cell death to promote cell survival during stress.] | \n", + "[Summary: These human genes are enriched in terms related to regulation and response to cellular stress.\\n\\nMechanism: The underlying biological mechanism is likely related to the response to various types of cellular stress, including oxidative stress and DNA damage.\\n\\n\\nHypothesis: These genes may be involved in regulating the response to cellular stress through various pathways, including the regulation of protein localization to organelles and the stabilization of proteins involved in stress response. Additionally, the negative regulation of cell proliferation and positive regulation of apoptotic process terms suggest a possible role in regulating cell survival or death decisions in response to stress.] | \n", + "0.94 | \n", + "153 | \n", + "
| 270 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "mtorc1-0 | \n", + "[Summary: The enriched terms shared among these genes are related to protein folding, metabolism, and immune response pathways.\\n\\nMechanism: These genes appear to share a connection through signaling pathways that regulate protein folding, metabolism, and immune response.\\n\\n] | \n", + "[Summary: Cellular metabolism\\n] | \n", + "0.81 | \n", + "243 | \n", + "
| 271 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "mtorc1-1 | \n", + "[Summary: Protein synthesis and folding\\nMechanism: Protein homeostasis regulation\\n] | \n", + "[Summary: Transport, metabolism, and protein folding are enriched functions for these genes.\\nMechanism: These genes are involved in regulating cellular metabolism and maintaining protein homeostasis.\\n\\n] | \n", + "0.88 | \n", + "119 | \n", + "
| 272 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "peroxisome-0 | \n", + "[Summary: These genes are involved in peroxisome biogenesis and organization.\\nMechanism: Peroxisome formation and maintenance pathway\\n] | \n", + "[Summary: The genes PEX1, PEX2, PEX3, PEX5, PEX6, and PEX7 are all involved in peroxisome biogenesis.\\nMechanism: Peroxisome biogenesis\\n\\nHypothesis: These genes are involved in the process of peroxisome biogenesis, which is the formation of new peroxisomes in the cell. Peroxisomes are organelles that perform various metabolic functions, including the breakdown of fatty acids and the detoxification of harmful substances. The enriched terms suggest that these genes are involved in the organization of the peroxisome membrane and matrix, as well as the import of proteins into the peroxisome. This could potentially be related to the localization and assembly of necessary components for peroxisome formation and function.] | \n", + "0.92 | \n", + "590 | \n", + "
| 273 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "peroxisome-1 | \n", + "[Summary: These genes are all involved in peroxisome biogenesis and maintenance.\\nMechanism: Peroxisomes are organelles that are involved in lipid metabolism and cellular signalling.\\n\\nHypothesis: These genes are likely involved in the regulation of peroxisome biogenesis and the maintenance of peroxisome membrane organization and fission. They may be involved in regulating lipid metabolism and cellular signalling processes that are mediated by peroxisomes.] | \n", + "[Summary: The common function of the given human genes is related to peroxisome biogenesis.\\n\\nMechanism: The peroxisome biogenesis process involves the formation of a membrane-bound organelle that contains enzymes involved in various metabolic pathways, including fatty acid degradation, plasmalogen biosynthesis, and bile acid synthesis. Peroxisomes play a vital role in cellular metabolism and are involved in various processes such as lipid metabolism, reactive oxygen species (ROS) detoxification, and the biosynthesis of specific signaling molecules.\\n\\n\\nHypothesis: The genes PEX2, PEX3, PEX6, PEX7, and PEX1 are all involved in peroxisome biogenesis. These genes encode proteins that are required for the assembly of peroxisomes and their proper function. Specifically, PEX1 and PEX6 encode ATPases involved in the translocation of peroxisomal matrix proteins into the organelle, while PEX2, PEX3, and PEX7 have roles in the early stages of peroxisome biogenesis, including membrane assembly and division. The enriched] | \n", + "0.93 | \n", + "564 | \n", + "
| 274 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "progeria-0 | \n", + "[Summary: The common function of the given genes is related to DNA damage repair, chromosome organization and regulation of transcription.\\nMechanism: The enriched terms suggest that these genes are involved in nuclear organization and DNA repair pathways. \\n] | \n", + "[Summary: These genes all play a role in the maintenance and regulation of nuclear structure and function, particularly in DNA repair and organization.\\nMechanism: These genes are involved in the nuclear lamina, a network of proteins that provides structural support to the nucleus and helps regulate gene expression. Dysregulation of the lamina can lead to DNA damage and aging-related diseases.\\n] | \n", + "0.91 | \n", + "139 | \n", + "
| 275 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "progeria-1 | \n", + "[Summary: The common function of the genes LMNA, WRN, and BANF1 is in DNA repair, chromatin organization, and cellular senescence.\\nMechanism: The nuclear envelope organization and maintenance\\n\\nHypothesis: LMNA, WRN, and BANF1 are involved in the maintenance of the nuclear envelope structure and function, which is crucial for chromatin organization and DNA repair. The disrupted functions of these genes can result in DNA damage accumulation, epigenetic abnormalities, and cellular senescence. These genes may act together in a network to regulate the nuclear envelope dynamics and facilitate DNA repair, thereby maintaining genome stability and cellular viability.] | \n", + "[Summary: Genes LMNA, WRN, and BANF1 are involved in chromatin organization and DNA repair.\\nMechanism: These genes are involved in maintaining nuclear architecture and stability.\\n\\nHypothesis: LMNA, WRN, and BANF1 are all involved in the regulation of chromatin organization and DNA repair, suggesting a potential link between nuclear architecture and genomic stability. These genes may function in pathways related to telomere maintenance, nuclear localization, nuclear lamina organization, and genome stability regulation. Overall, these findings suggest a potential mechanism by which changes in nuclear architecture and stability could lead to genomic instability and disease.] | \n", + "0.96 | \n", + "13 | \n", + "
| 276 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "regulation of presynaptic membrane potential-0 | \n", + "[Summary: The enriched terms from this list of genes are related to ion channel activity, particularly in relation to neurotransmission and synaptic signaling.\\n\\nMechanism: The genes on this list are involved in encoding different subunits of ion channels, most notably GABA and glutamate receptors, as well as voltage-gated potassium and sodium channels. These channels are crucial for synaptic transmission and the regulation of neuronal excitability.\\n\\n] | \n", + "[Summary: These genes are primarily involved in neurological processes and ion channel regulation. \\nMechanism: Regulation of ion channels in the nervous system.\\n\\nHypothesis: These genes are primarily involved in the regulation of ion channels in the nervous system, which affects processes such as nervous system development, synaptic transmission, and membrane potential regulation. The enrichment of terms related to ion transport and transmembrane transport suggest that these genes may play an important role in maintaining the balance of ion concentrations in neuronal cells, which is essential for proper neurological function. Additionally, the enrichment of terms related to neuron development suggests that these genes may play a role in shaping the nervous system during development.] | \n", + "0.93 | \n", + "340 | \n", + "
| 277 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "regulation of presynaptic membrane potential-1 | \n", + "[Summary: Ion channel activity and synaptic transmission-related processes are enriched in the listed genes.\\nMechanism: The genes are involved in synaptic plasticity, memory formation, and neuronal signaling.\\n] | \n", + "[Summary: Neurotransmission and Ion Channels are enriched functions in the given human genes.\\nMechanism: Signaling and excitatory neurotransmission.\\n\\n\\nHypothesis: The enriched functions suggest that these genes play a critical role in signaling pathways and neurotransmission in the central nervous system. Furthermore, the identified ion channels and receptors help mediate the excitatory and inhibitory communication between neurons, thus playing a critical role in neuronal development, learning, and memory.] | \n", + "0.92 | \n", + "303 | \n", + "
| 278 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "sensory ataxia-0 | \n", + "[Summary: The enriched terms found among the listed human genes suggest a common involvement in cellular metabolism, particularly in mitochondrial function, protein folding and degradation, and transportation across cellular membranes.\\nMechanism: These genes may be involved in the maintenance of cellular homeostasis and energy production.\\n\\nHypothesis: Many of the enriched terms are related to cellular stress pathways, suggesting that these genes may be involved in the response to stress and cellular damage. Additionally, the involvement of several genes related to mitochondrial function suggests that there may be a common underlying mechanism related to energy production and metabolism.] | \n", + "[Summary: Genes are involved in nervous system development and function. \\nMechanism: Myelination and axonal transport. \\n\\nHypothesis: The genes on the list are enriched for terms involved in nervous system development and function, including myelination, axon guidance, and neuron projection development. This suggests a role for these genes in the regulation of myelination and axonal transport, which are important processes for proper nervous system function. Dysfunction of these processes, due to mutations in genes such as PMP22 and SH3TC2, can lead to peripheral neuropathy and other neurological disorders.] | \n", + "0.87 | \n", + "82 | \n", + "
| 279 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "sensory ataxia-1 | \n", + "[Summary: Several of the genes are involved in nervous system development and function.\\nMechanism: Unknown, but potentially related to myelin formation and maintenance.\\n] | \n", + "[Summary: Genes related to neurological and cellular metabolism processes are over-represented.\\nMechanism: Metabolic and neurological processes\\n\\nHypothesis: These genes are involved in processes related to myelin sheath formation, cellular metabolism, and neurological development. Specifically, the genes NAGLU, PMP22, MPZ, EGR2, and TWNK are involved in myelin sheath formation, which is necessary for proper nerve function. FLVCR1, KPNA3, and AARS1 are involved in cellular metabolism, which has implications for cellular growth and function. Finally, DNAJC3, RNF170, and PIEZO2 are related to neurological development, which may be associated with neural plasticity and adaptation. Together, these genes suggest that there is an association between cellular metabolism, neurological development, and myelin sheath formation.] | \n", + "0.90 | \n", + "660 | \n", + "
| 280 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "term-GO:0007212-0 | \n", + "[Summary: The common function of the listed genes is related to G protein-coupled receptor signaling and neurotransmission.\\nMechanism: G protein-coupled receptor (GPCR) signaling\\n\\nHypothesis: The listed genes are involved in various aspects of G protein-coupled receptor (GPCR) signaling and neurotransmission. The enrichment of terms related to neurotransmitter receptor activity, GPCR signaling pathway, and regulation of neurotransmitter secretion suggests that these genes contribute to the communication between neurons in the brain. The dopamine receptor signaling pathway and adenylate cyclase-modulating GPCR signaling pathway terms suggest that these genes are particularly important in dopaminergic neurotransmission, which is involved in a wide range of processes including reward processing, motivation, and movement control. The involvement of these genes in dopaminergic neurotransmission may have implications for understanding and treating various neuropsychiatric disorders.] | \n", + "[Summary: G protein-coupled receptor signaling pathway.\\nMechanism: The genes are involved in the regulation of dopamine and prostaglandin signaling through G protein-coupled receptors.\\n] | \n", + "0.92 | \n", + "807 | \n", + "
| 281 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "term-GO:0007212-1 | \n", + "[Summary: Signaling and regulation via G-protein coupled receptors\\nMechanism: Activation of second messenger pathways\\n\\nHypothesis: These genes are all involved in signaling and regulation through G protein-coupled receptors (GPCRs), which are membrane proteins that activate intracellular signaling pathways upon binding with ligands such as neurotransmitters, hormones, or sensory signals. GPCR signaling pathways are transduced via G proteins, which consist of α, β, and γ subunits. The enriched terms suggest that these genes are involved in the regulation of G protein beta/gamma subunit complex binding, as well as the G protein coupled receptor signaling pathway. Dysfunction in these genes may lead to various diseases, including neuropsychiatric and cardiovascular disorders.] | \n", + "[Summary: G protein signaling and dopamine receptor activity are enriched in the list of human genes provided.\\nMechanism: G protein-coupled receptor (GPCR) signaling pathway and dopamine signaling pathway.\\n\\nHypothesis: The enriched genes in this list are involved in the GPCR and dopamine signaling pathways. GPCRs are the largest family of transmembrane receptors and play a crucial role in cellular signaling. The GPCR signaling pathway is responsible for several physiological processes like regulation of blood pressure, heart rate, immunity, and neurotransmission. The dopamine signaling pathway is responsible for reward, mood regulation, and movement. The enriched terms suggest the involvement of the GPCR signaling pathway and dopamine signaling pathway in regulating these physiological processes. The activation of adenylate cyclase and the role of Dopamine D1 receptor are important mechanistic pathways involved in the regulation of these physiological processes.] | \n", + "0.93 | \n", + "193 | \n", + "
| 282 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "tf-downreg-colorectal-0 | \n", + "[Summary: Transcriptional regulation and chromatin organization are enriched functions.\\nMechanism: These genes are involved in controlling gene expression and chromatin structure, which are crucial for cellular function and development.\\n\\nHypothesis: These genes may be involved in a common pathway related to transcriptional regulation and chromatin organization, such as the regulation of cell identity or differentiation, or the control of gene expression in response to external stimuli.] | \n", + "[Summary: Genes are enriched for transcription regulation, chromatin remodeling, and developmental processes.\\nMechanism: Transcriptional regulation\\n\\nHypothesis: The genes in this list are enriched for functions involved in transcriptional regulation, chromatin modification, and developmental processes. Specifically, the enriched terms suggest these genes play a role in protein-DNA complex assembly and response to stress. One underlying biological mechanism could involve the formation of multi-protein complexes involved in transcriptional regulation, including recruitment of chromatin remodelers and transcription factors, as well as response to cellular stress through activation of various signaling pathways.] | \n", + "0.95 | \n", + "227 | \n", + "
| 283 | \n", + "gpt-3.5-turbo | \n", + "no_synopsis | \n", + "tf-downreg-colorectal-1 | \n", + "[Summary: The common function among the given gene set is transcriptional regulation. \\nMechanism: The genes are involved in the regulation of various transcription factors, co-factors, and modifiers. \\n\\nHypothesis: The set of genes is involved in various stages of transcriptional regulation, from modifying chromatin structure to recruiting transcription factors and co-regulators. The enriched terms suggest that these genes may be involved in both positive and negative regulation of transcription, highlighting their importance in maintaining a fine balance of gene expression for proper cell function and development.] | \n", + "[Summary: These genes are enriched for terms related to transcriptional regulation and DNA binding.\\nMechanism: The mechanism likely involves the regulation of gene expression through DNA binding and transcriptional control.\\n\\n] | \n", + "0.91 | \n", + "397 | \n", + "
| 284 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "EDS-0 | \n", + "[Summary: The enriched terms are related to the extracellular matrix and connective tissue development.\\nMechanism: The genes are involved in the synthesis, processing, and organization of collagens and other extracellular matrix components.\\n] | \n", + "[Summary: The common function of the listed genes is related to connective tissue development, collagen biosynthetic processes, and extracellular matrix organization. \\n\\nMechanism: The enrichment of terms related to connective tissue and collagen biosynthesis suggests a potential underlying biological mechanism linking these genes to the pathogenesis of Ehlers-Danlos syndrome.\\n\\n] | \n", + "0.94 | \n", + "139 | \n", + "
| 285 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "EDS-1 | \n", + "[Summary: The common function among these genes is the regulation and formation of the extracellular matrix, which includes collagen fibril organization, dermatan sulfate biosynthetic process, proteoglycan biosynthetic process and connective tissue development.\\n\\nMechanism: These genes play a crucial role in the regulation and formation of the extracellular matrix, which is a scaffold-like structure comprising various proteins including collagen, and is essential in the development and maintenance of tissues and organs.\\n\\n\\nHypothesis: These genes play a role in regulating the organization and biosynthesis of the extracellular matrix, which is essential in the formation and maintenance of connective tissues. Dysregulation of these genes may contribute to various connective tissue disorders, including Ehlers-Danlos syndrome. This suggests that targeting the extracellular matrix and its related pathways may have potential therapeutic applications for these disorders.] | \n", + "[Summary: Genes involved in extracellular matrix organization and connective tissue development are enriched.\\nMechanism: These genes likely play a role in the synthesis, organization, and maintenance of the extracellular matrix and connective tissue.\\n\\n] | \n", + "0.94 | \n", + "725 | \n", + "
| 286 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "FA-0 | \n", + "[Summary: Fanconi anemia complementation pathway.\\n\\nMechanism: The Fanconi anemia (FA) pathway is a DNA repair pathway involved in the repair of inter-strand crosslinks and DNA double-strand breaks.\\n\\n\\nHypothesis: The FA pathway involves a series of proteins working together to repair damage to DNA that can cause various diseases, including cancer. The identification of this pathway provides insights into the mechanisms underlying DNA repair and may lead to improved methods of cancer treatment.] | \n", + "[Summary: These genes are involved in DNA repair and protein monoubiquitination, and are part of the Fanconi anemia nuclear complex. \\n\\nMechanism: The Fanconi anemia pathway plays a key role in the DNA repair process. \\n\\n] | \n", + "0.92 | \n", + "279 | \n", + "
| 287 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "FA-1 | \n", + "[Summary: The common function of these genes is DNA repair and protein monoubiquitination, specifically in the context of Fanconi anemia complementation groups. \\n\\nMechanism: Fanconi anemia is a genetic disorder characterized by genomic instability, bone marrow failure, and cancer susceptibility. It is caused by mutations in genes involved in DNA repair pathways, particularly the Fanconi anemia complementation group pathway. These genes work together to repair DNA damage and maintain genomic stability, and mutations in these genes can lead to the development of Fanconi anemia.\\n\\n\\nHypothesis: These genes work together in the Fanconi anemia complementation group pathway to repair DNA damage and maintain genomic stability. The pathway involves the monoubiquitination of FANCD2 and FANCI, leading to their recruitment to sites of DNA damage and the assembly of a repair complex involving other Fanconi anemia complementation group proteins, including those represented by the genes listed here. The complex repairs DNA damage via homologous recombination, which] | \n", + "[Summary: The enriched terms are related to DNA repair and protein monoubiquitination.\\nMechanism: These genes are involved in the Fanconi anemia pathway, which is a DNA damage response pathway that repairs interstrand DNA crosslinks.\\n] | \n", + "0.92 | \n", + "832 | \n", + "
| 288 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ADIPOGENESIS-0 | \n", + "[Summary: Mitochondrial function and energy metabolism are enriched in this list of genes.\\n\\nMechanism: These genes are involved in various processes such as ATP binding, enzyme activity, and transport, all of which are associated with mitochondrial function and energy metabolism.\\n\\n] | \n", + "[Summary: Several of the genes are involved in mitochondrial function, including electron transfer and ATP synthesis. Others are involved in lipid metabolism and transport, and some are involved in protein binding and signaling.\\n\\nMechanism: The enriched terms suggest a focus on mitochondrial function and metabolism, as well as protein and lipid transport and signaling.\\n\\n] | \n", + "0.94 | \n", + "91 | \n", + "
| 289 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ADIPOGENESIS-1 | \n", + "[Summary: Mitochondrial processes and metabolic function\\n\\nMechanism: The enriched terms suggest that these genes are involved in mitochondrial processes and metabolic function, with specific roles in energy production and mitochondrial regulation.\\n\\n] | \n", + "[Summary: Mitochondrial function, enzyme activity, and transporter activity\\nMechanism: Mitochondrial metabolism\\n] | \n", + "0.89 | \n", + "137 | \n", + "
| 290 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[Summary: Immune response and cytokine activity.\\n\\n] | \n", + "[Summary: Immune response-regulating genes\\n] | \n", + "0.87 | \n", + "7 | \n", + "
| 291 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[Summary: Immune system function and cytokine activity are enriched in the list of genes.\\n\\nMechanism: The common biological mechanism underlying the enriched terms is the regulation and activation of the immune system, particularly through cytokine signaling.\\n\\n] | \n", + "[Summary: These human genes are enriched in terms related to immune system, cytokine activity, chemokine receptor binding activity, and protein kinase activity.\\n\\n] | \n", + "0.92 | \n", + "99 | \n", + "
| 292 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[Summary: Many of the genes listed are involved in binding activities, such as nucleic acid binding, protein binding, and ion binding. A number of genes are also involved in metabolic processes, such as biosynthesis and dehydrogenase activity.\\n\\n] | \n", + "[Summary: Genes are involved in a variety of functions, including transport, enzyme activity, binding, and regulation of various processes. Enriched terms include protein phosphorylation, intracellular signaling pathways, and regulation of macromolecule metabolic process.\\n\\nMechanism: The enriched terms suggest that these genes are involved in signaling pathways and regulation of cellular processes. Specifically, protein phosphorylation appears to play a key role in the functions of these genes.\\n\\n] | \n", + "0.89 | \n", + "256 | \n", + "
| 293 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[Summary: Cell signaling and regulation of enzymatic activity\\nMechanism: These genes are involved in regulating cell signaling pathways, including cGMP biosynthesis, intracellular signal transduction and cell surface receptor signaling pathways. They also play a role in enzymatic activity, including phosphorylation, protein binding and transcription coactivator activity.\\n] | \n", + "[Summary: Genes are involved in various activities such as metal ion binding, enzymatic activity, and signal transduction.\\n\\n] | \n", + "0.89 | \n", + "250 | \n", + "
| 294 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ANGIOGENESIS-0 | \n", + "[Summary: Extracellular matrix structural constituents and proteins involved in cell signaling processes.\\n\\n] | \n", + "[Summary: Several genes are involved in extracellular matrix organization and cell signaling pathways, while others have roles in blood coagulation, lipid metabolism, and immunity.\\n\\n] | \n", + "0.91 | \n", + "75 | \n", + "
| 295 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ANGIOGENESIS-1 | \n", + "[Extracellular matrix organization and binding activity are the enriched terms in common among these genes.\\n\\nMechanism: The extracellular matrix (ECM) plays a crucial role in regulating cell behavior and maintaining tissue integrity. The enriched terms suggest that these genes all participate in ECM organization and binding, potentially contributing to processes such as cell adhesion, migration, and differentiation.\\n\\n] | \n", + "[Summary: Extracellular matrix organization and cell signaling\\nMechanism: Extracellular matrix regulation and cell signaling pathways\\n\\nHypothesis: These genes function in extracellular matrix organization and cell signaling pathways, involved in regulating the formation and maintenance of the extracellular matrix and cellular communication. They share enriched terms related to protein binding activity and positive regulation of intracellular signal transduction and are highly enriched for components of the collagen-containing extracellular matrix. This suggests a potential role in regulating collagen matrix structure, cell adhesion, and proliferation, as well as cell signaling cascades essential for tissue development and homeostasis.] | \n", + "0.93 | \n", + "324 | \n", + "
| 296 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-0 | \n", + "[Summary: These genes have functions related to cytoskeleton organization, cell adhesion, receptor binding, and kinase activity.\\n\\n] | \n", + "[Summary: These genes are involved in various cellular processes related to cytoskeletal organization, cell-cell communication, and intracellular signaling.\\n\\nMechanism: The common underlying biological mechanism may involve regulation of actin filament dynamics, which could impact processes such as cellular adhesion and migration, as well as intracellular signaling cascades.\\n\\n] | \n", + "0.92 | \n", + "249 | \n", + "
| 297 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-1 | \n", + "[Summary: These human genes are involved in various cellular functions and processes, including cell adhesion, cell signaling, and cytoskeleton organization. \\nMechanism: These genes likely function in a network of interrelated pathways involved in cellular processes. \\n\\n] | \n", + "[Summary: Cell adhesion and signaling\\nMechanism: Integrin-mediated signaling and cytoskeletal regulation\\n] | \n", + "0.88 | \n", + "165 | \n", + "
| 298 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_SURFACE-0 | \n", + "[Summary: Cell surface receptor activity and signal transduction are enriched in this list of genes.\\n\\nMechanism: These genes are involved in various processes such as cellular response, regulation of cellular processes, and intracellular signaling pathways. They function primarily as cell surface receptors, enzyme binding activity, and protein domain-specific binding activity.\\n\\n] | \n", + "[Summary: Several of the genes are involved in membrane transport and signaling, with a focus on plasma membrane and extracellular space.\\n\\nMechanism: These genes may be involved in the regulation of cellular signaling pathways and transport processes, particularly those related to the plasma membrane and extracellular space.\\n\\n] | \n", + "0.91 | \n", + "53 | \n", + "
| 299 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_SURFACE-1 | \n", + "[Summary: The enriched terms are related to membrane transport and signaling, with a focus on receptor activity and intracellular signaling.\\n\\nMechanism: These genes are primarily involved in the regulation of intracellular signaling pathways and membrane transport. \\n\\n] | \n", + "[Summary: The enriched terms include processes related to regulation and signaling, ion transport, cell adhesion and migration, and metabolic processes. \\n\\nMechanism: These genes may play roles in maintaining cellular homeostasis and responding to changes in the external environment through ion transport and signaling pathways. They may also act to regulate cell adhesion and migration, and participate in metabolic processes.\\n\\n] | \n", + "0.95 | \n", + "161 | \n", + "
| 300 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_APOPTOSIS-0 | \n", + "[Summary: These genes are involved in apoptosis, cytokine activity, and DNA-binding transcription factor activity.\\n\\n\\nHypothesis: These genes may be involved in pathways related to cell death and inflammation, such as the TNF signaling pathway or the p53 signaling pathway. They may also be involved in regulating gene expression through DNA-binding transcription factors.] | \n", + "[Summary: Genes in this list are primarily involved in apoptotic signaling pathways and immune response regulation.\\nMechanism: These genes act as modulators or effectors in apoptotic signaling pathways and immune response regulation. \\n\\n] | \n", + "0.91 | \n", + "136 | \n", + "
| 301 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_APOPTOSIS-1 | \n", + "[Summary: Genes involved in apoptotic signaling and cytokine activity.\\n\\n] | \n", + "[Summary: The enriched terms include apoptotic process, cytokine activity, and protein binding activity. \\n\\n] | \n", + "0.89 | \n", + "35 | \n", + "
| 302 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[Summary: The enriched terms indicate the genes are involved in lipid metabolism and transport.\\n\\nMechanism: The genes are involved in various processes related to the metabolism and transport of lipids and cholesterol, including ATP binding activity, and transmembrane transporter activity.\\n\\n] | \n", + "[Summary: These genes are involved in lipid and cholesterol metabolism, as well as peroxisomal and vitamin D-related processes.\\n\\nMechanism: These genes likely play a role in maintaining lipid and cholesterol homeostasis and metabolism, possibly through the regulation and transport of these molecules across cellular membranes.\\n\\n] | \n", + "0.92 | \n", + "37 | \n", + "
| 303 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[Summary: Several of the genes are involved in lipid metabolism and transport, particularly in the transport and binding of cholesterol and long-chain fatty acids. Peroxisomal proteins and functions are also enriched.\\n\\n] | \n", + "[Summary: Many of the listed genes are involved in lipid metabolism and transport, as well as peroxisome-related processes. \\n\\n\\nHypothesis: These genes are likely involved in the regulation and transport of various lipids and sterols, with a particular focus on the transport and metabolism of fatty acids and cholesterol in peroxisomes. ABC-type transporters may be involved in lipid uptake and efflux, while peroxisome-related processes may play a role in lipid metabolism and oxidation.] | \n", + "0.95 | \n", + "270 | \n", + "
| 304 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[Summary: Cholesterol biosynthesis and lipid metabolism.\\nMechanism: Genes involved in cholesterol biosynthesis and lipid metabolism are enriched in this list.\\n] | \n", + "[Summary: Cholesterol biosynthesis and metabolism genes.\\n\\nMechanism: These genes are involved in the biosynthesis and metabolism of cholesterol, a crucial molecule for cell membrane synthesis and steroid hormone production.\\n\\n] | \n", + "0.95 | \n", + "66 | \n", + "
| 305 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[Summary: Cholesterol biosynthesis and homeostasis, isoprenoid biosynthesis, and lipid metabolism are the enriched functional terms common among the given human genes.\\n\\nMechanism: These genes are involved in cholesterol biosynthesis and homeostasis, isoprenoid biosynthesis, and lipid metabolism. The mechanisms are related to the synthesis, transportation, and metabolism of cholesterol and other lipids.\\n\\n] | \n", + "[Summary: Cholesterol biosynthesis and lipid metabolism are the enriched terms across the provided genes.\\n\\nMechanism: The enriched terms suggest that the provided genes are involved in cholesterol biosynthesis and lipid metabolism, specifically the synthesis of isoprenoids and fatty acids.\\n\\n\\nHypothesis: These genes likely function in a coordinated pathway to support the synthesis of cholesterol, isoprenoids, and fatty acids within the body. This pathway may be involved in regulating cellular and systemic levels of these lipids to support proper cellular function and physiological processes, such as membrane structure and hormone production. Dysfunction in this pathway may contribute to the development of metabolic disorders, such as hyperlipidemia and atherosclerosis.] | \n", + "0.97 | \n", + "372 | \n", + "
| 306 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_COAGULATION-0 | \n", + "[Summary: The enriched terms for these genes include proteolysis, complement pathways, blood coagulation, and cell adhesion.\\n\\nMechanism: These genes all play a role in regulating the immune system and extracellular matrix.\\n\\n] | \n", + "[Summary: Several of these genes are involved in blood coagulation, complement activation, and metalloendopeptidase activity.\\n\\nMechanism: These genes participate in the regulation of proteolysis and enzyme inhibitors.\\n\\n] | \n", + "0.93 | \n", + "5 | \n", + "
| 307 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_COAGULATION-1 | \n", + "[Summary: Many of the genes listed are involved in the regulation of proteolysis, including metalloendopeptidase activity and serine-type endopeptidase activity, and are predicted to be involved in blood coagulation, complement activation, and negative regulation of proteolysis. \\n\\n] | \n", + "[Summary: The enriched terms suggest that the common function of these human genes involve diverse biological processes related to protein binding, enzymatic activity, and complement system. \\n\\n] | \n", + "0.87 | \n", + "89 | \n", + "
| 308 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_COMPLEMENT-0 | \n", + "[Summary: Genes involved in protease inhibition, protein binding, and enzyme activity.\\n\\nMechanism: The enriched terms suggest a potential underlying mechanism involving regulation of protease activity through protein binding and enzyme inhibition.\\n\\n] | \n", + "[Summary: Binding and catalytic activity\\n\\nHypothesis: These genes are involved in various types of binding and catalytic activities, which may include regulation of signaling pathways, transcriptional regulation, and enzyme activity in metabolic pathways. The enrichment of binding-related terms suggests that these genes may play a role in protein-protein interactions, protein-DNA interactions, metal ion coordination, and enzyme-substrate interactions. The involvement of ATP binding suggests these genes may also have a role in energy-dependent processes.] | \n", + "0.90 | \n", + "311 | \n", + "
| 309 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_COMPLEMENT-1 | \n", + "[Summary: These genes are involved in various functions, including protein binding activity, enzyme binding activity, and endopeptidase activity.\\n\\n] | \n", + "[Summary: Extracellular matrix, protease activity, and complement activation are enriched in the function of these genes.\\n\\n] | \n", + "0.91 | \n", + "24 | \n", + "
| 310 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_DNA_REPAIR-0 | \n", + "[Summary: Several genes are involved in DNA binding, RNA binding, and nucleotide metabolism. \\n\\n] | \n", + "[Summary: Many of the genes on this list are involved in DNA metabolism, transcription, and RNA processing. \\n\\n] | \n", + "0.94 | \n", + "15 | \n", + "
| 311 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_DNA_REPAIR-1 | \n", + "[Summary: These genes are involved in DNA replication, repair, and polymerization, RNA transcription, and metabolic processes.\\n\\nMechanism: These genes are likely part of a larger biological pathway involved in maintaining genome stability and function.\\n\\n] | \n", + "[Summary: Many of these genes are involved in DNA-related processes, including DNA replication, repair, and transcription. \\n\\n\\nHypothesis: The enriched terms suggest that these genes are part of a complex network involved in DNA processing, including binding to DNA and RNA molecules, maintaining nucleotide balance, and repairing DNA damage. The protein-macromolecule adaptor activity may be involved in coordinating these processes or facilitating interactions between proteins and genetic material.] | \n", + "0.92 | \n", + "247 | \n", + "
| 312 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_E2F_TARGETS-0 | \n", + "[Summary: Genes are primarily involved in DNA replication, cell cycle regulation, and chromatin organization.\\n\\nMechanism: These genes are likely involved in regulating the processes of DNA replication, the cell cycle, and chromatin organization.\\n\\n] | \n", + "[Summary: Genes involved in DNA replication, repair, and cell cycle regulation are enriched.\\n\\nMechanism: These genes are involved in processes related to DNA replication and repair, as well as regulation of the cell cycle, particularly in the G2 and M phases.\\n\\n] | \n", + "0.94 | \n", + "14 | \n", + "
| 313 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_E2F_TARGETS-1 | \n", + "[Summary: DNA-related functions are enriched among the given genes.\\nMechanism: These genes are involved in various processes related to DNA, such as DNA binding, repair, and replication.\\n\\n] | \n", + "[Summary: DNA binding and replication activities are enriched in the given gene list, indicating their involvement in DNA repair, replication, and regulation of cell cycle processes.\\n\\nMechanism: The enriched terms suggest that the genes in the list are involved in DNA binding, replication, and repair, which play essential roles in maintaining genomic stability.\\n\\n] | \n", + "0.93 | \n", + "177 | \n", + "
| 314 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[Summary: Extracellular matrix structural constituents and binding activities are statistically over-represented in this set of genes.\\n\\nMechanism: These genes are likely involved in extracellular matrix organization and cell-matrix interactions.\\n\\n] | \n", + "[Summary: These genes are involved in extracellular matrix organization and signaling pathways such as Wnt-protein binding, growth factor activity, and cytokine activity. \\n\\nMechanism: These genes work together to regulate the extracellular matrix and cellular signaling pathways that contribute to cellular processes such as development, tissue repair, and immunity.\\n\\n] | \n", + "0.92 | \n", + "121 | \n", + "
| 315 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[Summary: Extracellular matrix structural constituents and binding activities are enriched in these genes.\\n\\n] | \n", + "[Summary: The list of genes is enriched for functions related to extracellular matrix organization and regulation, including collagen binding, integrin binding, and heparin binding activity.\\n\\nMechanism: The genes in the list are involved in processes related to extracellular matrix regulation, including collagen synthesis and assembly, cell adhesion and migration, and protease inhibitor activity.\\n\\n] | \n", + "0.94 | \n", + "293 | \n", + "
| 316 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[Summary: These human genes are involved in a variety of functions related to binding and enzymatic activity, particularly involving calcium ion and nucleotide binding. They are also involved in several biological processes, including growth and development, gene transcription, and ion transport.\\n\\nMechanism: The common mechanism underlying these gene functions is likely related to the regulation and modulation of intracellular processes, particularly those involving binding and enzymatic activity. Calcium ion binding, for example, is a key regulator of many cellular processes, including muscle contraction, neurotransmitter release, and cell signaling.\\n\\n] | \n", + "[Summary: Transmembrane receptor and transporter activity, as well as DNA-binding transcription activator activity, are statistically over-represented in this list of genes.\\n\\nMechanism: These enriched terms suggest that the genes in this list are involved in membrane and nuclear signaling processes, including transcriptional regulation.\\n\\n] | \n", + "0.86 | \n", + "321 | \n", + "
| 317 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[Summary: Enriched terms relate to protein binding, transcription regulation, and transmembrane transport activity.\\n\\n] | \n", + "[Summary: Cell signaling and transcription regulation\\nMechanism: Enzyme and receptor activity, nucleic acid binding, transcriptional regulation\\n] | \n", + "0.86 | \n", + "27 | \n", + "
| 318 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[Summary: Transmembrane transporter activity and binding activity are enriched terms in the functions of the given genes.\\n\\nMechanism: These genes are involved in the transport of metabolites across membranes and regulation of protein-protein interactions, possibly contributing to maintenance of cellular homeostasis.\\n\\n] | \n", + "[Summary: This list of human genes is enriched for terms related to protein and enzyme activity, binding activity, and cellular transport.\\n\\nMechanism: These genes likely play important roles in various cellular processes, including protein and enzyme activity, binding and transport of molecules, and regulation of cellular growth and development.\\n\\n] | \n", + "0.93 | \n", + "30 | \n", + "
| 319 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[Summary: Several genes are involved in enzymatic activities (e.g. oxidoreductase, dehydrogenase), while others are involved in binding activities (e.g. protein binding, chemokine binding, lipid binding). Many genes are also predicted to be involved in several processes, including cell signaling, transcription regulation, and protein kinase activity.\\n\\n] | \n", + "[Summary: These genes are involved in various biological processes, but the enriched terms suggest a focus on binding activity and molecular transport.\\n\\nMechanism: The common biological mechanism for these genes is likely related to molecular interactions and transport within cells.\\n\\n] | \n", + "0.89 | \n", + "69 | \n", + "
| 320 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[Summary: Enzyme activity and metabolism.\\nMechanism: Metabolism, specifically, fatty acid metabolism and energy production.\\n\\n\\nHypothesis: These genes are involved in the metabolism of fatty acids and the production of energy through the tricarboxylic acid cycle. They enable the binding, breakdown, and transfer of acyl-CoA, which is important in the catabolism of fatty acids for energy production. These metabolic processes are vital for maintaining cellular function and homeostasis.] | \n", + "[Summary: Metabolism of fatty acids and carboxylic acids\\nMechanism: Fatty acid oxidation and elongation pathways, as well as carboxylic acid metabolism pathways\\n\\n] | \n", + "0.87 | \n", + "325 | \n", + "
| 321 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[Summary: Enzyme activity and binding activity are the most common functions among the genes in the list.\\n\\nMechanism: The genes in this list encode proteins that are involved in catalyzing chemical reactions (enzyme activity) and binding to other molecules (binding activity).\\n\\n] | \n", + "[Summary: These genes are mostly involved in oxidation-reduction processes and metabolic pathways, specifically lipid and fatty acid metabolism. \\n\\n] | \n", + "0.84 | \n", + "131 | \n", + "
| 322 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-0 | \n", + "[Summary: These genes are involved in various molecular functions related to DNA binding and activity, including DNA replication, transcription, and chromatin binding. \\nMechanism: These genes are likely involved in modulating gene expression and chromatin structure. \\n\\n] | \n", + "[Summary: These genes enable several functions related to DNA binding, transcription regulation, protein binding, histone modification, and protein kinase activity. \\n\\nMechanism: These genes are involved in regulating gene expression and DNA-related processes such as DNA replication, repair, and chromosome segregation. \\n\\n] | \n", + "0.96 | \n", + "53 | \n", + "
| 323 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-1 | \n", + "[Summary: These genes are involved in DNA binding and transcription factor activity, protein kinase and phosphatase activity, cytoskeletal protein binding, and microtubule binding activity.\\n\\n] | \n", + "[Summary: The genes are involved in DNA binding/transcription factor activity, protein kinase activity, and binding activity, and play a role in mitosis, DNA replication, and gene expression regulation. \\n\\nMechanism: These genes are involved in processes related to cell cycle regulation and gene expression control, likely through interactions with DNA, RNA, and protein molecules. \\n\\n] | \n", + "0.95 | \n", + "193 | \n", + "
| 324 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_GLYCOLYSIS-0 | \n", + "[Summary: Glycosylation and carbohydrate metabolism are enriched functions in this list of genes.\\n\\nMechanism: Glycosylation is a key process in carbohydrate metabolism, involving the addition of carbohydrate groups to proteins and lipids to form glycoproteins and glycolipids, respectively. These modifications are critical for proper protein folding, stability, and secretion, as well as for cell-cell recognition and signaling.\\n\\n\\nHypothesis: The enriched functions in these genes suggest a critical role for glycosylation and carbohydrate metabolism in a variety of physiological processes and perhaps a possible link between glycosylation and pathologies. Future studies could explore the molecular mechanisms underlying these processes and their role in disease pathogenesis.] | \n", + "[Summary: Glycosylation and carbohydrate metabolism related genes are enriched in this list.\\n\\nMechanism: The genes in this list are involved in various steps of glycosylation and carbohydrate metabolism pathways.\\n\\n] | \n", + "0.95 | \n", + "566 | \n", + "
| 325 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_GLYCOLYSIS-1 | \n", + "[Summary: Enriched terms are involved in carbohydrate metabolism, specifically glycosaminoglycan and glycoprotein biosynthesis.\\n\\nMechanism: These genes all code for enzymes involved in carbohydrate metabolism, particularly in the biosynthesis of glycosaminoglycans and glycoproteins.\\n\\n] | \n", + "[Summary: Enriched terms among these genes are involved in carbohydrate metabolism, enzyme activity, and binding activity.\\n\\nMechanism: These genes may be involved in a pathway that regulates carbohydrate metabolism, including glycosylation, synthesis of glucose, and synthesis and breakdown of glycogen. The genes may also play a role in enzyme activity and binding activity in various cellular processes.\\n\\n] | \n", + "0.95 | \n", + "122 | \n", + "
| 326 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[Summary: Genes are involved in a variety of cellular processes, including cell adhesion, signaling, and development.\\n\\nMechanism: These genes appear to converge on pathways related to cellular communication, regulation of gene expression, and cytoskeletal organization.\\n\\n] | \n", + "[Summary: The enriched terms for these genes reveal involvement in various cellular processes, including signal transduction, development, and gene regulation.\\n\\nMechanism: The underlying biological mechanism for these enriched terms involve complex cellular processes that are regulated by multiple genes and signaling pathways.\\n\\n] | \n", + "0.91 | \n", + "59 | \n", + "
| 327 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[Summary: Cell signaling and adhesion, transcriptional regulation, and nervous system development are common functions among the given genes.\\n\\nMechanism: These genes seem to be involved in the regulation of various signaling pathways, which contribute to important biological processes.\\n\\n] | \n", + "[Summary: Genes are involved in various processes such as cell adhesion, transcription regulation, and signal transduction. \\nMechanism: Biological mechanism involves regulation of gene expression and signal transduction pathways. \\n] | \n", + "0.92 | \n", + "57 | \n", + "
| 328 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_HEME_METABOLISM-0 | \n", + "[Summary: These genes are involved in various biological processes, including enzymatic activities, transcriptional regulation, and ion transport. The enriched terms include heme binding, protein binding activity, transcription factor activity, and transmembrane transporter activity.\\n\\nMechanism: The underlying biological mechanism involves the regulation of various metabolic pathways and cellular processes, such as DNA transcription, ion transport, and protein function.\\n\\n] | \n", + "[Summary: Several of the genes on the list are involved in binding and transportation activity, as well as enzyme activity.\\n\\nMechanism: These genes may play a role in metabolic and cellular processes through the transport and binding of various molecules, as well as enzymatic activity.\\n\\n] | \n", + "0.93 | \n", + "188 | \n", + "
| 329 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_HEME_METABOLISM-1 | \n", + "[Summary: Transport and binding activity \\n\\nHypothesis: These genes may be involved in pathways related to transport regulation, signaling, redox homeostasis, and gene expression. Further studies may explore the role of these genes in these cellular processes.] | \n", + "[Mechanism: Protein binding activity\\n\\nHypothesis: The common mechanism among these genes is their protein binding activity, which includes enzyme binding activity, protein domain specific binding activity, protein heterodimerization activity, identical protein binding activity, and protein homodimerization activity. These genes may interact with and regulate each other's activity through their protein binding domains, leading to coordinated cellular processes. Alternatively, they may play a role in the assembly of larger protein complexes necessary for various cellular functions.] | \n", + "0.90 | \n", + "327 | \n", + "
| 330 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_HYPOXIA-0 | \n", + "[Summary: Enriched terms show functions related to carbohydrate metabolism, enzyme binding and activity, signaling receptor binding, and DNA-binding transcription factor activity.\\n\\nMechanism: These genes may be involved in various biological mechanisms, such as carbohydrate metabolism, gene expression regulation, and receptor signaling pathways.\\n\\n] | \n", + "[Summary: Many of the genes listed are involved in binding, catalytic activity, and enzyme activity. \\nMechanism: These genes are likely involved in metabolic processes and signaling pathways. \\n\\n\\nHypothesis: These genes are involved in a complex network of metabolic processes and signaling pathways, potentially involving kinases, transcription factors, and calcium signaling. They may contribute to the regulation of enzyme activity, protein binding, and metabolic pathways in the body.] | \n", + "0.90 | \n", + "139 | \n", + "
| 331 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_HYPOXIA-1 | \n", + "[Summary: Enriched terms indicate genes involved in metabolic activities, specifically related to glucose metabolism and kinase activities, as well as transcriptional regulation and signaling.\\n\\nMechanism: These genes likely play a role in various cellular processes involved in metabolism, gene regulation, and signaling cascades.\\n\\n] | \n", + "[Summary: Functions enriched in this list of genes include binding activities (such as protein, ion, and growth factor binding) and enzymatic activities (such as kinase, dehydrogenase, and transferase activity). \\n\\nMechanism: These common functions suggest that the genes in this list are involved in various cellular processes that require binding and enzymatic activities, such as signal transduction, metabolism, and cell growth and differentiation.\\n\\n] | \n", + "0.90 | \n", + "121 | \n", + "
| 332 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[Summary: Regulation of cytokines and immune responses.\\nMechanism: Modulation of cytokine signaling and immune response pathways.\\n\\nHypothesis: These genes are involved in regulating cytokine signaling and immune response pathways, potentially modulating the response to infection or other immune challenges. They may play a role in the regulation of lymphocyte activation and differentiation, including T cell costimulation and negative regulation of activation, and have been implicated in defense responses to pathogens. Additionally, these genes appear to be involved in cytokine signaling regulation through modulation of cytokine receptor binding and interleukin binding activity.] | \n", + "[Summary: The common function of the listed genes is binding activity, including protein and DNA binding. \\n\\n] | \n", + "0.82 | \n", + "578 | \n", + "
| 333 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[Summary: Enriched terms are related to immune function and cytokine activity.\\n\\n] | \n", + "[Summary: Signaling and cytokine receptor activity, protein binding activity, enzyme activity, DNA binding activity, RNA binding activity, several processes including apoptosis and cellular response to cytokines.\\n\\n] | \n", + "0.84 | \n", + "134 | \n", + "
| 334 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[Summary: Cytokine and growth factor signaling pathways\\nMechanism: These genes are all involved in the process of cytokine and growth factor signaling pathways which regulate a wide range of biological processes.\\n] | \n", + "[Summary: Cytokine and growth factor receptor activity\\nMechanism: Signal transduction\\n] | \n", + "0.91 | \n", + "127 | \n", + "
| 335 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[Summary: Cytokine signaling and immune response\\nMechanism: These genes are involved in cytokine and chemokine receptor binding and cytokine-mediated signaling pathways, particularly those related to immune response and defense against other organisms.\\n\\n] | \n", + "[Summary: The enriched terms suggest that these genes are involved in cytokine activity and signaling pathways.\\nMechanism: These genes are likely involved in the regulation of the immune system through cytokines and signaling pathways.\\n] | \n", + "0.92 | \n", + "18 | \n", + "
| 336 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[Summary: These genes are involved in various functions relating to cytokine and chemokine activity, enzyme binding activity, receptor activity, and ion transport.\\n\\n\\nHypothesis: These genes play a role in immune system function, possibly involved in chemotaxis and signal transduction pathways through cytokine and chemokine activity, as well as ion transport in cell signaling. The genes may also be involved in enzyme binding and receptor activity, which could potentially affect various biological processes and disease pathways.] | \n", + "[Summary: Signaling and cell communication through the immune system and cytokines.\\nMechanism: The genes listed enable cytokine activity, cytokine receptor activity, G protein-coupled receptor activity, and enzyme binding activity, with a particular emphasis on the immune system. \\n] | \n", + "0.91 | \n", + "251 | \n", + "
| 337 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[Summary: These genes are involved in various biological processes, including receptor and transporter activity, cytokine activity, and signal transduction.\\n\\n] | \n", + "[Summary: Cell signaling and receptor binding activity are enriched in the list of genes.\\n\\nMechanism: These genes are involved in cellular signaling, including binding to receptors and activation of downstream pathways.\\n\\n] | \n", + "0.91 | \n", + "63 | \n", + "
| 338 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[Summary: Immune response genes that are involved in cytokine activity, defense response to other organisms, and negative regulation of viral entry into host cells. \\n\\nMechanism: These genes are likely involved in the innate immune response to infection, particularly in the modulation of viral infection and replication. \\n\\n] | \n", + "[Summary: Many of the genes listed are involved in immune response and antigen processing and presentation, including cytokines, chemokines, and interferon-related genes. Additionally, several genes are involved in RNA processing and editing.\\n\\n\\nHypothesis: These genes may be involved in immune recognition and response to foreign pathogens, potentially through antigen presentation and cytokine/chemokine-mediated immune cell recruitment and activation. The RNA-related genes may be involved in post-transcriptional regulation of immune-related genes.] | \n", + "0.91 | \n", + "230 | \n", + "
| 339 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[Summary: These genes are involved in immune response, defense against virus, negative regulation of protein secretion, regulation of leukocyte chemotaxis, RNA binding, and regulation of transcription.\\n\\nMechanism: The biological mechanism is likely the activation of the immune response, specifically the interferon response.\\n\\n] | \n", + "[Summary: Many of the genes are involved in immune response and defense against viruses, as well as regulation of protein activity.\\n\\nMechanism: The enriched terms suggest an underlying biological mechanism of antiviral defense and immune response pathways.\\n\\n] | \n", + "0.91 | \n", + "69 | \n", + "
| 340 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[Summary: Immune response and cytokine signaling-related genes.\\n\\n] | \n", + "[Summary: Immune system processes and regulation are enriched in the list of genes.\\n\\nMechanism: These genes are involved in various immune system processes, from cytokine and chemokine activity to transcription factor binding and protein homodimerization. \\n\\n\\nHypothesis: The enriched immune system processes and regulation may be involved in the regulation and response to external stimuli, such as infections or tissue damage, and the maintenance of internal homeostasis. The different gene functions may work together in a network to activate or inhibit immune responses and protect the body from harmful agents.] | \n", + "0.89 | \n", + "550 | \n", + "
| 341 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[Summary: Immune system activity, particularly in response to viral infection, is the overarching theme among the functions of these genes.\\nMechanism: These genes are involved in various aspects of the immune response, including innate antiviral defense, antigen presentation, cytokine signaling, and regulation of immune cell activation and proliferation.\\n] | \n", + "[Summary: Genes involved in immune response, from antigen presentation to cytokine signaling and antiviral defense.\\n\\nMechanism: These genes are involved in various aspects of the immune response, including antigen presentation through MHC class I and II complexes, cytokine signaling through STAT proteins, and antiviral defense through interferon-stimulated genes.\\n\\n] | \n", + "0.95 | \n", + "10 | \n", + "
| 342 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[Summary: Ion transport and binding activity\\nMechanism: Ion channel and transporter activity\\n\\nHypothesis: These genes are involved in various ion transport mechanisms and have binding activity for different ions, including calcium and sodium: potassium:chloride. They may be part of a larger pathway involved in regulating ion concentration and signaling in the cell.] | \n", + "[Summary: Protein binding and enzyme activity.\\n\\n\\nHypothesis: The overrepresented terms suggest that these genes may be involved in a complex protein-protein interaction network, with many proteins acting as enzymes that catalyze a reaction and interact with other proteins through binding activity. Additionally, many of these proteins may act as transcription factors, influencing gene expression by binding to DNA and regulating transcription. Ion binding activity may also be involved in many of these processes, as ions are important cofactors for many enzymes and can influence protein structure and function.] | \n", + "0.90 | \n", + "247 | \n", + "
| 343 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[Summary: The enriched terms are related to binding activity and transport, specifically involving ion, protein, and nucleoside.\\n\\n\\nMechanism: The genes in this list are involved in regulating binding activity and transport, likely through ion channels and protein-protein interactions.\\n\\n\\n] | \n", + "[Summary: Genes involved in binding and enzymatic activities, as well as regulation of cellular processes.\\n\\n] | \n", + "0.88 | \n", + "180 | \n", + "
| 344 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[Summary: Several genes are involved in binding activity, such as protein binding, ion binding, and receptor binding. Additionally, some genes are involved in enzyme activity and transcription activator activity. \\n\\n] | \n", + "[Summary: Genes involved in binding activity, enzymatic activity, and protein regulation.\\nMechanism: These genes play a role in cellular processes such as signaling, metabolism, and transcriptional regulation.\\n\\n] | \n", + "0.93 | \n", + "4 | \n", + "
| 345 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[Summary: Many of the genes in the list enable various binding activities and are involved in regulation of cellular processes.\\n\\n] | \n", + "[Summary: Protein binding and enzymatic activity\\n] | \n", + "0.85 | \n", + "80 | \n", + "
| 346 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[Summary: Genes involved in cytoskeleton organization, microtubule binding, and GTPase regulation.\\n\\nMechanism: These genes are predicted to be involved in various aspects of cytoskeleton organization and microtubule regulation, including microtubule binding, kinetochore binding, and actin filament binding. They are also predicted to be involved in the regulation of GTPases, which have been shown to play critical roles in cytoskeletal organization.\\n\\n] | \n", + "[Summary: Several genes are involved in cytoskeleton organization and regulation, including microtubule binding, actin binding, and GTPase activator activity.\\n\\nMechanism: The regulation of cytoskeleton stability and dynamics is crucial for many cellular processes, including cell division, migration, and differentiation. These genes likely play key roles in maintaining cytoskeleton integrity and regulating its rearrangement through protein-protein interactions and enzymatic activities.\\n\\n] | \n", + "0.96 | \n", + "38 | \n", + "
| 347 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[Summary: The enriched terms suggest that these genes are involved in microtubule organization and mitosis.\\n\\nMechanism: These genes play a role in regulating microtubule organization and mitosis, potentially through interactions with other proteins in the cytoskeleton and spindle apparatus.\\n\\n] | \n", + "[Summary: Genes are primarily involved in microtubule binding and regulation, as well as cell division processes such as mitosis and cytokinesis. \\n\\n] | \n", + "0.90 | \n", + "145 | \n", + "
| 348 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-0 | \n", + "[Summary: Many of the genes are involved in binding activities, including RNA binding, protein binding, and ion binding, and several are involved in enzymatic activity such as oxidoreductase and kinase activity. \\n\\nMechanism: The enriched functions suggest that these genes are involved in protein synthesis and processing, as well as intracellular signaling and metabolism. \\n\\n] | \n", + "[Summary: Many of the genes listed are involved in protein or RNA binding, enzymatic activity, and structural components of cells. \\n\\n] | \n", + "0.94 | \n", + "243 | \n", + "
| 349 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-1 | \n", + "[Summary: These genes are involved in several cellular processes, including protein binding and enzyme activity. \\n\\n] | \n", + "[Summary: The enriched terms across these genes suggest a common theme of protein folding, transport, and degradation. \\n\\nMechanism: These genes are involved in the regulation of protein folding, transport, and degradation, likely through the ubiquitin-proteasome system and endoplasmic reticulum-associated degradation pathway.\\n\\n] | \n", + "0.90 | \n", + "214 | \n", + "
| 350 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-0 | \n", + "[Summary: Protein synthesis and folding\\n\\n] | \n", + "[Summary: Ribosome and protein synthesis-related activity\\nMechanism: Protein synthesis and ribosome biogenesis\\n\\nHypothesis: The enriched terms suggest that the genes in this list are involved in fundamental cellular processes related to protein synthesis and ribosome biogenesis. They are likely necessary for proper folding, transport, binding, and localization of mRNA and ribosomes, which are essential for protein synthesis. The genes on the list may function together to regulate these processes, playing key roles in fine-tuning protein production during development, cellular differentiation, and stress responses.] | \n", + "0.86 | \n", + "581 | \n", + "
| 351 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-1 | \n", + "[Summary: These genes are involved in nucleic acid binding, RNA processing, protein folding, and structural constituents of ribosomes.\\n\\n] | \n", + "[Summary: RNA processing and binding activity\\n\\n] | \n", + "0.90 | \n", + "89 | \n", + "
| 352 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-0 | \n", + "[Summary: These genes are predominantly involved in RNA and protein processing, with many of them predicted to have RNA binding activity and be involved in rRNA processing. They also play roles in cell cycle regulation and mitochondrial function.\\n\\nMechanism: These genes likely function together in various pathways involved in RNA and protein processing, including rRNA processing, mRNA catabolism, and RNA maturation.\\n\\n] | \n", + "[Summary: This set of human genes is enriched for terms related to RNA processing, specifically rRNA processing and biogenesis. \\n\\nMechanism: These genes likely participate in a common biological pathway related to ribosome biogenesis and function.\\n\\n] | \n", + "0.92 | \n", + "172 | \n", + "
| 353 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-1 | \n", + "[Summary: The enriched terms from these genes suggest involvement in various aspects of RNA processing and nucleolar function.\\n\\nMechanism: These genes encode proteins involved in RNA processing and nucleolar function.\\n\\n] | \n", + "[Summary: Genes involved in RNA processing, rRNA processing, and ribosomal biogenesis.\\n\\nMechanism: These genes contribute to the production and processing of ribosomal RNA (rRNA) involved in ribosomal biogenesis. rRNA molecules are important components of ribosomes, which are responsible for protein synthesis in cells.\\n\\n] | \n", + "0.90 | \n", + "103 | \n", + "
| 354 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MYOGENESIS-0 | \n", + "[Summary: The common function among the genes is related to muscle function and regulation.\\n\\nMechanism: The genes are all involved in the muscle cell structure, regulation, and function, including contraction, signaling, and development.\\n\\n] | \n", + "[Summary: These human genes are enriched for terms related to muscle structure and function, including actin binding and ATP activity.\\n\\nMechanism: These genes likely play a role in muscle development and function, as well as related processes such as calcium ion binding and molecular adaptor activity.\\n\\n] | \n", + "0.90 | \n", + "65 | \n", + "
| 355 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_MYOGENESIS-1 | \n", + "[Summary: Muscle structure and function\\n\\n] | \n", + "[Summary: Muscle and cytoskeletal proteins are enriched in this list of genes.\\n\\n] | \n", + "0.83 | \n", + "39 | \n", + "
| 356 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-0 | \n", + "[Summary: Notch signaling pathway and protein ubiquitination are enriched functions among the given genes.\\n\\nMechanism: The enriched functions suggest that these genes are involved in a biological pathway related to the regulation of Notch signaling pathway and protein ubiquitination.\\n\\n] | \n", + "[Summary: The enriched terms suggest that the listed genes are involved in various aspects of cellular signaling pathways, including Notch, Wnt, and ubiquitin-mediated protein degradation.\\n\\nMechanism: The mechanism underlying the commonalities in function may be related to the fact that many of these genes are involved in the regulation of gene expression and cellular signaling pathways that are critical for embryonic development and tissue homeostasis.\\n\\n] | \n", + "0.93 | \n", + "173 | \n", + "
| 357 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-1 | \n", + "[Summary: The enriched terms include \"Notch signaling pathway,\" \"protein ubiquitination,\" \"negative regulation of cell differentiation,\" and \"regulation of DNA-templated transcription.\"\\n\\nMechanism: These genes are involved in processes related to intracellular signaling and protein regulation.\\n\\n\\nHypothesis: These genes are involved in a complex regulatory network that fine-tunes protein levels and intracellular signaling pathways to ensure proper cell differentiation and development. The Notch signaling pathway is a key pathway involved in cell differentiation and is regulated by ubiquitination and transcriptional control. The enriched terms likely reflect the importance of these processes in maintaining proper cell function and development.] | \n", + "[Summary: Notch signaling pathway and protein ubiquitination are enriched terms among these genes.\\nMechanism: These genes are involved in the regulation of cell differentiation, stem cell population maintenance, and DNA-templated transcription, which are processes that require the Notch signaling pathway for their proper function. Additionally, several of these genes are involved in ubiquitination, a process that targets proteins for degradation or signaling.\\n] | \n", + "0.97 | \n", + "288 | \n", + "
| 358 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[Summary: Genes in this list are involved in various aspects of mitochondrial function and metabolism, including electron transport chain activity, ATP synthesis, and metabolism of acyl-CoA and ketone bodies.\\n\\n\\nHypothesis: These genes are involved in different parts of mitochondrial metabolism and energy production, but they all work together to maintain proper mitochondrial function. Dysregulation of these genes could lead to disruptions in the electron transport chain and oxidative phosphorylation, which could contribute to mitochondrial dysfunction and metabolic disorders. Further research is needed to fully understand the underlying pathways and mechanisms by which these genes interact to maintain mitochondrial homeostasis.] | \n", + "[Summary: Mitochondrial respiratory chain complex activity.\\n\\nHypothesis: Mitochondria are the powerhouse of the cell and play a crucial role in energy production, most notably through oxidative phosphorylation in which electrons pass through a series of complexes in the mitochondrial respiratory chain to generate ATP. The enriched terms of this gene list, such as electron transfer activity, NADH dehydrogenase (ubiquinone) activity, and ubiquitin protein ligase binding activity, directly relate to the functionality of the mitochondrial respiratory chain. Additionally, the RNA binding activity and protein homodimerization activity suggest the regulation and maintenance of these complexes. The metal ion binding activity could also be related to the involvement of metal ions, such as iron or copper, in electron transport.] | \n", + "0.89 | \n", + "92 | \n", + "
| 359 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[Summary: These human genes have functions related to mitochondrial respiratory chain complexes and enzyme activity, as well as ion and molecule transport across mitochondrial membranes.\\n\\nMechanism: These genes are involved in the electron transport chain in the mitochondria. The electron transport chain generates ATP by transferring electrons from NADH and other electron donors to oxygen.\\n\\n] | \n", + "[Summary: Several of these genes are involved in mitochondrial functions such as respiratory chain complex activity and ATP synthase activity. They also play roles in metabolic processes such as electron transfer activity and oxidoreductase activity.\\n\\n] | \n", + "0.95 | \n", + "142 | \n", + "
| 360 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_P53_PATHWAY-0 | \n", + "[Summary: Enriched terms include regulation of apoptotic process, protein binding activity, and DNA-binding transcription factor activity. \\n\\nMechanism: These genes are involved in regulating apoptosis and controlling cell death. They also play a role in gene regulation and transcription factor activity through protein binding. \\n\\n] | \n", + "[Summary: These genes are involved in various functions, including DNA binding, protein binding, enzyme activity, transcription factor activity, and growth factor activity.\\n\\n] | \n", + "0.91 | \n", + "157 | \n", + "
| 361 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_P53_PATHWAY-1 | \n", + "[Summary: RNA binding and transcription factor activity are enriched in these genes.\\nMechanism: These genes are involved in regulating gene expression at the transcriptional level and RNA processing.\\n] | \n", + "[Summary: These genes are involved in a variety of functions, including DNA binding, protein binding, and kinase activity.\\n\\n] | \n", + "0.89 | \n", + "76 | \n", + "
| 362 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[Summary: Genes are involved in various processes including glucose homeostasis, insulin secretion, and transcription regulation.\\n\\nMechanism: Genes work together to regulate glucose homeostasis and insulin secretion.\\n\\n] | \n", + "[Summary: Several of the genes are involved in glucose metabolism and regulation of insulin secretion.\\n\\nMechanism: These genes likely play a role in the regulation of blood sugar levels and insulin secretion through various cellular mechanisms.\\n\\n] | \n", + "0.96 | \n", + "28 | \n", + "
| 363 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[Summary: Genes related to glucose homeostasis, insulin secretion, and glucose metabolism are enriched.\\n\\n\\nHypothesis: These genes may be involved in a pathway or mechanism related to glucose regulation and diabetes, potentially influencing glucose uptake, storage, and secretion.] | \n", + "[Summary: Many of the genes are involved in insulin secretion or glucose metabolism, suggesting a potential role in diabetes. Additionally, several genes are involved in transcriptional regulation or regulation of gene expression.\\n\\n\\nHypothesis: \\nThe enriched terms suggest that several of these genes may be involved in a common regulatory pathway controlling insulin secretion and glucose metabolism. Specifically, the transcriptional regulation of genes involved in insulin secretion and glucose metabolism may be mediated by RNA polymerase II-specific transcription factors, which can bind to specific cis-regulatory regions of these genes to control their expression. Negative regulatory factors can suppress gene expression, while positive regulatory factors can increase expression. Dysfunction in any of these genes, therefore, could lead to defects in insulin secretion or glucose metabolism, potentially contributing to the development of type 1 or type 2 diabetes mellitus.] | \n", + "0.94 | \n", + "704 | \n", + "
| 364 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PEROXISOME-0 | \n", + "[Summary: Several of the genes listed are involved in transport functions and enzyme activities related to lipid and fatty acid metabolism. Additionally, some genes are involved in binding and catalytic functions related to retinoids and steroids.\\n\\n\\nHypothesis: These genes are involved in several functions that are key to cellular metabolism and homeostasis. Lipid and fatty acid metabolism are essential for maintaining membrane integrity and cellular signaling processes. Transporters and enzymes related to these functions are necessary for proper uptake, utilization, and metabolism of lipids and fatty acids. Additionally, retinoids and steroids are important signaling molecules that can be involved in metabolic processes and cellular differentiation. The presence of these genes suggests that dysregulation of lipid, fatty acid, retinoid, or steroid metabolism could lead to disease states such as metabolic disorders, cancer, or developmental abnormalities.] | \n", + "[Summary: The enriched terms suggest that these genes are involved in lipid metabolism and transport, as well as binding and catalysis.\\n\\nMechanism: These genes likely function together in cellular lipid metabolism and transport pathways, potentially in peroxisomes or mitochondria.\\n\\n] | \n", + "0.93 | \n", + "686 | \n", + "
| 365 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PEROXISOME-1 | \n", + "[Summary: Most of the genes are involved in lipid or fatty acid metabolism and transport, including long-chain fatty acid-CoA ligase activity, palmitoyl-CoA oxidase activity, arachidonate-CoA ligase activity, very long-chain fatty acid-CoA ligase activity, and several other related terms.\\n\\nMechanism: These genes likely play a role in regulating lipid homeostasis and transport, possibly through peroxisome biogenesis and function, as several genes also have peroxisome-targeting sequence binding activity.\\n\\n] | \n", + "[Summary: Many of these genes are involved in lipid metabolism and transport, mitochondrial function, and DNA repair. \\n\\nMechanism: These genes may be involved in maintaining cellular homeostasis by regulating lipid metabolism and mitochondrial function, as well as protecting DNA from damage. \\n\\n] | \n", + "0.92 | \n", + "214 | \n", + "
| 366 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[Summary: Genes are involved in various cellular processes, including protein kinase activity, cytoskeleton structure, lipid metabolism, and protein binding activity.\\n\\nMechanism: These genes are involved in different pathways that regulate cellular signaling and metabolic processes.\\n\\n] | \n", + "[Summary: Genes in this list are largely involved in signal transduction pathways, including protein kinase activity, G protein-coupled receptor binding activity, and transcription factor binding activity.\\n\\nMechanism: These genes likely function in several interconnected signaling pathways, including the MAPK/ERK pathway, PI3K/Akt pathway, and NF-kappaB pathway.\\n\\n] | \n", + "0.92 | \n", + "81 | \n", + "
| 367 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[Summary: Several of the genes are involved in intracellular signal transduction and several processes related to protein phosphorylation. \\n\\n] | \n", + "[Summary: Intracellular signal transduction and protein phosphorylation.\\nMechanism: These genes are involved in intracellular signal transduction processes which involve the phosphorylation of proteins.\\n] | \n", + "0.95 | \n", + "62 | \n", + "
| 368 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-0 | \n", + "[Summary: The enriched terms involve the transport and organization of cellular components, particularly in Golgi-related processes.\\n\\nMechanism: These genes likely contribute to the regulation of cellular transport and trafficking pathways involved in Golgi function and organization.\\n\\n] | \n", + "[Summary: Golgi apparatus-related processes are enriched in this list of genes.\\n\\nMechanism: The genes in this list are involved in various processes related to Golgi apparatus homeostasis, organization, transport, and vesicle-mediated recycling.\\n\\n] | \n", + "0.93 | \n", + "39 | \n", + "
| 369 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-1 | \n", + "[Summary: Intracellular vesicle transport and protein localization\\nMechanism: Vesicle-medidated transport pathways\\n] | \n", + "[Summary: This set of genes is enriched for functions related to intracellular membrane trafficking and transport.\\n\\n\\nHypothesis: These genes are involved in various steps of intracellular transport and vesicle-mediated trafficking between the endoplasmic reticulum and the Golgi complex. The enriched terms are likely reflections of this shared functional theme. It is possible that the proteins encoded by these genes interact with each other to form complexes or pathways that regulate this process. Further investigation may reveal more details about the specific mechanisms involved in these functions.] | \n", + "0.87 | \n", + "492 | \n", + "
| 370 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[Summary: Genes involved in cell redox homeostasis and antioxidant activity are enriched.\\n\\nMechanism: These genes function in maintaining the balance of redox reactions in cells and protecting against oxidative damage.\\n\\n] | \n", + "[Summary: Cell redox homeostasis and response to oxidative stress are enriched functional themes among the listed genes.\\n\\nMechanism: Genes in this group function in maintaining cellular redox balance by regulating the activity of reactive oxygen species (ROS) and oxidative stress response pathways. \\n\\n] | \n", + "0.94 | \n", + "82 | \n", + "
| 371 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[Summary: Cell redox homeostasis and oxidative stress response\\nMechanism: Regulating and maintaining redox balance within cells to prevent oxidative damage\\n\\nHypothesis: These genes play important roles in maintaining cellular redox homeostasis and responding to oxidative stress. This includes antioxidant activity and the regulation of glutathione peroxidase and superoxide dismutase activities. Additionally, these genes are involved in NADH dehydrogenase activity and mitochondrial respiratory chain complex I assembly, both of which are crucial for cellular respiration and energy production. Together, these processes ensure the proper functioning of cells and protect against oxidative damage.] | \n", + "[Summary: Cell redox homeostasis and response to oxidative stress are enriched terms in the gene list.\\n\\nMechanism: These genes are involved in maintaining cellular redox balance by regulating oxidant detoxification pathways and responding to oxidative stress.\\n\\n] | \n", + "0.95 | \n", + "439 | \n", + "
| 372 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-0 | \n", + "[Summary: These genes are involved in a variety of processes including protein binding, enzyme activity, and ion transport. They are enriched for terms related to kinase activity, protein binding, and nucleotide binding.\\n\\nMechanism: These genes may be involved in the regulation of cell signaling and communication pathways through the activity and binding of kinases, proteins, and nucleotides.\\n\\n] | \n", + "[Summary: This list of human genes is highly enriched in genes involved in protein binding and kinase activity, as well as in genes involved in cell cycle regulation and gene expression.\\nMechanism: The enriched terms suggest that these genes are involved in cellular processes that require the binding and modification of proteins, particularly during cell cycle regulation and gene expression.\\n] | \n", + "0.95 | \n", + "2 | \n", + "
| 373 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-1 | \n", + "[Summary: The enriched terms include protein binding and enzymatic activity, involvement in several processes such as cell signaling, transcription, and metabolism, and localization to specific cellular structures.\\n\\nMechanism: These genes are involved in various biological processes that rely on protein-protein interactions, enzymatic activity, and regulation of various cellular functions.\\n\\n\\nHypothesis: These enriched terms suggest that the genes are involved in various biological pathways that are essential for maintaining cellular functions, including protein folding, transcription, signaling, and regulation of metabolism. These genes may also play a role in cellular localization and transport of specific molecules. Overall, these genes are integral to maintaining cellular homeostasis and their dysregulation could contribute to various diseases.] | \n", + "[Summary: Many of the identified genes are involved in cellular processes such as protein binding, enzyme activator/inhibitor activity, and ATP binding activity.\\n\\nMechanism: The underlying biological mechanism may involve regulating cellular processes through protein interactions and/or enzyme regulation.\\n\\n] | \n", + "0.93 | \n", + "552 | \n", + "
| 374 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[Summary: Genes involved in transforming growth factor beta (TGF-β) receptor signaling and related pathways are over-represented.\\n\\nMechanism: TGF-β receptor signaling is central to the regulation of cell growth and differentiation and is involved in numerous biological processes.\\n\\n] | \n", + "[Summary: The enriched terms are related to cellular signaling and development processes, particularly those involving the transforming growth factor-beta (TGF-beta) signaling pathway.\\n\\nMechanism: These genes are involved in the TGF-beta signaling pathway, which regulates cellular processes such as proliferation, differentiation, and apoptosis.\\n\\n] | \n", + "0.92 | \n", + "66 | \n", + "
| 375 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[Summary: Genes involved in various aspects of signal transduction and regulation of gene expression.\\n\\n] | \n", + "[Summary: Signaling through TGF-beta superfamily and BMP receptor-related pathways\\nMechanism: TGF-beta and BMP ligands bind to type II receptors, which activate type I receptors. The activated type I receptors phosphorylate SMAD transcription factors, which activate or repress target gene expression.\\n] | \n", + "0.84 | \n", + "199 | \n", + "
| 376 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[Summary: The enriched terms for these genes suggest a role in immune response, cytokine activity, DNA-binding transcription factor activity, and enzyme binding activity.\\n\\nMechanism: These genes may play a role in activating or regulating the immune response and cytokine production through DNA-binding transcription factor activity and enzyme binding activity.\\n\\n] | \n", + "[Summary: Transcription regulation and cytokine activity.\\n\\nHypothesis: These genes may be involved in the regulation of immune responses, cellular differentiation, and tissue growth and repair. They may interact with signaling pathways involved in cytokine production and response, such as the JAK-STAT pathway and the NF-kappaB pathway.] | \n", + "0.91 | \n", + "25 | \n", + "
| 377 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[Summary: Genes on the list are involved in cytokine activity, DNA-binding transcription activities, and several enzymatic activities.\\n\\n] | \n", + "[Summary: The enriched terms are related to immune system processes and cytokine signaling pathways.\\nMechanism: These genes are involved in regulating cytokine receptor activity and immune system signaling pathways, likely through activation of MAP kinase and transcription factor pathways.\\n\\n] | \n", + "0.88 | \n", + "156 | \n", + "
| 378 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[Summary: These genes are predominantly involved in protein processing, modification, and transport. \\n\\nMechanism: These genes are involved in various stages of protein synthesis, folding, and transport, including post-translational modifications, protein chaperoning, and trafficking. \\n\\n] | \n", + "[Summary: Many of the genes are involved in protein folding and chaperone activity, RNA binding and transcriptional regulation, and RNA processing and degradation.\\n\\nMechanism: The common mechanism might be related to the regulation of protein homeostasis, with these genes functioning in different aspects of protein folding, RNA binding and processing, and transcriptional regulation.\\n\\n] | \n", + "0.93 | \n", + "100 | \n", + "
| 379 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[Summary: All of the genes are involved in molecular functions related to RNA, protein, and ribosomal binding activity.\\nMechanism: These genes likely play a role in the regulation of transcription, translation, and protein folding.\\n] | \n", + "[Summary: These genes are involved in various cellular processes, with a common theme of RNA and protein regulation, as well as involvement in endoplasmic reticulum (ER) stress response pathways.\\n\\nMechanism: These genes may be involved in regulating RNA and protein synthesis and processing, as well as responding to cellular stress, particularly ER stress.\\n\\n] | \n", + "0.92 | \n", + "127 | \n", + "
| 380 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-0 | \n", + "[Summary: Extracellular matrix structural constituent, growth factor binding, protein kinase activity, nucleotide binding, transcription factor activity, protein binding.\\n\\n] | \n", + "[Summary: Extracellular matrix structural constituent and protein binding activity are enriched functions amongst the given human genes.\\nMechanism: These genes may play a role in cellular adhesion, migration, and signal transduction processes.\\n] | \n", + "0.91 | \n", + "72 | \n", + "
| 381 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-1 | \n", + "[Summary: Extracellular matrix structural constituents and binding activity.\\nMechanism: Extracellular matrix formation and maintenance.\\n\\n] | \n", + "[Summary: Extracellular matrix structural constituents, protein binding, transcription activator activity, and receptor binding are enriched terms among these genes.\\nMechanism: The enriched terms suggest that these genes may be involved in cell signaling pathways and extracellular matrix formation.\\n] | \n", + "0.90 | \n", + "163 | \n", + "
| 382 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-0 | \n", + "[Summary: Many of the enriched terms relate to protein binding and enzyme activity.\\n\\n] | \n", + "[Summary: Enriched terms suggest involvement in protein binding, enzymatic activity, and transcriptional regulation.\\nMechanism: These genes likely play a role in various cellular processes that involve protein-protein interactions, enzymatic reactions, and transcriptional regulation.\\n\\n] | \n", + "0.92 | \n", + "201 | \n", + "
| 383 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-1 | \n", + "[Summary: Genes enriched for ion transport, enzyme activity, DNA-binding, and protein binding\\n\\nMechanism: These genes likely play a role in various cellular processes including ion transport, metabolic processes, and gene expression regulation.\\n\\n] | \n", + "[Summary: Molecular Function Inhibitor Activity and Protein Binding Activity\\nMechanism: Molecular inhibition of various cellular processes\\n] | \n", + "0.83 | \n", + "107 | \n", + "
| 384 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[Summary: Genes are involved in Wnt signaling pathway and regulation of transcription, with a focus on negative regulation of canonical Wnt signaling pathway. \\n\\nMechanism: The genes listed are all involved in the Wnt signaling pathway, specifically the negative regulation of canonical Wnt signaling pathway. \\n\\n] | \n", + "[Summary: Genes are involved in the Wnt signaling pathway and regulation of transcription by RNA polymerase II.\\nMechanism: The identified genes all function in the Wnt signaling pathway and particularly in the regulation of transcription by RNA polymerase II. This pathway plays a crucial role in embryonic development and cellular proliferation, and dysregulation can contribute to the development of multiple diseases, including cancer and developmental disorders.\\n] | \n", + "0.95 | \n", + "156 | \n", + "
| 385 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[Summary: These genes are involved in multiple signaling pathways, including Wnt and Notch signaling pathways, as well as protein degradation processes such as ubiquitination and proteolysis.\\nMechanism: These genes function to regulate cell proliferation, differentiation, and fate through activation or inhibition of specific signaling pathways.\\n\\nHypothesis: These genes function to maintain cellular homeostasis by regulating important signaling pathways and protein degradation processes. Dysregulation of these pathways may lead to abnormal cell growth, differentiation, and function, contributing to the development of various diseases such as cancer and neurodegenerative disorders.] | \n", + "[Summary: Genes involved in Wnt signaling pathway and regulation of gene expression.\\nMechanism: Wnt signaling pathway regulates gene expression through the interaction of Wnt ligands with Frizzled receptors and subsequent activation of downstream signaling pathways.\\n\\nHypothesis: The enrichment of genes involved in Wnt signaling and regulation of gene expression suggests a potential role in developmental processes, as well as potential implications in cancer and neurodegenerative diseases. The dysregulation of Wnt signaling has been implicated in multiple cancers, pointing to the importance of these genes in cellular growth and proliferation. Additionally, the involvement of PSEN2 in amyloid-beta formation highlights the potential role of Wnt signaling in Alzheimer's disease pathology.] | \n", + "0.91 | \n", + "107 | \n", + "
| 386 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "T cell proliferation-0 | \n", + "[Summary: Genes are involved in several processes including intracellular signaling, regulation of immune response, cell recognition, and response to bacterium.\\n\\nMechanism: These genes are mostly involved in intracellular signaling pathways, especially in the regulation of immune response.\\n\\n] | \n", + "[Summary: Signaling and receptor binding activity\\n] | \n", + "0.80 | \n", + "242 | \n", + "
| 387 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "T cell proliferation-1 | \n", + "[Summary: Genes enriched in immune system processes, particularly T cell activation, cytokine production, and regulation of gene expression.\\n\\nMechanism: These genes likely function together to regulate the immune response, specifically in T cells. They contribute to T cell activation, cytokine production, and the regulation of gene expression at multiple levels.\\n\\n] | \n", + "[Summary: Immune-related genes with a focus on T cell regulation and signaling.\\nMechanism: T cell activation and signaling pathway.\\n] | \n", + "0.92 | \n", + "234 | \n", + "
| 388 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "Yamanaka-TFs-0 | \n", + "[Summary: These four genes are involved in transcription regulation and have DNA-binding activity. They are also involved in several cellular processes, such as gene expression regulation, cell proliferation, and differentiation.\\nMechanism: The enriched terms are likely involved in regulating gene expression and cellular differentiation through the binding and regulation of transcription factors.\\n\\n] | \n", + "[Summary: Transcriptional regulation and gene expression.\\nMechanism: Gene expression regulation.\\n\\nHypothesis: All the genes listed are involved in transcriptional regulation and gene expression. All of these genes have DNA-binding transcription factor activity, and a role in the regulation of gene expression. They are involved in positive or negative regulation of transcription by RNA polymerase II, and act upstream of or within several processes such as endodermal cell fate specification, and regulation of biosynthesis and metabolic processes. These genes seem to be part of a broader pathway or mechanism involved in gene expression regulation.] | \n", + "0.92 | \n", + "252 | \n", + "
| 389 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "Yamanaka-TFs-1 | \n", + "[Summary: Transcriptional regulation and developmental processes\\n\\nMechanism: Transcriptional regulation and cell fate specification\\n\\n] | \n", + "[Summary: Transcription regulation and gene expression\\nMechanism: Transcriptional regulation\\n] | \n", + "0.94 | \n", + "40 | \n", + "
| 390 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "amigo-example-0 | \n", + "[Summary: The enriched terms describe genes involved in extracellular matrix organization, cell signal transduction, and blood coagulation.\\n\\nMechanism: The genes share functions necessary for proper extracellular matrix organization and remodeling, including interactions with integrins and collagen-containing matrix components. They also share cell signaling pathways involved in growth factor binding and receptor activity, as well as regulation of intracellular signal transduction. Finally, several of the genes are involved in blood coagulation and lipid metabolism.\\n\\n] | \n", + "[Summary: Extracellular matrix components and their interactions with the cell surface are enriched functions in this gene set.\\n\\nMechanism: These genes are involved in cell-matrix adhesion, collagen fibril organization, and extracellular matrix protein binding and organization. They also have roles in the regulation and binding of lipoproteins.\\n\\n] | \n", + "0.93 | \n", + "226 | \n", + "
| 391 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "amigo-example-1 | \n", + "[Summary: Extracellular matrix structure and function, integrin binding, growth factor activity, and response to external stimuli are enriched functions amongst the listed genes.\\n\\nMechanism: The enriched functions suggest that these genes play a crucial role in tissue development, organization, and homeostasis. They also participate in cellular communication, response to external signals, and signal transduction, possibly shaping key pathways involved in external stimuli responsiveness.\\n\\n] | \n", + "[Summary: Genes with diverse functions including extracellular matrix structural constituents, integrin and Notch binding activities, and chemokine activity are enriched for terms related to cell adhesion, migration, and regulation of protein metabolic processes. \\nMechanism: Extracellular matrix remodeling, integrin signaling, and chemokine signaling pathways are likely involved in the common functions of these genes.\\n] | \n", + "0.93 | \n", + "71 | \n", + "
| 392 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_0-0 | \n", + "[Summary: These genes are enriched for functions involved in protein binding, ion channel activity, transcriptional regulation, and ubiquitin-protein ligase activity.\\n\\nMechanism: The underlying biological mechanism may involve signaling pathways involved in protein regulation, ion transport, and gene expression.\\n\\n] | \n", + "[Summary: Several genes are involved in various aspects of protein binding activity and regulation of gene expression, with a focus on transcription factor binding activity.\\n\\nMechanism: The enriched terms suggest a role for these genes in regulating gene expression at the transcriptional level, likely through interaction with DNA and other proteins involved in transcriptional regulation.\\n\\n] | \n", + "0.93 | \n", + "77 | \n", + "
| 393 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_0-1 | \n", + "[Summary: Genes involved in binding activities, ion channel activity, and transcription factor activity.\\nMechanism: These genes are involved in regulating cellular processes by controlling the binding of molecules, ion flow, and gene expression.\\n] | \n", + "[Summary: The common function among these genes is the ability to enable binding activities, including metal ion binding, protein domain specific binding, DNA-binding transcription factor activity, and ubiquitin protein ligase activity. They are also involved in several processes, including cell proliferation, development, and regulation of signaling pathways.\\n\\nMechanism: These genes likely play a role in regulating various cellular processes through their binding activities, either by promoting or inhibiting specific protein interactions or by modifying signaling pathways through enzymatic activity.\\n\\n] | \n", + "0.93 | \n", + "363 | \n", + "
| 394 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_1002-0 | \n", + "[Summary: Genes related to muscle contraction, specifically those involved in myofibril assembly and regulation of muscle adaptation.\\n\\nMechanism: These genes are involved in the structural organization of the myofibril and the regulation of muscle contraction through their functions in actin and myosin binding, tropomyosin binding, and calcium ion binding.\\n\\n] | \n", + "[Summary: Enriched terms include muscle contraction, regulation of muscle adaptation, and protein ubiquitination. \\n\\nMechanism: The genes in this list are primarily involved in muscle development and function, as well as protein ubiquitination. \\n\\n\\nHypothesis: The enriched terms suggest that these genes may play a role in regulating muscle growth and adaptation through protein ubiquitination and other mechanisms.] | \n", + "0.88 | \n", + "55 | \n", + "
| 395 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_1002-1 | \n", + "[Summary: Genes involved in muscle contraction and regulation are statistically over-represented in this list.\\n\\nMechanism: These genes likely play a role in the regulation and contraction of muscle tissue.\\n\\n] | \n", + "[Summary: Genes are mostly involved in muscle contraction and structure, ion channel activity, and protein ubiquitination.\\n\\n] | \n", + "0.89 | \n", + "83 | \n", + "
| 396 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "endocytosis-0 | \n", + "[Summary: Receptor-mediated endocytosis and protein transport processes are enriched in these genes.\\nMechanism: These genes play important roles in endocytosis and the transport of proteins between organelles.\\n] | \n", + "[Summary: The enriched terms for these genes are related to endocytosis, cellular adhesion, and regulation of signal transduction pathways.\\n\\nMechanism: These genes are involved in various processes such as endocytosis, protein degradation, and signal transduction. They regulate several cellular functions such as cellular adhesion, plasma membrane organization, and lipid transport.\\n\\n\\nHypothesis: The enriched terms suggest that these genes are involved in the regulation of endocytic processes, which are essential for the uptake of various molecules from the extracellular environment. They also play a role in the organization of plasma membrane, which is crucial for cell signaling and signal transduction. The genes are part of the network that regulates cellular adhesion and cytoskeleton organization. They also participate in the regulation of lipid transport, which is essential for maintaining cellular physiology.] | \n", + "0.92 | \n", + "716 | \n", + "
| 397 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "endocytosis-1 | \n", + "[Summary: These genes are involved in various processes related to intracellular transport and signaling, including endocytosis, lysosomal function, and receptor activity.\\nMechanism: These genes likely play a role in cellular transport and communication pathways, with some genes directly involved in intracellular trafficking and others affecting signaling pathways related to immune response and metabolism.\\n] | \n", + "[Summary: All genes are involved in membrane-related processes, including endocytosis, protein transport, and cell signaling.\\nMechanism: These genes are essential for membrane traffic and organization.\\n] | \n", + "0.94 | \n", + "208 | \n", + "
| 398 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "glycolysis-gocam-0 | \n", + "[Summary: Enzymes involved in glycolytic processes and carbohydrate metabolism.\\nMechanism: Glycolysis\\n] | \n", + "[Summary: These genes are involved in various processes related to carbohydrate metabolism and cellular energy homeostasis.\\n\\nMechanism: The common mechanism underlying the enriched terms is the regulation of glycolysis and energy metabolism in cells.\\n\\n] | \n", + "0.90 | \n", + "150 | \n", + "
| 399 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "glycolysis-gocam-1 | \n", + "[Summary: Genes are involved in metabolic processes and cellular development.\\nMechanism: Glycolysis pathway.\\n] | \n", + "[Summary: The common function of these genes is glycolysis and carbohydrate metabolism.\\nMechanism: These genes are involved in the breakdown of glucose to produce energy in the form of ATP. \\n] | \n", + "0.92 | \n", + "82 | \n", + "
| 400 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "go-postsynapse-calcium-transmembrane-0 | \n", + "[Summary: Genes involved in calcium ion transport and signaling, as well as neurotransmitter receptor activity, are statistically over-represented. \\n\\nMechanism: These genes likely play a role in synaptic transmission and neuronal signaling. \\n\\n] | \n", + "[Summary: The enriched terms include calcium ion transport, voltage-gated calcium channel activity, glutamate receptor activity, and acetylcholine-gated channel complex.\\n\\nMechanism: These genes are involved in calcium signaling, particularly in calcium ion transport and voltage-gated calcium channel activity. They also play a role in neurotransmission, specifically in the activity of glutamate and acetylcholine-gated channels.\\n\\n] | \n", + "0.94 | \n", + "189 | \n", + "
| 401 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "go-postsynapse-calcium-transmembrane-1 | \n", + "[Summary: Calcium signaling and neurotransmission\\nMechanism: Genes encode for ion channels and regulatory proteins involved in calcium-mediated neurotransmission.\\n\\nHypothesis: These genes play a critical role in regulating calcium-mediated neurotransmission, including depolarization, synaptic transmission, and the regulation of neurotransmitter levels. This suggests a potential involvement in various neurological disorders such as epilepsy, schizophrenia, and Alzheimer's disease. Several of the genes are also involved in calcium transport and homeostasis, which may have implications in muscle function and calcium signaling in other tissues.] | \n", + "[Summary: Calcium signaling plays a major role in the function of the genes listed, including calcium channel activity, regulation of cytosolic calcium ion concentration, and calcium ion transmembrane import.\\n\\nMechanism: Calcium signals can activate a variety of pathways, including second messenger systems and ion channel activation, leading to changes in intracellular signaling and gene expression.\\n\\n] | \n", + "0.92 | \n", + "245 | \n", + "
| 402 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "go-reg-autophagy-pkra-0 | \n", + "[Summary: Several of the genes are involved in signal transduction and regulation of protein kinase activity.\\n\\n\\nHypothesis: Many of these genes play roles in the regulation of signal transduction and pathways related to protein kinase activity. The enriched terms likely reflect the general role these genes play in the control and modulation of these mechanisms. Specifically, the involvement of many of these genes in TOR signaling, macroautophagy, and regulation of cyclin-dependent protein serine/threonine kinase activity suggest possible roles in cell cycle regulation and cancer development.] | \n", + "[Summary: Protein phosphorylation and kinase activity regulation\\nMechanism: Enzymatic activity and protein-protein interactions\\n\\nHypothesis: This set of genes is enriched in functions related to kinase activity regulation and signaling pathways that involve protein phosphorylation. Many of these genes enable protein kinase binding, activator or inhibitor activity, and participate in processes that involve protein phosphorylation. These processes include intracellular signal transduction, TOR signaling, apoptotic signaling pathway, and positive regulation of metabolic processes. The underlying biological mechanism is likely linked to the interactions between these proteins, with many of them being located in protein-containing complexes and regulatory pathways.] | \n", + "0.95 | \n", + "172 | \n", + "
| 403 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "go-reg-autophagy-pkra-1 | \n", + "[Summary: The enriched terms for this list of genes are intracellular signaling and apoptosis.\\n\\nMechanism: These genes are involved in various intracellular signaling pathways, particularly the PI3K signaling pathway, which is known to play a role in the regulation of cellular processes such as proliferation, differentiation, and survival. They are also involved in the regulation of apoptosis, which is a programmed cell death pathway responsible for the elimination of abnormal or damaged cells.\\n\\n] | \n", + "[Summary: The enriched terms for these genes are related to intracellular signaling and regulation of cell processes.\\nMechanism: These genes are mainly involved in regulation of protein kinase activity and intracellular signal transduction, which contribute to the homeostasis of cellular processes.\\n\\n] | \n", + "0.94 | \n", + "200 | \n", + "
| 404 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[Summary: The enriched terms are centered around the catabolism of complex carbohydrates, specifically glycosphingolipids, glycoproteins, and chitin, as well as the breakdown of hyaluronan.\\n\\nMechanism: The genes with enriched functions are involved in various steps of complex carbohydrate catabolism, including enzymatic breakdown of specific glycosyl bonds and trimming of terminally located mannose and glucose residues. These processes likely occur in intracellular membrane-bound organelles, such as lysosomes.\\n\\n] | \n", + "[Summary: These genes are involved in various processes related to the breakdown and metabolism of carbohydrates and glycoproteins.\\n\\nMechanism: The enriched terms suggest a common mechanism of carbohydrate and glycoprotein degradation through the activity of various hydrolases, including alpha- and beta-glucosidases, alpha- and beta-mannosidases, and multiple hyaluronidases.\\n\\n] | \n", + "0.93 | \n", + "138 | \n", + "
| 405 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[Summary: Many of the genes listed are involved in carbohydrate metabolism and catabolic processes, including the processing and breakdown of glycans, glycoproteins, glycolipids, and other complex carbohydrates. Some genes are involved in the catabolism of specific substances such as chitin and fucose. \\n\\nMechanism: This group of genes likely represents a group of enzymes involved in the breakdown of various types of carbohydrates and sugars in the body. \\n\\n] | \n", + "[Summary: These genes are involved in the catabolism and modification of various carbohydrates, such as hyaluronic acid, chitin, glycoproteins, glycolipids, and sugar monomers. Many of the genes encode glycosidase enzymes that enable the breakdown of specific sugars. \\n\\n] | \n", + "0.95 | \n", + "190 | \n", + "
| 406 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "ig-receptor-binding-2022-0 | \n", + "[Summary: These genes are involved in immunoglobulin receptor binding activity and activation of the immune response.\\nMechanism: The genes encode for the variable region of the immunoglobulin heavy and light chain, which are expressed by B-cells in response to foreign antigens, and enable the recognition and binding of those antigens. \\n] | \n", + "[Summary: Enrichment in immunoglobulin receptor binding activity and antigen binding activity suggests a function related to immune response.\\n\\nMechanism: These genes encode immunoglobulins or immunoglobulin-related proteins involved in the production of antibodies.\\n\\n] | \n", + "0.93 | \n", + "71 | \n", + "
| 407 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "ig-receptor-binding-2022-1 | \n", + "[Summary: These genes are predicted to be involved in various processes related to the activation and defense response of the immune system. \\n\\nMechanism: These genes are involved in the production of immunoglobulin proteins, also known as antibodies, which are key components of the adaptive immune response system. \\n\\n\\nHypothesis: These genes are involved in the activation and defense response of the immune system through the production of immunoglobulin proteins. Antibodies bind to pathogens, marking them for destruction by other components of the immune system. The enriched terms suggest that these genes are particularly involved in the humoral immune response, which involves the production and secretion of antibodies into the bloodstream. Additionally, these genes may play a role in regulating the organization and differentiation of immune cells, such as monocytes.] | \n", + "[Summary: Genes involved in the activation of immune response, defense response to other organisms and antigen binding activity.\\nMechanism: Immune response pathway\\n] | \n", + "0.92 | \n", + "715 | \n", + "
| 408 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "meiosis I-0 | \n", + "[Summary: These genes are primarily involved in meiotic processes, such as homologous chromosome pairing and recombination, as well as DNA repair.\\n\\nMechanism: These genes likely play a role in the proper segregation of chromosomes during meiosis, which is crucial for the formation of viable gametes.\\n\\n] | \n", + "[Summary: Majority of the genes listed are involved in meiotic DNA recombination and repair.\\nMechanism: Meiotic DNA recombination and repair.\\n] | \n", + "0.93 | \n", + "160 | \n", + "
| 409 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "meiosis I-1 | \n", + "[Summary: Enrichment analysis of human genes reveals a common function in meiotic recombination and double-strand break repair via homologous recombination.\\n\\nMechanism: Meiotic recombination and double-strand break repair via homologous recombination are vital processes for the proper segregation of homologous chromosomes during meiosis. Several of the genes identified in the enrichment analysis are involved in these processes, either directly or indirectly.\\n\\n] | \n", + "[Summary: These genes are primarily involved in meiotic recombination and chromosomal segregation, as well as various DNA repair processes.\\nMechanism: These genes likely function together to ensure proper chromosome segregation and correct genetic transmission during meiosis, and to maintain genomic stability through DNA repair mechanisms.\\n] | \n", + "0.90 | \n", + "122 | \n", + "
| 410 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "molecular sequestering-0 | \n", + "[Summary: Molecular sequestering and protein binding activity seem to be common functions among these genes.\\nMechanism: These genes may be involved in regulating the localization and availability of important molecules and proteins within cells.\\n\\n\\nHypothesis: The genes identified in this analysis may play a role in maintaining cellular homeostasis by regulating the availability and localization of important molecules and proteins. This function may be particularly important in response to stress and infection, as many of the enriched terms relate to these processes. The common function of molecular sequestering may involve the sequestration of molecules which could be detrimental to cellular function if present in excess (e.g. iron ion or oxysterols). The common function of protein binding activity could involve the regulation of protein trafficking and localization. Together, these genes may play a role in optimizing cellular function and protecting cells from damage.] | \n", + "[Summary: Protein sequestering and binding activities are enriched across the listed genes.\\n\\nMechanism: The enriched terms suggest that protein sequestering and binding play a significant role in the function of the listed genes.\\n\\n\\nHypothesis: Protein sequestering and binding are essential mechanisms in controlling the cellular localization and activity of proteins. These mechanisms may affect several processes, including intracellular transport, transcriptional regulation, and signal transduction.] | \n", + "0.95 | \n", + "480 | \n", + "
| 411 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "molecular sequestering-1 | \n", + "[Summary: Molecular sequestering activity, regulation of gene expression, positive regulation of protein ubiquitination, and sequestering of metal ion are enriched functions among the given human genes.\\n\\nMechanism: These genes are involved in the regulation and control of various cellular processes by sequestering certain molecules or ions, influencing cellular response to stress, and regulating gene expression. The enriched functions are primarily related to cellular regulation and signaling pathways.\\n\\n] | \n", + "[Summary: Several of the genes listed are involved in molecular sequestering or binding activity, and are located in various cellular compartments. Many are also implicated in immune responses and regulation of gene expression.\\n\\nMechanism: The enriched terms suggest that these genes are involved in cellular processes related to regulation of gene expression, immune responses, and cellular signaling pathways.\\n\\n\\nHypothesis: These genes may play a role in regulating immune responses and cellular signaling pathways, by sequestering or binding to various molecules and regulating the expression of genes involved in these processes.] | \n", + "0.93 | \n", + "125 | \n", + "
| 412 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "mtorc1-0 | \n", + "[Summary: Many of the genes are involved in binding activities, including RNA binding, protein binding, and ion binding, and several are involved in enzymatic activity such as oxidoreductase and kinase activity. \\n\\nMechanism: The enriched functions suggest that these genes are involved in protein synthesis and processing, as well as intracellular signaling and metabolism. \\n\\n] | \n", + "[Summary: Many of the genes listed are involved in protein or RNA binding, enzymatic activity, and structural components of cells. \\n\\n] | \n", + "0.94 | \n", + "243 | \n", + "
| 413 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "mtorc1-1 | \n", + "[Summary: These genes are involved in various cellular functions, including protein binding, catalytic activity, and transporter activity. The enriched terms are related to cellular metabolic processes, protein folding, and DNA binding.\\n\\nMechanism: These genes likely contribute to cellular metabolism and homeostasis through various catalytic and transport mechanisms, as well as protein folding and DNA regulation.\\n\\n] | \n", + "[Summary: The genes in this list are involved in various functions related to cellular processes including protein binding, enzyme activity, and transporter activity.\\n\\nMechanism: The underlying biological mechanism or pathway is likely related to cellular processes involved in protein homeostasis and metabolism.\\n\\n] | \n", + "0.95 | \n", + "103 | \n", + "
| 414 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "peroxisome-0 | \n", + "[Summary: Genes involved in peroxisomal biogenesis and protein import.\\n\\nMechanism: These genes are part of the peroxisome biogenesis pathway, which involves the recognition, targeting, and import of proteins into the peroxisomal membrane and matrix.\\n\\n] | \n", + "[Summary: Genes involved in peroxisome biogenesis and protein import into peroxisome matrix.\\nMechanism: Peroxisome biogenesis and protein import pathway.\\n] | \n", + "0.98 | \n", + "97 | \n", + "
| 415 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "peroxisome-1 | \n", + "[Summary: Genes involved in peroxisomal biogenesis and protein import into peroxisomes.\\nMechanism: Peroxisomal biogenesis and protein import mechanism.\\n\\nHypothesis: These genes are involved in the mechanism of peroxisomal biogenesis and protein import into peroxisomes. The enriched terms suggest that this process involves specific lipid binding activities, ATP binding and hydrolysis, and ubiquitin-dependent protein binding in order to ensure proper folding, import, and localization of proteins within peroxisomes. Dysfunctions in these genes can lead to peroxisomal biogenesis disorders, such as Heimler syndrome and rhizomelic chondrodysplasia punctata type 1.] | \n", + "[Summary: These genes are all involved in peroxisome biogenesis and protein import into the peroxisome.\\n\\nMechanism: These genes all encode for proteins involved in the same biological process of peroxisomal biogenesis, which is the formation of peroxisomes and the import of proteins into the peroxisome.\\n\\n] | \n", + "0.96 | \n", + "361 | \n", + "
| 416 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "progeria-0 | \n", + "[Summary: These genes are involved in several processes related to DNA and cellular response, including chromatin regulation, DNA metabolic process, and cellular senescence. \\nMechanism: These genes are likely involved in maintaining genomic stability and responding to environmental stressors.\\n\\n] | \n", + "[Summary: These genes are all involved in DNA metabolism and chromatin regulation.\\nMechanism: These genes are all involved in maintaining the stability and integrity of the genome, particularly at the nuclear envelope and telomeres. They may also play a role in regulating cellular senescence processes.\\n] | \n", + "0.97 | \n", + "9 | \n", + "
| 417 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "progeria-1 | \n", + "[Summary: These genes are involved in DNA-related processes and cellular responses to stress, and are implicated in several diseases.\\nMechanism: The enriched terms suggest a possible role in DNA damage response and repair mechanisms, as well as cellular senescence.\\n\\nHypothesis: These genes may be part of a network involved in maintaining genomic stability and cellular homeostasis, particularly in response to stressors such as DNA damage. Dysfunction of this network may lead to increased cellular senescence and disease.] | \n", + "[Summary: Genes involved in DNA repair and maintenance with possible roles in aging and age-related diseases.\\nMechanism: DNA damage repair and telomere maintenance pathways.\\n] | \n", + "0.91 | \n", + "351 | \n", + "
| 418 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "regulation of presynaptic membrane potential-0 | \n", + "[Summary: The enriched terms are related to ion channels and synaptic transmission, including ligand-gated monoatomic ion channel activity, regulation of presynaptic/presynaptic membrane potential, and several transmembrane transport processes. \\n\\nMechanism: These genes all play a role in regulating synaptic transmission through ion channels. \\n\\n] | \n", + "[Summary: The enriched terms are related to ion channel activity, transmembrane transport, and neurotransmitter signaling pathways.\\nMechanism: These genes all play a role in regulating the flow of ions across cell membranes in neurons.\\n\\nHypothesis: These genes are involved in regulating the membrane potential and synaptic transmission in neurons. The GABA and glutamate signaling pathways are important modulators of neural activity, and the ion channels identified here play key roles in regulating the activity of these signaling pathways. The inward rectifier potassium channels help to maintain the resting potential of neurons, while the voltage-gated ion channels play a critical role in generating action potentials. Together, these genes likely play a key role in the regulation of neural activity and synaptic plasticity.] | \n", + "0.96 | \n", + "487 | \n", + "
| 419 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "regulation of presynaptic membrane potential-1 | \n", + "[Summary: Ion channel activity and neurotransmission are enriched functions among the listed genes, with a focus on GABA and glutamate signaling pathways. \\n\\nMechanism: The genes in the list are involved in regulating ion channel activity and neurotransmission, particularly through GABA and glutamate signaling pathways. \\n\\n] | \n", + "[Summary: These genes are involved in ion channel activity, specifically ligand-gated monoatomic ion channel activity and voltage-gated ion channel activity.\\nMechanism: The genes in this list contribute to the regulation of membrane potential and synaptic transmission in the nervous system.\\n] | \n", + "0.94 | \n", + "31 | \n", + "
| 420 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "sensory ataxia-0 | \n", + "[Summary: Genes are primarily involved in the peripheral nervous system, myelination, and neurological disorders.\\nMechanism: The enriched terms suggest that these genes primarily function in the peripheral nervous system and myelination.\\n\\nHypothesis: These genes are all involved in the development and maintenance of the peripheral nervous system and myelination. Dysregulation or mutation of these genes likely leads to neuropathic disorders.] | \n", + "[Summary: Genes are involved in various processes in the development and maintenance of the nervous system, specifically peripheral nerves and myelination, as well as nucleic acid and protein metabolism.\\n\\nMechanism: The enriched terms suggest a common underlying biological mechanism in the formation and maintenance of the peripheral nervous system and myelination, as well as in nucleic acid and protein metabolism.\\n\\n\\nHypothesis: The enrichment of terms related to Charcot-Marie-Tooth disease and myelination suggest that these genes play an important role in peripheral nervous system development and maintenance, specifically in the formation and maintenance of myelin. The enrichment of terms related to protein folding and nucleic acid metabolism suggest that these genes also have a role in maintaining and regulating the overall metabolic processes of cells. The involvement of genes in mitochondrial function suggests a possible link between peripheral nerve function and mitochondrial metabolism.] | \n", + "0.95 | \n", + "562 | \n", + "
| 421 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "sensory ataxia-1 | \n", + "[Summary: Genes are predominantly involved in peripheral nervous system development, myelination and maintenance, and mitochondria-related functions with a subset involved in protein ubiquitination and cellular response to mechanical stimulus. \\n\\nMechanism: The primary biological mechanism underlying these enriched terms is likely the maintenance of neuronal function and homeostasis, with specific pathways including mitochondrial metabolism and protein degradation/regulation.\\n\\n] | \n", + "[Summary: Genes are primarily involved in neurological and neuromuscular diseases and developmental disorders.\\n\\nHypothesis: These genes may be involved in the regulation of nervous system development and myelination, as well as mitochondrial dysfunction, which could lead to the development of neurological and neuromuscular diseases. The role of protein ubiquitination in these processes is unclear and requires further investigation.] | \n", + "0.92 | \n", + "45 | \n", + "
| 422 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "term-GO:0007212-0 | \n", + "[Summary: G protein-coupled receptor signaling pathway and dopamine receptor signaling pathway are statistically over-represented in the gene functions.\\n\\nMechanism: The genes listed are involved in intracellular signaling pathways that are activated by G protein-coupled receptors and dopamine neurotransmitter receptors. The signaling cascades triggered by these receptors are essential for many physiological processes, including neurotransmission, hormone secretion, and muscle contraction.\\n\\n] | \n", + "[Summary: The enriched terms suggest that these genes are involved in dopamine receptor signaling pathway, including adenylate cyclase activation, calcium ion concentration regulation, and G protein-coupled receptor pathway.\\n\\nMechanism: These genes are involved in dopamine receptor signaling, which regulates various cellular processes via the activation of adenylate cyclase, calcium ion concentration, and G protein-coupled receptor pathways.\\n\\n] | \n", + "0.93 | \n", + "48 | \n", + "
| 423 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "term-GO:0007212-1 | \n", + "[Summary: The list of genes is enriched in terms related to G protein-coupled receptor signaling pathways and dopamine neurotransmitter activity.\\n\\nMechanism: These genes are involved in the regulation of intracellular signaling cascades, particularly those involving G protein-coupled receptors. Dopamine neurotransmitter activity appears to be a common thread linking many of these genes.\\n\\n] | \n", + "[Summary: The enriched terms in common for this list of genes are related to G protein-coupled receptor signaling pathways, dopamine neurotransmitter receptor activity, and adenylate cyclase activity.\\n\\nMechanism: These genes are involved in pathways that regulate cellular signaling, including dopamine-mediated signaling and cyclic AMP (cAMP) signaling pathways.\\n\\n\\nHypothesis: These genes are involved in the regulation of signaling pathways, particularly those involved in dopamine-mediated signaling and cyclic AMP (cAMP) signaling. They may contribute to the development of neurological and metabolic disorders, including Alzheimer's disease, Parkinson's disease, hypertension, and type 2 diabetes mellitus. More research is needed to fully understand the underlying biological mechanisms and pathways involved in these diseases.] | \n", + "0.97 | \n", + "443 | \n", + "
| 424 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "tf-downreg-colorectal-0 | \n", + "[Summary: Genes are involved in transcriptional regulation and DNA binding activities.\\nMechanism: Transcriptional regulation through DNA-binding activities.\\n] | \n", + "[Summary: These genes are involved in DNA-binding transcription regulation and are located in various cellular components, including the nucleus and chromatin. \\nMechanism: These genes are likely involved in regulating genetic expression and the transcriptional machinery.\\n] | \n", + "0.93 | \n", + "115 | \n", + "
| 425 | \n", + "gpt-3.5-turbo | \n", + "ontological_synopsis | \n", + "tf-downreg-colorectal-1 | \n", + "[Summary: DNA-binding transcription factor activity and regulation of DNA-templated transcription.\\nMechanism: These genes are involved in the regulation of gene expression via DNA-binding transcription factor activity and DNA-templated transcription.\\n] | \n", + "[Summary: DNA binding transcription factor activity, regulation of DNA-templated transcription, gene expression regulation, and nucleosome disassembly are statistically enriched functions in these genes.\\nMechanism: These genes are involved in transcriptional regulation, including regulation of DNA binding and gene expression.\\n] | \n", + "0.95 | \n", + "77 | \n", + "
| 426 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "EDS-0 | \n", + "[ The list of genes includes several connective tissue related genes, such as those related to the tenascin protein family and collagen chains of type I-V, which are responsible for the formation of strong and stable connective fibers. There are also several genes related to the binding and folding of proteins, and the immune response mediated by the complement system. Further, there are genes associated with glycosaminoglycan synthesis and dermatan sulfate metabolism. The commonalities among these genes is involvement in connective tissue formation and repair, structure and binding of proteins, and immune response.\\n\\nMechanism: These genes function in a variety of biological processes, including wound healing, glycosaminoglycan synthesis, and immune response. Through their specific roles, these proteins are able to facilitate the formation and maintenance of strong and stable connective tissue, to bind and fold proteins, and to mediate the innate immune response. Furthermore, genetic mutations in these genes are associated with a variety of Ehlers-Danlos syndromes, further indicating the importance of these proteins in connective tissues.\\n\\n] | \n", + "[\\n\\nSummary: Genes analyzed are associated with or involved in collagen biosynthesis, modification or turnover, extracellular matrix maturation, and transcriptional regulation. \\nMechanism: These genes likely function in the coordination and regulation of collagen production, fiber formation, and tissue informatics. \\n] | \n", + "0.89 | \n", + "841 | \n", + "
| 427 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "EDS-1 | \n", + "[\\nSummary: Enriched term analysis reveals that the human genes described here are largely involved in collagen maturation, glycosaminoglycan synthesis, transcriptional regulation, and zinc transport. \\nMechanism: These genes likely take part in the functions of the endoplasmic reticulum and Golgi apparatus, as well as mediating processes involved in cell differentiation and tumorigenesis. \\n] | \n", + "[\\nSummary: This gene list consists of genes involved in tissue development, collagen and extracellular matrix production, and immunity response. \\nMechanism: These genes all seem to be involved in tissue development and the formation of extracellular matrix components such as collagen and physical complexes such as C1 and fibril-forming collagens. In addition, some of the genes are associated with immunity processes like phagocytosis and inflammation.\\n \\n] | \n", + "0.90 | \n", + "65 | \n", + "
| 428 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "FA-0 | \n", + "[\\nSummary: The enriched terms involve DNA repair, homologous recombination and phosphorylation, as they are commonly found among a group of genes associated with Fanconi Anemia.\\nMechanism: These genes act in a coordinated manner to perform DNA repair, homologous recombination and control chromosomal stability.\\n] | \n", + "[\\nSummary: This gene list is composed of human genes involved in DNA damage repairs and genome maintenance.\\nMechanism: These genes are involved in the mechanisms to detect and repair DNA damages caused by environmental stressors by facilitating the formation of the nuclear protein complex.\\n] | \n", + "0.87 | \n", + "21 | \n", + "
| 429 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "FA-1 | \n", + "[\\nSummary: The genes identified in this list are involved in DNA repair and maintenance of chromosome stability, specifically the homologous recombination pathway for double-strand DNA repair.\\nMechanism: These genes play key roles in a number of processes, including DNA repair, monoubiquitination of FANCD2 and FANCI, Holliday junction resolution, and binding to the RAD51 recombinase. \\n] | \n", + "[ \\nSummary: The genes analyzed in this enrichment test are all associated with the Fanconi anemia complementation group (FANC) and are known to be involved in the repair of DNA lesions, stabilization of genome stability, and maintenance of homologous recombination.\\n\\nMechanism: These genes likely play a role in a common biological cell pathway, acting as components of multiple nucleoprotein complexes, endonucleases, and homologous recombination proteins in order to facilitate DNA repair and prevent chromosome instability.\\n\\n] | \n", + "0.92 | \n", + "140 | \n", + "
| 430 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ADIPOGENESIS-0 | \n", + "[\\n\\nSummary: Several genes in the list encode proteins involved in the metabolism of fatty acids, including the formation and break down of lipids, synthesis of essential fatty acids, and transport of fatty acid synthase. Additionally, many of the genes encode proteins involved in the functioning of the mitochondria, including relating to the electron transport chains, antioxidant and redox systems, and synthesis of key metabolic components.\\n\\nMechanism: The commonality among these genes is that they encode proteins essential for normal functioning of the mitochondria, oxidative metabolism of fuels, and lipid metabolism, all of which are important for normal cellular functioning and growth.\\n\\n] | \n", + "[ \\n\\nSummary: The list of genes appear to be primarily involved in metabolic and energy production processes, as well as some related to membrane assembly and transcription factors.\\n\\nMechanism: The genes listed appear to be involved in controlling multiple pathways within the cell, such as energy production, enzymatic activity, transcription, and assembly of membranes.\\n\\n] | \n", + "0.92 | \n", + "327 | \n", + "
| 431 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ADIPOGENESIS-1 | \n", + "[ Cellular metabolism and energy production is enriched in this group of genes, likely related to their role in production and transport of proteins, enzymes, and energy.\\n\\nMechanism: The genes likely act together to produce and convert energy into a useable form and to transport proteins between cellular compartments.\\n\\n] | \n", + "[ Enriched terms related to energy metabolism (ATP production, mitochondrial respiratory chain, electron transfer and fatty acid elongation) and protein binding/assembly/transport mechanisms (RNA/DNA binding and transport, ubiquitination and phosphorylation, microtubule binding and lipid transport) are highly represented in this list of genes.\\n\\nMechanism: These genes are mainly involved in energy production, protein modification, and transport processes. Energy production is carried out by multiple substrates including NADP, copper, zinc, and ubiquinone. The electron transfer chain is powered by cytochrome c oxidase, ATP5PO and ME1. Fatty acid elongation is handled by ELOVL6, while protein transportation is enabled by several CBL-type E3 ubiquitin ligases, ABC transporters and ATPases. Protein binding and assembly mechanisms are handled by many proteins with multiple domains, including G3BP2, VEGFB, and GHITM.\\n\\n] | \n", + "0.90 | \n", + "604 | \n", + "
| 432 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[\\nThe list of genes is associated with multiple biological processes, including immune/cytokine responses, protein synthesis, transcription, and cell surface signaling. Enriched terms include: immune/cytokine responses; protein synthesis; transcription; cell surface signaling; receptor activation; ubiquitination; calcification; and ATP binding.\\nMechanism: The enriched terms associated with this list of genes describe key biological processes that regulate a variety of cellular activities. In particular, cytokines play a key role in the immune response, transcription is necessary for gene expression, and cell surface signaling is necessary for receptor activation. Furthermore, ubiquitination is involved in protein degradation, calcification is necessary for cellular processes such as bone formation, and ATP binding is necessary for energy production. \\n] | \n", + "[\\n\\nSummary: This list of genes are involved in a variety of physiological processes, including developmental morphogenesis, cell signalling, cytokine and chemokine production and regulation, antimicrobial defence, plasma protein regulation, immune and inflammatory regulation and transcriptional regulation.\\n\\nMechanism: Many of these gene functions are related to various cell signalling pathways involving cytokines and receptors, as well as regulation of transcription factors, protein kinases and proteases, as well as glycoproteins and receptor proteins of various classes.\\n\\n] | \n", + "0.91 | \n", + "284 | \n", + "
| 433 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[\\n\\nSummary: The list of genes report a variety of terms related to protein synthesis and cellular regulation functions.\\n\\nMechanism: These genes are involved in a variety of metabolic, cell signaling, transcription and immunoregulatory pathways.\\n\\n] | \n", + "[ \\nSummary: Analysis of the given human genes reveals an enrichment for terms of cell membrane associated proteins and cytokines, as well as associated pathways of transcriptional regulation, protein synthesis, and immune response regulation. \\nMechanism: This enrichment of terms suggests that there is a complex network of pathways at play that enable important processes such as cell communication, cell activation, and immune response.\\n] | \n", + "0.90 | \n", + "193 | \n", + "
| 434 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[\\nThe list of terms includes functions related to protein tyrosine phosphatase (PTP) family, protein kinases, transcription factors, lectins, adhesion molecules, and cyclins. The underlying biological mechanism is likely related to a variety of cell signaling pathways and regulation of gene transcription, protein synthesis and turnover, and cell adhesion. ] | \n", + "[ \\nSummary: These genes are involved in a variety of protein-related processes, such as binding, catalyzing, and regulating proteins, as well as in modulation, hydrolase activity, phosphorylation, and regulation of metabolism, transport, and signaling.\\n\\nMechanism: The genes are involved in a variety of pathways, such as cellular stress response, vesicle trafficking, DNA replication, transcription, lipid and cholesterol metabolism, and hormone signaling.\\n\\n] | \n", + "0.88 | \n", + "101 | \n", + "
| 435 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[ In this list of genes, they predominantly function in regulating cell proliferation, transcription, signaling pathways, structural components and metabolism of proteins, lipids, and carbohydrates; many of which are involved in cell adhesion or binding activity. Specifically, they are involved in regulating gene expression and DNA binding, catalyzing protein kinase and oxidoreductase reactions, anchoring kinase complexes to microtubules, binding to receptors, transporting molecules, binding and hydrolyzing peptides and lipids, and catalyzing the interconversion of polyols and ketoses. Hypothesis: These genes thus likely work by regulating signaling pathways, gene expression, and varying cell structures to enable a wide variety of cellular processes and activities.\\n\\nMechanism: Through the regulation of signaling pathways, gene expression, and cell structures, these genes enable a wide variety of cellular processes.\\n\\n] | \n", + "[\\nThe list of genes is related to various cellular functions such as transcriptional regulation, protein kinase activity, protein binding, RNA binding, signal transduction, proteolytic enzyme activity, DNA binding, membrane transport, cell cycle, regulation, protein modification, peptidase, calcium binding, and others. The common molecular processes which are associated with these genes include regulation of transcription, signal transduction, transport, and protein modification.\\n\\nMechanism: The underlying molecular mechanisms behind the commonalities in gene functions are likely related to signal transduction and control of gene expression. Signal transduction involves the transmission of a signal from a cell's environment to the inside of the cell. Once the signal has been received and processed, it is relayed by the production of downstream molecules, such as transcription factors and other signaling proteins, which will ultimately lead to changes in gene expression and cellular behavior. Protein modification also plays a key role in signal transduction as well as in the regulation and processing of cellular components, such as proteins and lipids, necessary for normal cellular functioning.\\n\\n] | \n", + "0.92 | \n", + "284 | \n", + "
| 436 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ANGIOGENESIS-0 | \n", + "[COULD NOT PARSE] | \n", + "[ \\nSummary: This gene list encodes related proteins for key functional pathways including lipoprotein metabolism, coagulation, hemostasis, cytokinases, chemokines, receptors, transporters, cytokines, secreted extracellular matrix proteins, serpins and proteoglycans.\\nMechanism: These processes involve activation or regulation of enzymes or other proteins involved in cell adhesion and migration, signaling, cell proliferation, apoptosis, transcriptional regulation, tissue development and regeneration, and immune response.\\n] | \n", + "0.70 | \n", + "509 | \n", + "
| 437 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ANGIOGENESIS-1 | \n", + "[\\nThe list of human genes provided are involved in a wide range of functions such as matrix remodeling, cell adhesion, extracellular signal transduction, iron metabolism and regulation of microvasculature. The list of genes are enriched for processes related to cell adhesion, extracellular matrix remodeling, signal transduction, protease inhibition and transcriptional regulation.\\n\\nMechanism: The enrichment of genes for the processes listed above suggests the coordination of these processes to maintain tissue homeostasis, forming a complex network that involves interactions between extracellular matrix-receptors, cytokines and chemokines, and intracellular signalling pathways.\\n\\n] | \n", + "[ \\nThis list of genes includes a variety of molecules that are involved in a range of biological processes such as tissue morphogenesis, cell adhesion, cell migration, cell survival, signal transduction, cell cycle regulation, scaffolding, apoptosis, extracellular matrix production, platelet aggregation and others. Most of these molecules are involved in processes related to cell-cell or cell-matrix interaction and in particular, formation and/or maintenance of the extracellular matrix.\\n\\nMechanism: These genes likely function in the formation and/or maintenance of the extracellular matrix via a number of processes. Specifically, these genes may be involved in processes such as regulation of cell-cell interactions and cell-matrix interactions, production and secretion of extracellular matrix proteins, processing of proteoglycans and glycoproteins, scaffolding, cell cycle control, signal transduction, and cell adhesion. These processes are likely to be involved in the control of tissue morphogenesis, cell migration and survival, platelet aggregation, and apoptosis.\\n\\n] | \n", + "0.94 | \n", + "395 | \n", + "
| 438 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-0 | \n", + "[\\n\\nSummary: The genes identified are mostly involved in protein-protein interactions, intracellular and extracellular adhesion, and regulation of calcium-dependent processes.\\n\\nMechanism: Protein-protein interactions, cell adhesion, intracellular signaling of calcium-dependent processes.\\n\\n] | \n", + "[ The genes listed are primarily involved in cell adhesion, signaling, and cytoskeletal stabilizing functions. This is evidenced by over-represented terms related to cell adhesion, such as \"integrin\", \"cadherin\", \"lectin\", \"nectin\"; terms related to signaling, such as \"MAP kinase\", \"protein tyrosine kinase\", \"guanine nucleotide binding protein\", \"GTPase\"; and terms related to cytoskeletal stabilizing functions, such as \"actin\", \"fascin\", \"laminin\", and \"myosin\". Hypothesis of underlying mechanism: The combined functions of the genes suggested are associated with cell motility, development, growth, and division in response to extracellular stimuli and signals.\\n\\nSummary: Genes associated with cell adhesion, signaling, and cytoskeletal stabilizing functions.\\nMechanism: Cell motility, development, growth, and division in response to extracellular stimuli and signals.\\n] | \n", + "0.90 | \n", + "587 | \n", + "
| 439 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-1 | \n", + "[\\nThe list of human genes analyzed in this enrichment test are associated with functions related to cell adhesion, signal transduction, and cytoskeletal and extracellular matrix (ECM) proteins. The enriched terms include cell adhesion, signal transduction, actin binding and assembly, membrane localization, ECM protein binding and assembly, integrin binding, calcium and phosphorylation-dependent regulation, neuron regulation, and receptor regulation. \\n\\nMechanism: The underlying biological mechanism that these genes are involved in is related to the regulation of cell adhesion, signal transduction, and cytoskeletal and ECM proteins. This includes signal transduction and cell adhesion mediated by various proteins such as integrins, cadherins, adhesion receptors, and kinases, as well as actin binding and assembly, membrane localization, ECM protein binding and assembly, and phosphorylation-dependent regulation. In neurons, there is regulation of axon guidance, regulation of synapse formation, and regulation of signaling pathways that control neuronal development and plasticity. \\n\\n] | \n", + "[ After performing a term enrichment test of these genes, we have identified a number of commonalities in their functions, including cell adhesion, signaling, scaffolding and cytoskeleton maintenance. These functions are typically mediated by proteins involved in the regulation of extracellular matrix, integrins, claudins, nectins, protein kinases and cadherins, suggesting a common pathway of interaction between membrane-bound receptors and cytoplasmic components.\\n\\nMechanism: These commonalities collectively suggest a pathway involving the regulation of signaling transduction, cell adhesion and cytoskeletal organization by a series of membrane-bound receptors and signals originating in the cytoplasm.\\n\\n] | \n", + "0.93 | \n", + "382 | \n", + "
| 440 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_SURFACE-0 | \n", + "[ The commonality in the functions of these genes is their involvement in cell-matrix adhesion and cell signalling, including signal transduction, membrane proteins, and transcriptional coactivation. The underlying mechanisms likely involve signal recognition and regulating the flow of information to and from the cell, as well as transmembrane transport and receptor-mediated endocytosis.\\n\\nMechanism: Signal recognition and regulation of the flow of information to and from the cell, as well as transmembrane transport and receptor-mediated endocytosis.\\n\\n] | \n", + "[\\n\\nSummary: The genes described in the list are associated with cell adhesion and communication, cell metabolism and transport, receptor-mediated endocytosis, cell-matrix adherence, tissue growth, transcriptional regulation, glycosylation, and signaling.\\n\\nMechanism: The genes are involved in processes such as cell-to-cell adhesion, protein folding, and communication via cell surface proteins; receptor-mediated endocytosis; glycosylphosphatidylinositol and GPI-anchored cell surface proteins; cation transport ATPase; transcriptional coactivation; interleukin signaling and hormone-dependence; heparan sulfate proteoglycan and heparin-binding; and cell-matrix adhesion \\n\\n] | \n", + "0.92 | \n", + "117 | \n", + "
| 441 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_APICAL_SURFACE-1 | \n", + "[\\nThe gene summaries indicate a common association with proteins that mediate cell adhesion, signal transduction, cell-matrix interactions and regulation of cellular growth and differentiation. This suggests a common mechanism of extracellular communication and regulation between cells, mediated by the action of a diverse set of proteins. The enriched terms include cell-matrix adhesion; cell-matrix interactions; carbohydrate binding activity; cell adhesion; receptor activity; signal transduction; positive regulation of cell proliferation; negative regulation of axon regeneration; ankyrin binding; and protein tyrosine kinase.\\n\\nMechanism: The underlying biological mechanism is that a diverse set of proteins interact with one another and external signals, forming an interconnected network of extracellular communication and regulation that mediates cell adhesion, signal transduction, cell-matrix interactions and regulation of cellular growth and differentiation.\\n\\n] | \n", + "[\\n\\nSummary: This list of genes is involved in cell signalling, adhesion, growth regulation, protein folding, cation transport, ligand binding, and other cellular functions.\\n\\nMechanism: These genes are likely involved in cell signalling pathways and signalling molecules that regulate cell growth, differentiation, and homeostasis.\\n\\n] | \n", + "0.91 | \n", + "642 | \n", + "
| 442 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_APOPTOSIS-0 | \n", + "[ Analysis indicates the gene functions enriched in these terms are those involved in apoptosis, cytoplasmic signaling, transcriptional regulation, protein binding, and cellular organization.\\n\\nMechanism: The underlying biological mechanism involves regulation of apoptosis/cell death pathways, as be indicated by the presence of genes like FAS, CASP, BCL-2, BNIP3L, MADD, PEA15, etc. This is further supported by gene functions enabling signaling via G-protein coupled receptors and transcriptional regulation by factors like EGR3, LEF1, etc. Additionally, many involved genes are related to protein binding in order to modulate the activity of these processes, as well as maintain cellular organization, implied by membrane proteins like APP, BCAP31, IFITM3, CD38, CD44, etc.\\n\\n] | \n", + "[ The majority of the human genes on the list are involved in cell death processes, specifically apoptosis, and a wide range of activities associated with transcriptional regulation and DNA binding. A significant portion of the genes are associated with the TNF receptor superfamily, and the BCL-2 protein family, both of which are involved in cell death processes. Common enriched terms in the list include: apoptosis, transcriptional regulation, DNA binding, TNF receptor superfamily, and BCL-2 protein family.\\n\\nMechanism: Apoptotic pathways including caspase activation, BCL-2 protein family and death agonists, in addition to DNA binding of transcription factors and cytokine signaling, are likely to be important mechanisms in the human genes on the list.\\n\\n] | \n", + "0.91 | \n", + "15 | \n", + "
| 443 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_APOPTOSIS-1 | \n", + "[ \\nSummary: This list of gene functions involve mostly cell death processes, signaling, cytoplasmic and nuclear proteins, transcriptional activities, and enzymes for cell processing, as well as toxin removal and receptor binding. \\nMechanism: Cell death processes involve the activation or inhibition of specific enzymes and proteins that interact with cell membrane receptors, signal cell apoptosis, modulate transcriptional activities and regulate reversible and irreversible cytoplasmic and nuclear protein activities. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "506 | \n", + "
| 444 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[ \\nSummary: The list of genes has been enriched with terms related to ATP-binding, transport, fatty acid desaturase, oxidation-reduction, enzyme catalysis, and transcription factors. \\nMechanism: The list of genes encodes a range of proteins whose functions are related to catalysis and transport of molecules, as well as transcription and regulation of hormones and neurotransmitters. \\n] | \n", + "[\\nThe gene summaries correspond to proteins which have enzyme and binding activities related to lipid metabolism, membrane transportation, steroid catalyzation, hormone activation and deactivation, and antioxidant activity.\\nHypothesis: The underlying biological mechanism is likely to involve the crosstalk between different activities in different cellular compartments, such as cytoplasm, nucleus, and peroxisomes, to regulate fatty acid metabolism, signal transduction and other cellular processes. \\n] | \n", + "0.89 | \n", + "117 | \n", + "
| 445 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[ \\nSummary: Genes in the list are involved in protein transport and synthesis, lipid metabolism, oxidation-reduction, hormone regulation, and transcription regulation.\\nMechanism: Genes in the list are involved in a variety of molecular and biochemical processes, such as protein import and export, oxidation-reduction, drug metabolism, hormone regulation, transcription regulation, fatty acid and cholesterol signaling, enzyme regulation, and the breakdown of malonyl-CoA.\\n] | \n", + "[ The list of human genes provided in this term enrichment test appears to be mostly related to enzymes, transporters, and receptors involved in lipid metabolism and transport, as well as in other metabolic pathways like bile acids synthesis, sulfur metabolism, and oxidative stress response. Notably, protein import into peroxisomes is over-represented by PEX6, PEX7, and PEX26. \\n\\nMechanism: The above proteins are likely to be involved in metabolic pathways contributing to lipid metabolism, transport, and oxidation.\\n\\n] | \n", + "0.90 | \n", + "48 | \n", + "
| 446 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[ The list of genes provided appears to be involved in a number of different physiological functions, including cell adhesion, lipid metabolism, energy generation, growth, receptor activity, signaling pathways, apoptosis regulation, transcription regulation, and cholesterol metabolism. Mechanism: The underlying biological mechanism may be related to changes in membrane properties and intracellular signaling, as well as regulation of gene expression, metabolism, and other cellular processes. ] | \n", + "[\\nOur analysis of the list of human genes has revealed that many of the functions of these genes are related to cell regulation, metabolism, and transport. Specifically, the genes are involved in regulating cell growth and adhesion, lipid metabolism, cholesterol synthesis and breakdown, protein homodimerization and packing, enzymatic reactions, hormone regulation, and gene transcription. These gene functions are enriched in areas such as cell motility, energy generation, amino acid synthesis and degradation, glycoprotein synthesis, sterol biosynthesis and degradation, lipid metabolism and transport, and transcriptional regulation. \\n\\nMechanism: The underlying biological mechanism likely involves the coordination of these processes in order to maintain cellular homeostasis and to respond to a variety of environmental stimuli. In this way, cells can signal and respond to changes in their internal and external environments.\\n\\n] | \n", + "0.95 | \n", + "438 | \n", + "
| 447 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[ This gene list is largely composed of genes and their associated proteins involved in processes related to cell growth, metabolism, and cholesterol biosynthesis. The terms that are enriched include lipid metabolism, phospholipid binding proteins, fatty acid desaturase, ATP-binding cassette proteins, sterol biosynthesis, and cytochrome P450 family proteins.Mechanism: The mechanisms underlying these processes involve the synthesis and degradation of essential fatty acids, lipids, and sterols, and the regulation of cell growth and adhesion through transcription factors, receptor-ligand interactions, and transfer of molecules across intracellular and extracellular membranes.] | \n", + "[ \\nSummary: Enriched terms were identified related to cholesterol synthesis, lipid metabolism, fatty acid desaturation, and cell growth/regulation.\\nMechanism: These genes play a role in the regulation of cholesterol and other lipids, as well as amino acids, fatty acid desaturation and biosynthesis, growth, and cell cycle regulation. \\n] | \n", + "0.93 | \n", + "345 | \n", + "
| 448 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_COAGULATION-0 | \n", + "[ The provided list of genes is primarily involved in the regulation of the complement system and blood clotting, as well as in the processing of proteins and peptides. Mechanism: The genes play a role in the innate immune response by modulating the complement system, helping to break down peptides and proteins, regulating inflammation, and in the control of blood clotting. ] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "361 | \n", + "
| 449 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_COAGULATION-1 | \n", + "[ This gene list is enriched for many serine proteases and proteins involved in coagulation, complement activation, metalloproteases, transcriptional regulators and transcription factors. Hypothesis: These genes are involved in extracellular matrix turnover, cell-cell adhesion and signal transduction pathways, as well as processes related to tissue morphogenesis. ] | \n", + "[ \\nSummary: The list of genes are associated with various functions involved in proteolysis, hemostasis, bone growth, morphogenesis, tissue development, lipoprotein regulation, and regulation of the complement system.\\n\\nMechanism: These genes are involved in mechanisms such as proteolysis, hemostasis, bone growth, morphogenesis, tissue development, lipoprotein regulation, and complement system regulation.\\n\\n] | \n", + "0.90 | \n", + "43 | \n", + "
| 450 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_COMPLEMENT-0 | \n", + "[ \\nSummary: The enriched terms found from the list of genes involve proteins associated with cell signaling, structure/stability, metabolism, and vitamin K/clotting. \\n\\nMechanism: These proteins work together to regulate cell signaling pathways and pathways involved in inflammation and metabolism. Additionally, these genes are involved in vitamin K/clotting pathways, cytoskeletal structure/stability and cell membrane strengthening. \\n\\n] | \n", + "[ This list comprises genes with roles in immune and inflammatory processes, cell regulation and development, cell signalling, cell adhesion, and cell metabolism. Many of these genes play roles in modulating the activity of kinases, members of the proteasome complex, and members of the serpin, cysteine-aspartic acid protease (casp) family, and in particular caspase-9 and caspase-3, both of which have roles in apoptosis and inflammation signalling. There are also proteins important in complement activation and coagulation, such as factor V, X, and VII and their receptors, as well as proteins that modulate interferon-induced signalling, such as IRF1, IRF2, and IRF7.\\n\\nMechanism: This list shows that these genes play roles in diverse pathways, such as cell development, cell signalling, cell regulation, cell adhesion and metabolism, complement activation, coagulation, and interferon-induced signalling.\\n\\n] | \n", + "0.89 | \n", + "475 | \n", + "
| 451 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_COMPLEMENT-1 | \n", + "[\\nSummary: The list of genes are mainly involved in protein production, cell surface glycoprotein regulation, complement activation and signalling pathways.\\n] | \n", + "[\\n\\nSummary: The genes included in this list encode proteins involved in cell signaling, adhesion, protease activity, and cytoskeletal and metabolic processes.\\n\\nMechanism: The proteins encoded by the genes in this list are important in a variety of cellular processes including cell adhesion, transcriptional regulation, protease activity, and metabolic and cytoskeletal functions.\\n\\n] | \n", + "0.91 | \n", + "225 | \n", + "
| 452 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_DNA_REPAIR-0 | \n", + "[COULD NOT PARSE] | \n", + "[\\n\\nSummary: The human genes in this list are involved in functions such as DNA binding, transcription control, post-splicing, and RNA polymerase II functions. \\nMechanism: These genes are involved in multiple functions involved in the maintenance of DNA structure and transcription, such as DNA repair, post-splicing, andRNA polymerase II-related functions.\\n] | \n", + "0.68 | \n", + "341 | \n", + "
| 453 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_DNA_REPAIR-1 | \n", + "[\\n\\nSummary: We have identified 18 enriched terms associated with the functions of the given list of genes. These functions include DNA binding, transcription, DNA repair and mRNA processing.\\n\\nMechanism: The commonalities between the functions of the given list of genes suggest that they are involved in facilitating DNA binding and transcription regulation, DNA repair, mRNA splicing and mRNA processing activities.\\n\\n] | \n", + "[\\nSummary: The genes found in this list primarily involve DNA repair, transcription, and mRNA metabolism.\\nMechanism: The genes are involved in the transcription and DNA repair process, which includes enzyme binding, RNA binding, DNA, protein, and chromosomal binding activities, as well as the activity of DNA and RNA polymerases, phosphorolysis, gene silencing, and protein ubiquitination.\\n] | \n", + "0.92 | \n", + "27 | \n", + "
| 454 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_E2F_TARGETS-0 | \n", + "[ \\n\\nSummary: This term enrichment test identified highly conserved proteins and protein complexes that play a role in DNA replication, repair and transcription, chromatin binding and modification, and cell cycle regulation.\\n\\nMechanism: The enrichment test suggests that these genes are essential for maintaining their respective functions, as well as for responding to DNA damage, replication blocks and cell cycle regulation.\\n\\n] | \n", + "[\\nSummary: The enriched terms from the given gene list suggest that these genes are involved in DNA replication and repair, chromatin regulation, and RNA processing.\\nMechanism: These processes involve the coordination and control of proteins, DNA sequences, and metabolites such as calcium ions.\\n] | \n", + "0.91 | \n", + "132 | \n", + "
| 455 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_E2F_TARGETS-1 | \n", + "[\\nGene functions related to the regulation of nucleic acid binding and metabolism, chromatin, protein modification, DNA replication, and cell cycle regulation are enriched in the list of genes provided above. These process appear to be interrelated and part of a larger cellular pathway.\\n\\nMechanism:\\nThe mechanism underlying these gene functions seems to involve the control of the cell cycle, DNA binding and metabolism, chromatin dynamics, and protein modification and turnover. These processes are regulated by a complex network of interactions between various proteins, DNA modifications, and histone modifications, which help control the assembly and disassembly of different chromatin structures. This in turn affects DNA replication, transcription, and translation of proteins required for various cellular processes.\\n\\n] | \n", + "[\\nSummary: This list of genes is involved in a variety of functions, such as DNA replication, nuclear import and export, RNA binding, chromatin regulation and modification, protein degradation, cell cycle control, and DNA repair.\\n\\nMechanism: These genes are involved in many processes related to maintaining genomic stability, including DNA replication, DNA repair, and chromatin regulation.\\n\\n] | \n", + "0.93 | \n", + "433 | \n", + "
| 456 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[ The genes presented in this list are primarily involved in cell signaling, extracellular matrix formation and cell adhesion. Furthermore, many of the genes play a role in connective tissue formation and related structural processes.\\n\\nMechanism: Genes involved in cell signaling, extracellular matrix formation, and cell adhesion are integral in their roles in producing cell structure and maintaining connective tissue structure and integrity. These genes work together to allow cells to communicate properly and modulate processes such as inflammation and tissue repair. Additionally, cell signaling and cytokines produced by these genes contribute to angiogenesis, metabolic regulation, and tissue growth and development. \\n\\n] | \n", + "[ \\nSummary: Enriched gene functions were identified related to extracellular matrix glycoproteins, collagen, actin binding and regulation, cell adhesion and signaling, cytokine regulation and signaling, peptidase genes, and growth factor family members.\\n\\nMechanism: Members of these gene families play important roles in the regulation of cell signaling pathways, cell migration, cell growth and differentiation, hemostasis and inflammation, and various other biological processes.\\n\\n] | \n", + "0.91 | \n", + "245 | \n", + "
| 457 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[\\nThis list of genes is strongly associated with extracellular matrix and collagen production, with members of the integrin, laminin, dystrophin, fibronectin, von Willebrand Factor, and fibulin families involved. Enriched terms include extracellular matrix proteins, collagen, laminin, fibronectin, von Willebrand Factor, integrin, dystrophin, and fibulin proteins.\\n\\nMechanism: \\nThese proteins are involved in extracellular matrix production and organization, which is critical for cell-to-cell and cell-to-environment interaction. This involves extracellular matrix proteins that facilitate connection and communication between cells, as well as structural proteins such as collagen and laminin that provide stability and rigidity. In addition, these proteins are involved in cell adhesion, migration, and proliferation. By forming interconnecting complexes, these proteins work together to mediate multiple biological processes, from cell development to tissue and organ formation. \\n\\n] | \n", + "[ \\nSummary: The genes included in this list encode proteins that are involved in structural support and maintainance of cell components, such as extracellular matrix proteins, integrins, collagen, fibrillin, tropomyosin and myosin proteins.\\nMany of them have roles related to regulatory cell functions, such as cell adhesion, growth and signalling pathways.\\nMechanism: These proteins play a role in the maintainance and regulation of cell structure, linking the extracellular environment to the intracellular environment, enabling cell-cell interactions, and modulating cell behaviour and signalling.\\n] | \n", + "0.92 | \n", + "385 | \n", + "
| 458 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[ The enriched terms in this list of genes include proteins related to peptide binding, cell membrane structure modification, DNA binding, fatty acid metabolism, hormone receptor binding, signalling transcription, GTPase activation, adenylate cyclase modulation, kinase activity, endocytosis, glycoprotein production, growth factor binding, histone modification, phospholipid metabolism and zinc-binding. The underlying biological mechanisms and pathways involve proteins involved in intracellular and intercellular signalling, as well as chromatin remodelling and membrane trafficking. \\n\\nMechanism: Membrane trafficking, cellular signalling and chromatin remodelling. \\n\\n] | \n", + "[ Enriched terms involved in signal transduction, gene expression, transport, and membrane protein functions.\\n\\nMechanism: Signal transduction, gene expression and transport functions may occur as a result of interaction between proteins encoded by the genes, as well as interaction between nucleic acids such as DNA, RNA, and chromatin. This can be regulated by post-translational modifications such as methylation, phosphorylations, and acylation, as well as by binding of other proteins and ligands. Membrane proteins allow for communication between the cytoplasm and outside environment and facilitate the transport of molecules.\\n\\n] | \n", + "0.92 | \n", + "37 | \n", + "
| 459 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[ \\n\\nSummary: The genes described in this list are mainly involved in the regulation and manipulation of protein functions, such as DNA-binding, signaling pathways, post-translational modification, protein binding, and metabolic activity.\\n\\nMechanism: Many of the genes involved are involved in metabolic pathways and regulation, and interactions between proteins, such as through DNA-binding, signaling pathways, and post-translational modification.\\n\\n] | \n", + "[ Gene functions were identified enriched for cytoskeletal organization, DNA binding transcription regulation, membrane transport and receptor signalling.\\nMechanism: Commonalities in gene functions is associated with cellular and signal transduction pathways, involving several mechanisms including membrane transport, DNA-binding transcription regulation, cell adhesion, cytokine and growth factor signalling, and the expression of structural components of muscle and epithelial cells.\\n] | \n", + "0.87 | \n", + "37 | \n", + "
| 460 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[\\n\\nSummary: Genes involved in regulation of cell signaling, including protein kinases, transcription factors, calcium ion binding, glycobiology, and hormone receptors. \\nMechanism: All the genes operate at the cellular signaling level to mediate various biological functions such as cell adhesion, protein folding, and gene expression. \\n] | \n", + "[\\nSummary: The human gene list provided consists of genes involved in a variety of cellular functions, including regulation of G protein signalling, ion channel transport, membrane receptor signalling, cytoskeletal protein scaffolding, enzyme regulation and glycoprotein modulation. \\n] | \n", + "0.90 | \n", + "52 | \n", + "
| 461 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[ The genes identified are largely involved in membrane and transmembrane processes, ion transport, cell adhesion and growth, metabolizing enzymes, disease processes, and protein signaling and processing. Mechanism: These genes are involved in processes related to cell physiology, adhesion, growth and development, and reparative pathways, as well as immune and disease processes. ] | \n", + "[\\nSummary: The genes listed are involved in various cellular functions, including signal transduction, gene transcription, ion transport and binding, protein-protein interaction and post-translational modifications.\\nMechanism: These genes have been found to encode proteins that are involved in diverse cell functions, including signal transduction, structural proteins, transcription factors, transporters, kinases and phosphatases, and their associated regulatory proteins.\\n] | \n", + "0.91 | \n", + "94 | \n", + "
| 462 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[ \\n\\nSummary: There is an enrichment for metabolic and energy regulation processes involving multiple enzymes and proteins connecting with metabolites, nucleotides, fatty acids, and other molecules.\\n\\nMechanism: These genes seem to be involved in metabolic pathways leading to the formation of intermediate metabolites and energy transportation in the body.\\n\\n] | \n", + "[\\n\\nSummary: This list includes 51 human genes involved in metabolic, biosynthetic, enzymatic, and regulatory pathways and processes. The majority of these genes encode proteins involved in metabolic functions, such as glycolysis, oxidation-reduction processes, and polyamine metabolism.\\n\\nMechanism: The commonalities between these genes are related to their roles in metabolic and enzymatic processes throughout cells. These proteins are involved in catalyzing and regulating nucleotide and amino acid metabolism, fatty acid oxidation and synthesis, polyamine metabolism, and enzyme activity.\\n\\n] | \n", + "0.93 | \n", + "237 | \n", + "
| 463 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[ The summaries of these human genes suggest that the majority of them are involved in metabolism-related processes, specifically in the processing and transport of fatty acids and oxidoreductases. There is also evidence that these genes may be involved in growth and development, such as for aiding in morphogenesis, cell differentiation, and protein-macromolecule adaptor activity. The enriched terms that represent these processes are \"metabolism,\" \"fatty acid transport and processing,\" \"oxidoreductase,\" \"morphogenesis,\" \"cell differentiation,\" and \"protein-macromolecule adaptor activity.\" \\n\\nMechanism: The underlying biological mechanism might involve the genetic regulation of enzymes responsible for fatty acid and metabolite transport and transformation. Additionally, the gene products of these genes might be involved in signaling cascades that lead to morphogenesis and cell differentiation. \\n\\n] | \n", + "[\\nThe gene list contains genes associated with metabolic activities such as enzymatic components of tricarboxylic acid cycle, fatty acid binding proteins, aldehyde dehydrogenases and enzyme processes related to electron transfer, including pyruvate dehydrogenase, NAD-retinol dehydrogenase, succinate dehydrogenase, etc. The underlying biological mechanism involves the process of metabolic energy conversion, which involves the coordination of various enzymatic components.\\n\\nMechanism: Metabolic energy conversion coordinates various enzymatic components.\\n\\n] | \n", + "0.90 | \n", + "349 | \n", + "
| 464 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-0 | \n", + "[ \\n\\nSummary: The provided gene list is mainly involved in functions related to cell cycle regulation, chromatin/histone modification, and transcription.\\n\\nMechanism: These genes are involved in a variety of biological processes related to cell cycle regulation, chromatin/histone modifications, protein kinase activity, ATP-binding, and RNA binding.\\n\\n] | \n", + "[\\nSummary: The genes in the list encode proteins involved in cell signalling and regulation pathways, epigenetic regulation, nuclear transport, mitosis, mRNA processing, protein modification, DNA replication and repair, and chromatin structure.\\nMechanism: This analysis suggests that these genes are responsible for various critical cellular functions and pathways, such as transcriptional regulation, epigenetic remodeling, nuclear transport, post-translational modifications, DNA replication and repair, chromatin structure, and mitosis.\\n] | \n", + "0.94 | \n", + "190 | \n", + "
| 465 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-1 | \n", + "[ Enriched terms among this list of genes point to functions related to cell division, DNA and RNA binding, transcriptional regulation, chromatin restructuring, and protein kinase activity. This set of genes appears to have enriched terms related to nuclear and cytoplasmic transport, nucleic acid metabolic functions, and histone certain activities. Mechanism: The collection of processes related to the functions of these genes appear to function in a coordinated way, with many proteins involved in multiple pathways that work together to maintain cell division, DNA integrity, gene expression, and the structural organization of chromatin. These processes appear to be primarily regulated by an array of proteins with phosphorylation, methylation, acetylation, and ubiquitination activities. ] | \n", + "[ \\nSummary: The human genes in this list are involved in various critical functions related to cellular development, including nucleocytoplasmic transport, histone acetylation, chromatin-associated processes, cell cycle regulation, and transcriptional regulation.\\n] | \n", + "0.90 | \n", + "532 | \n", + "
| 466 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_GLYCOLYSIS-0 | \n", + "[\\n\\nSummary: The list of genes have similar functions in cellular pathways such as glycoprotein metabolism, phosphorylation, cell adhesion, transcription, nucleotide metabolism, energy production, and others.\\n\\nMechanism: Many of these genes are involved in phosphorylation, which helps to regulate cellular activity. This includes regulation of cell adhesion and transcription, as well as energy production and nucleotide metabolism.\\n\\n] | \n", + "[\\n] | \n", + "0.73 | \n", + "432 | \n", + "
| 467 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_GLYCOLYSIS-1 | \n", + "[ Biological processes related to development, glycosylation, and metabolism of proteins, lipids, and carbohydrates are enriched based on the list of genes given.\\n\\nMechanism: The genes identified encode for enzymes, receptors, and proteins that support functions in several biological mechanisms, including protein and carbohydrate metabolism, post-translational modification, binding, and transport.\\n\\n] | \n", + "[\\nSummary: Analysis of the summaries of these genes reveal that the majority are involved in enzymatic functions, binding, transporting, and metabolism of molecules, including ions and sugars.\\nMechanism: These genes likely have an underlying biological mechanism of enzyme catalysis and/or binding affinity affecting the metabolism of molecules, including ions and sugars, as well as modulating transcription, cytoskeletal structure, and cell adhesion.\\n] | \n", + "0.89 | \n", + "51 | \n", + "
| 468 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[ \\nSummary: The list contains 22 genes involved in signal transduction, transcription and cell adhesion, primarily within the nervous system.\\n] | \n", + "[\\nThis gene set is involved in a variety of cellular functions, such as cell adhesion, neural development, transcription factor regulation, signal transduction, and extracellular protein interaction. These genes are over-represented in processes related to endocytosis, growth factor binding, and receptor-mediated pathways. The hypothesis is that these genes are involved in pathways associated with the regulation of neuron survival, differentiation, and youthfulness.\\n\\nMechanism: This gene set is hypothesised to be involved in signalling pathways related to neuron survival, differentiation, and development. These pathways are probable mediated by endocytosis, growth factor binding, and receptors.\\n\\n] | \n", + "0.89 | \n", + "563 | \n", + "
| 469 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[ This set of genes are mainly involved in neuron signalling and cell adhesion, and all contribute to cellular processes such as growth, differentiation, motility and development. Mechanism: These genes are predominantly involved in intracellular signal transduction pathways, which lead to the activation of transcription factors or the production of secretory proteins. ] | \n", + "[\\nThis is a list of 20 human genes, most of which are associated with neural development and axon guidance. Several of these genes are involved in receptor-mediated endocytosis, G-protein coupled receptors, cell adhesion, gene transcription and post-translational regulation. The enriched terms include structure-specific proteins, receptor-mediated endocytosis, G-protein coupled receptors, cell adhesion, gene transcription, and post-translational regulation. \\nMechanism: These genes are involved in the regulation of various processes such as cell motility, cell differentiation and cell migration, and formation of complex systems such as axon networks, which involves a variety of cellular pathways. ] | \n", + "0.93 | \n", + "333 | \n", + "
| 470 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_HEME_METABOLISM-0 | \n", + "[ \\n\\nSummary: The list of genes described relate to the processing and binding of protein molecules, cytokinesis, transcriptional regulation, metabolic and enzymatic functions, formation of cell cortex, transport, and several other cellular processes.\\n\\nMechanism: Many of the genes are associated with the formation and modification of proteins, including phosphorylation and acetylation, playing an important role in cell membrane and cytoskeleton structure, catalyzing metabolic reactants, and trafficking. \\n\\n] | \n", + "[\\nAnalysis of the above list of genes revealed that a considerable number of them are involved in processes such as protein binding, transcription, catalyzing reactions (including enzymatic reactions), and GTPase activating protein activation. This indicates that these genes play a role in a wide range of biological processes related to cellular and subcellular processes. In particular, these genes are involved in functions such as histone deacetylation, carbohydrate and lipid metabolism, receptor binding and signaling, DNA binding, and DNA packaging.\\n\\nMechanism:\\nMany of the genes listed are related to binding either other molecules or DNAs, as well as catalyzing various reactions. These processes likely work together to allow cells to properly function, as well as for their internal structures to be regulated and maintained, such as for the types of molecules necessary for cellular and subcellular processes. Additionally, transcription is another process heavily involved, as many of the genes are associated with regulating the expression of other genes. \\n\\n] | \n", + "0.93 | \n", + "563 | \n", + "
| 471 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_HEME_METABOLISM-1 | \n", + "[ The list of human genes appear to be involved in transcription and post-transcriptional regulation, regulation of glycolysis and pyruvate metabolism, glutathione metabolism, proteolysis, transcriptional regulation, and ubiquitination. \\n\\nMechanism: The genes may be involved in regulation and modulation of pathways that control cell structure, function, maturation and apoptosis.\\n\\n] | \n", + "[ \\nSummary: The list of human genes encompass a variety of processes such as DNA binding, histone acetylation, protein binding, transcription regulation, and leucine residue modification.\\n\\nMechanism: The underlying biological mechanism involves the regulation of gene expression, protein and nucleic acid metabolism, and signal transduction.\\n\\n] | \n", + "0.90 | \n", + "40 | \n", + "
| 472 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_HYPOXIA-0 | \n", + "[ \\n\\nSummary: Genes involved in regulating a variety of metabolic functions such as glycolysis, phosphorylation, protein kinase activity, proteolytic degradation, extracellular matrix assembly and maintenance, and transcription regulation.\\n\\nMechanism: Genes are involved in different aspects of metabolic regulation responsible for the control of cellular processes such as cell cycle and proliferation, energy homeostasis, inflammation, and the communication between cells. \\n\\n] | \n", + "[ The list of genes provided encodes many different proteins involved in metabolic regulation, cell signaling, and post-translational modification. The most enriched term is: “cell signaling”; other terms include “metabolic regulation” and “post-translational modification”.\\n\\nMechanism: The mechanism underlying the enriched terms is that many of the encoded proteins are involved in different pathways that ultimately regulate and control the cell processes, such as cellular signaling, metabolic regulation, post-translational modification, and more. These proteins work together in a complex network to control cell activities. \\n\\n] | \n", + "0.89 | \n", + "157 | \n", + "
| 473 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_HYPOXIA-1 | \n", + "[\\nThe list of genes is mainly involved in metabolic and transcription processes. The genes enable physical functions such as carbohydrate binding, phosphorylation, and filamin binding, as well as regulate apoptosis, proliferation and growth. The biological mechanism involves cytoplasmic processing, lipoprotein metabolism, cell-binding and signaling pathways.\\n\\nMechanism: Metabolic, Transcription, and Cytoplasmic Processes\\n] | \n", + "[\\n\\nSummary: A large majority of the genes are involved in the regulation of a wide range of cellular functions including those related to cellular transport, metabolic processes, scaffolding, transcriptional regulation, cell cycle control, transcription factor activity and phosphorylation.\\n\\nMechanism: These genes-through their diverse roles in the regulation of cell transport, metabolic processes, scaffolding, transcriptional regulation, cell cycle control, transcription factor activity and phosphorylation-form the backbone of numerous cellular functions. \\n\\n] | \n", + "0.91 | \n", + "139 | \n", + "
| 474 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[\\n cells proliferate and differentiation, metabolism and gene regulation, cytokine signaling and antigen recognition, transcription factors and membrane-associated proteins.\\nMechanism: A wide range of mechanisms are involved, including regulation of cell proliferation and differentiation, metabolism, gene regulation, cytokine signaling, and antigen recognition. Common enriched terms include cell cycle regulation, receptor signaling, membrane-associated proteins, and transcription factors.\\nHypothesis: The underlying biological mechanism involves a wide range of processes related to cell proliferation, differentiation, metabolism, gene regulation, cytokine signaling, and antigen recognition. These processes are mediated by various membrane-associated proteins and transcription factors.\\n] | \n", + "[ The enriched terms from the analysis of this list of genes indicate that they are all primarily involved in interaction with other macromolecules or with receptors, or in structure and cell adhesion. Many of the genes are associated with the regulation of transcription factors, such as the TNF receptor family, and others are associated with enzyme regulation or the production of cytokines. The underlying hypothesis is that these genes represent a variety of pathways that help regulate various aspects of cell function and communication.\\n\\nMechanism: The mechanism behind the term enrichment relates to the protein-protein interactions and cell adhesion that is regulated by these genes.\\n\\n] | \n", + "0.90 | \n", + "101 | \n", + "
| 475 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[ The list of genes can be divided into several classes related to their functions, including signaling (MAPKAPK2, PHLDA1, CSF2, CD86, etc.), cell adhesion (SELL, CD79B, CD44, etc.), receptor activity (P2RX4, TNFSF4, IGF2R, etc.) and protein kinase activity (PRAF2, CAPG, PTCH1, etc.). These genes are involved in diverse physiological processes, such as signal transduction, membrane transport, immune response, cell cycle and apoptosis. Mechanism: The enriched terms indicate that these genes are involved in signal transduction and cellular processes at the molecular level, such as GTP binding, protein homodimerization, nucleic acid binding, and protein kinase activity. ] | \n", + "[\\nSummary: A list of human genes and their functions were analyzed and enrichment terms related to intracellular signaling, cell adhesion, and membrane proteins were identified.\\nMechanism and ] | \n", + "0.91 | \n", + "484 | \n", + "
| 476 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[\\nSummary: The list of genes is associated with inflammation, cell growth, and development processes primarily involving cytokine signaling pathways. \\nMechanism: Signaling pathways comprise cytokine signals of various types coupled to various types of receptors and transmembrane proteins, with downstream activations of various protein kinases, transcription factors, and modulators of cell cycle progression.\\n] | \n", + "[ \\nSummary: Twenty-eight genes that encode proteins involved in immune/inflammatory responses, growth regulation, and signal transduction were found to be enriched in terms of functions related to cytokine receptors, chemokines, TGF-beta superfamily, transcriptional regulation, protein tyrosine phosphatases, and protein kinases. \\n\\nMechanism: These genes are involved in immune and inflammatory responses, growth regulation, and signal transduction by influencing cell proliferation, differentiation, and apoptosis.\\n\\n] | \n", + "0.93 | \n", + "107 | \n", + "
| 477 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE] | \n", + "1.00 | \n", + "0 | \n", + "
| 478 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[ The list of genes are mainly involved in receptor binding, cytokine signalling, and regulation of inflammation, cell cycle and growth. \\nMechanism: These genes likely represent critical components of complex pathways involving cell growth, immune signalling and inflammation, as well as the coordination of cell cycle and apoptosis.\\n] | \n", + "[ \\nSummary: A majority of the gene functions on this list are related to protein-coupling, receptors, cell surface and membrane-associated proteins, and cytokine-related components.\\nMechanism: Cell membrane, receptor-coupled, and ligand-binding activities.\\n] | \n", + "0.88 | \n", + "77 | \n", + "
| 479 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[ Cells have an inherent potential to interact with each other, responding to proteins that traffic signals across the membrane which may modulate cytokines, immunoactivators, lipids, and transcription factors to form different types of signaling pathways and biological processes. Mechanism: Interaction or binding of proteins or receptors with lipids, cytokines, transcription factors, or hormones triggers signaling events across the membrane, consequently modulating the gene expression of the cell. ] | \n", + "[ Genes in this list are predominantly involved in receptor binding, signaling, membrane transport, calcium binding and transmembrane transport. The enrichment of these specific functions suggest the underlying biological mechanism involves immune responses, cytokine signaling and communication between the nucleus and cytoplasm of cells. \\n\\nMechanism: Genes in this list have functions in receptor binding, signaling, membrane transport, calcium binding and transmembrane transport which are involved in immune responses, cytokine signaling, and nuclear/cytoplasm communication.\\n\\n] | \n", + "0.87 | \n", + "77 | \n", + "
| 480 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[\\nThe list of genes related to human genetics is statistically enriched for genes involved in immune response and regulation, protein-binding and modification, subunit-binding and regulation in macromolecular complexes (such as proteasomes & MHC), and RNA-binding and modification. \\nMechanism: The enriched terms identified above support the underlying biological mechanism of protein-protein interactions, ligand binding, gene transcriptional regulation, signal transduction and other essential processes essential to maintaining cell homeostasis. \\n] | \n", + "[ This list of genes are enriched for modulating processes related to cell signaling, immune response, and gene regulation, mainly through interacting with ligands, receptors and enzymes, and RNA or DNA binding activity. \\nMechanism: The enriched genes are involved in pathways that lead to protein activation, degradation, ubiquitination, and participation in RNA or DNA binding.\\n] | \n", + "0.92 | \n", + "170 | \n", + "
| 481 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[ \\n\\nSummary: The gene list is composed of transcriptional regulators, tumor suppressors, proteases, catalysts, membrane proteins and receptor proteins, which are involved in immune response, defense response, mRNA stabilization, mRNA editing, protein ubiquitination, protein methylation, and cell proliferation. \\nMechanism: These genes are involved in regulating the expression of other gene pathways, controlling cellular growth and activation, recognition of external or internal signals, or altering the properties of a macromolecule through enzymatic action, leading to shifts in growth and metabolism. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "592 | \n", + "
| 482 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[ Genes in this list are associated with immune regulation, DNA binding, RNA binding, protein ubiquitination, anti-viral response, cytokine signaling, and inflammation.\\n\\nMechanism: These genes are involved in pathways that regulate immune responses, such as the induction of cytokines, the recognition of viral DNA, the binding of RNA and DNA, the ubiquitination of proteins, and the activation of inflammatory pathways.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.67 | \n", + "406 | \n", + "
| 483 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[ \\n\\nSummary: This list of human genes has been found to be involved in various processes related to inflammation, immune cell signaling and development, immune regulation and cellular metabolism.\\n\\nMechanism: These genes may be involved in pathways related to the regulation of innate and adaptive immunity, as well as pathways related to metabolic and transcriptional regulation, DNA binding and RNA binding activities.\\n\\n] | \n", + "[ This gene set is enriched for terms related to transcriptional regulation, enzyme activity, binding ability, protein structures, and cell signalling. There is a wide array of proteins involved in cytokine and growth factor signalling, immunity, and transcription factors, as well as a range of proteins carrying out important enzymatic functions.\\n\\nMechanism: The genes in this gene set are all involved in a variety of pathways and processes related to cellular signalling, protein production, gene expression, immune response, enzyme activity, and DNA binding activities, given their involvement in different transcriptional and binding processes.\\n\\n] | \n", + "0.89 | \n", + "231 | \n", + "
| 484 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[\\n\\nSummary: Genes listed are involved in a variety of cellular activities, including protein-binding, transcriptional regulation, cell adhesion, cell membrane channel activity, protein metabolism/modification, and receptor signalling.\\n\\nMechanism: The enriched terms represent the wide-ranging cellular activities of the listed genes, exemplifying they operate within multiple pathways and networks to form a complex system of molecular interactions.\\n\\n] | \n", + "[ The genes in this list are predominantly involved in the regulation of ion channels and ion transport proteins, as well as receptor proteins, calcium binding proteins and various enzymes involved in cell signaling and metabolic processes. \\nMechanism: These proteins play important roles in the regulation of various processes ranging from cell adhesion to cytokine/growth factor signaling and hormone-regulation as well as metabolism. \\n] | \n", + "0.90 | \n", + "13 | \n", + "
| 485 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[ After performing a term enrichment test on the list of human genes and their descriptions, the enriched terms found to be statistically over-represented are related to proteins that are responsible for cellular growth and development, movement, action potentials, calcium binding, steroid binding and metabolism, transcription factors, and binding of various molecules such as ATP, RNA, G proteins, and DNA-binding. The underlying biological mechanisms involve the integrative action of various proteins that are essential for various physiological and developmental processes, including those related to reproduction and metabolism.\\n\\nMechanism: Integrative action of proteins related to cellular growth, development, movement, action potentials, calcium binding, steroid binding and metabolism, transcription factors, and binding of various molecules. \\n\\n] | \n", + "[\\nSummary: The list of genes are involved in a variety of functions including catalyzing reaction, membrane transport, signaling, DNA-binding, transcription, extracellular signaling, and calcium-ion binding.\\n\\nMechanism: These genes play a role in operating a variety of biological pathways related to immune system signaling, cell growth and maintenance, cell communication, hormone regulation, transcription, development, and metabolism.\\n\\n] | \n", + "0.88 | \n", + "417 | \n", + "
| 486 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[ Enriched terms and mechanisms related to cell adhesion, regulation of growth factors and cytokines, calcium activation, and transcriptional regulation.\\n\\nMechanism: The genes involved are related to a range of important cell process, such as cell adhesion and calcium signaling, as well as the regulation of growth factors, cytokines, and gene transcription. These functions are essential for cellular growth and development, and are the basis for many of the body's responses to a variety of stimuli.\\n\\n] | \n", + "[ Enriched terms related to protein structure and functions, including membrane-associated proteins, peptidases, receptor proteins, DNA-binding proteins, kinases, and transcription factors involved in transcriptional regulation. Mechanism: These proteins are involved in many biological processes, including blood pressure regulation, electrolyte balance, signal transduction, transcriptional regulation, ion transport, muscle contraction, immunologic regulation and cytokine production, cell cycle control, apoptosis, cell adhesion, and tumorigenesis. ] | \n", + "0.89 | \n", + "50 | \n", + "
| 487 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[ \\nSummary: The list of terms is mostly associated with proteins and their cellular roles, such as binding to cell membrane, binding to DNA, catalyzing reactions, activating pathways, and regulating cytokines, growth factors, and transcription.\\nMechanism: The human genes are involved in regulating growth, development, metabolic and immunological processes through the functioning of the encoded proteins.\\n] | \n", + "[\\nSummary: Gene functions enriched in this list include receptor functions, protease production, cell adhesion, development, immune regulation, inflammation, protein family structural functions, GTPase activities, transcription factor functions, transcription regulation, post-translational modifications, endocytic receptor-ligand interactions, ligand functions, serine protease inhibitor functions, interaction with plasma membrane components, small molecule energy production and transport, transcriptional binding and regulatory protein family functions, and DNA binding. \\nMechanism: A variety of gene functions are enriched in this list, including receptor functions, protease production, cell adhesion, development, immune regulation, inflammation, protein family structural functions, GTPase activities, transcriptional regulation, transcription factor functions, post-translational modification functions, endocytic receptor-ligand interactions, ligand functions, serine protease inhibitor functions, interactions with plasma membrane components, small molecule energy production and transport, transcriptional binding and regulatory protein family functions, and DNA binding. These functions likely play a role in a variety of biological processes, including signal transduction, cell proliferation, development, growth factor signal transduction, metabolic regulation and stress response. \\n] | \n", + "0.89 | \n", + "993 | \n", + "
| 488 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[\\nThe given genes are primarily involved in regulation and control of cell morphological and structural processes, such as cytoskeletal organization, centrosome interaction, DNA interaction, and GTPase regulation.\\nHypothesis: These genes are likely to be involved in a variety of biological pathways that control cell morphology and structure, such as organization of the cytoskeleton, centrosome dynamics, DNA replication and maintenance of chromatin structure through interactions with GTPases and their associated proteins.\\n] | \n", + "[\\nSummary: This list of genes has numerous important functions related to regulation of the cytoskeleton, cellular communication, cellular development and DNA transcription/translation and repair.\\nMechanism: These functions are critical for maintaining proper cellular morphology, adhesion, and organelle trafficking as well as for initiating and regulating cellular signaling pathways and gene expression.\\n] | \n", + "0.90 | \n", + "120 | \n", + "
| 489 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[\\nThe list of genes consist of proteins involved in the maintenance of cell architecture, cell cycle regulation, microtubule-binding, and chromosome segregation. Most of the proteins are involved in GTPase and nucleotide exchange regulation, cellular signaling, chromatin remodeling, cytoskeleton structure, DNA replication, cell adhesion, and actin binding and regulation.\\n\\nMechanism:\\nThe proteins suggested in the list are involved in a variety of regulatory pathways that are integral to the maintenance of proper cellular architecture and organization. These pathways include cellular signaling, chromatin remodeling, cytoskeleton structure, DNA replication, cell adhesion, and actin binding and regulation.\\n\\n] | \n", + "[\\n\\nSummary: The list of genes encodes proteins which are associated with various regulatory processes in the cell, including binding to and/or activating GTPases, structural maintanance of the cytoskeleton, and control over cell cycle or apoptosis.\\n\\nMechanism: These proteins are likely involved in the regulation of the cell via interactions with proteins such as Rho GTPases or guanine nucleotide exchange factors (GEFs), or participation in the cell cycle, apoptosis, or structure of the cell.\\n\\n] | \n", + "0.95 | \n", + "215 | \n", + "
| 490 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-0 | \n", + "[ Genes related to the list are enriched for activities related to protein biosynthesis, transport and signaling, metabolism, and gene expression control. Mechanism: Genes related to the list are involved in integral processes of the cell, such as metabolism and gene expression control, which are facilitated by protein synthesis, transport and signaling. ] | \n", + "[ This list of human genes is enriched for functions related to cellular homeostasis, including protein synthesis, metabolism, protein folding, ubiquitination, transcription, DNA binding and damage control, development, and regulation of cellular pathways.\\n\\nMechanism: These genes are enriched for factors involved in various cellular processes necessary for maintaining homeostasis. These include protein synthesis, redox balance, fatty acid and energy metabolism, protein folding, ubiquitination, protein-protein interaction, transcription, and DNA damage control. In addition, these genes are enriched for factors that regulate various cellular pathways, including apoptosis, the cell cycle, and protein degradation.\\n\\n] | \n", + "0.92 | \n", + "364 | \n", + "
| 491 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-1 | \n", + "[ These genes perform important functions related to protein synthesis and metabolism, including binding, ubiquitination, transcription, and enzyme activity. They are involved in processes such as protein folding, chaperoning, cell cycle regulation, lipid metabolism, glucose uptake, and cytoskeleton formation. Mechanism: These genes share common functions related to protein synthesis and metabolism, and their expressions are mutually regulated to interact with one another and create pathways that lead to the desired outcomes. ] | \n", + "[\\nThe human genes found in the list are primarily involved in metabolic processes, cellular homeostasis, and chromatin regulation. Specifically, ATP production, amino acid homeostasis and metabolism, stress response, transcription and mRNA regulation, chaperones and proteasome degradation pathways, and lipid metabolism are all found to be enriched terms with known correlation to each other. Many of the proteins noted have both metabolic and protein-degradation pathways, indicating potential regulatory mechanisms in place for metabolic and homeostatic processes.\\n\\nMechanism: \\n\\nThe metabolic pathway systems are regulated by a combination of transcription and degradation pathways. Proteins involved in these pathways, such as chaperones, proteasomes, and enzymes regulate the transcription of genes and the degradation of proteins for a tight control of homeostatic and metabolic processes. Additionally, lipid and amino acid metabolism are regulated by clusters of enzymes, indicating a need for integration between multiple proteins.\\n\\n] | \n", + "0.90 | \n", + "510 | \n", + "
| 492 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-0 | \n", + "[\\nThe list of genes are involved in the processes of transcription, translation, and post-translational modification, which are essential for protein synthesis and function in the cell. Enriched terms include transcription, translation, mRNA binding, ribosome subunits, splicing factors, post-translational modification, cytoplasmic proteins, nuclear proteins, DNA binding and unwinding proteins subunits of the nuclear lamina, and proteins associated with the spliceosome. \\nMechanism: These gene functions are part of the essential biological mechanism of protein synthesis in a cell, which is a complex process that requires the coordination of multiple processes, including transcription, translation, and post-translational modifications. \\n] | \n", + "[\\n\\nSummary: The genes studied are involved in a variety of functions that together form a transcription and translation network, primarily related to translation initiation, RNA binding, and ubiquitination.\\n\\nMechanism: The genes involved form a transcription and translation network that is used to control gene expression and regulation.\\n\\n] | \n", + "0.91 | \n", + "404 | \n", + "
| 493 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-1 | \n", + "[ The genes in this list are largely related to mRNA and protein synthesis, nucleic acid binding and transport, and post-translational modification activities.\\n\\nMechanism: This list of genes likely represents the many steps involved in the synthesis and transport of proteins, from the initial transcription of mRNA and its associated splicing factors, to the polymerase activities, aminoacylation, and trafficking of proteins in and out of the nucleus and into the mitochondria.\\n\\n] | \n", + "[ \\nThe list of genes includes proteins that are involved in several processes, such as ribosome formation, RNA binding, DNA unwinding, nucleocytoplasmic transport, SUMO binding, mRNA splicing, nucleic acid binding, and protein acetylation.\\n\\nMechanism: \\nThese genes are enriched for proteins and processes related to gene expression, posttransslational modification of proteins, and protein synthesis. Through these processes, cells control the expression of genes, activate and inactivate proteins, regulate the cytoplasmic environment, and control the metabolism of macromolecules.\\n\\n] | \n", + "0.93 | \n", + "103 | \n", + "
| 494 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-0 | \n", + "[ The list of genes is associated with functions related to ribosome biogenesis, RNA binding and splicing, cell proliferation, cell cycle progression, and chromatin binding.\\n\\nMechanism: The list of genes is likely involved in the regulation and maintenance of ribosome biogenesis and cell proliferation through pre-rRNA processing, DNA replication-dependent chromatin assembly, and regulation of signal transduction.\\n\\n] | \n", + "[ \\n\\nSummary: This set of genes is involved in protein binding, transcriptional regulation, cellular processes such as cell cycle progression, protein chaperoning, and cell proliferation, nuclear localization, RNA binding activity, pre-rRNA processing, and ribosome biogenesis. \\n\\nMechanism: Many of the genes in this list encode proteins involved in pre-rRNA processing, ribosome biogenesis, transcriptional regulation, and protein binding activities that are fundamental in cell cycle progression and regulation of cellular processes.\\n\\n] | \n", + "0.94 | \n", + "118 | \n", + "
| 495 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-1 | \n", + "[ Genes from this list encode proteins that are involved in a variety of cellular processes, such as transcription, RNA processing, protein folding, DNA replication and repair, and cell cycle regulation. ] | \n", + "[ This list of genes encodes a number of proteins that are involved in RNA processing, nucleolar function, mitochondrial function, nuclear signaling and protein folding. The enriched terms include RNA binding activities, rRNA processing, protein homodimerization, cell proliferation, signal transduction, ribosome biogenesis, protein folding, and mitochondrial transcription factor activity. Mechanism: The underlying biological mechanism might involve a complex network of interactions involving proteins encoded by these genes, that lead to successful cellular processes such as ribosome biogenesis, RNA processing, mitogenesis, and protein folding. ] | \n", + "0.93 | \n", + "448 | \n", + "
| 496 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MYOGENESIS-0 | \n", + "[ \\nSummary: The list of genes contain genes related to motor protein activity, calcium signaling, muscle contraction, transcriptional regulation, intracellular fatty acid-binding, binding of ligands, and several other related processes.\\n\\nMechanism: Many of these genes encode electric conductance, actin filaments, and membrane proteins. They are involved in processes such as ion channels, muscle contraction, calcium sequestration and release, regulation of transcription, and phosphorylation of proteins. These processes occur in response to changes in the external environment or internal signals.\\n\\n] | \n", + "[\\nSummary: The list of genes consists of genes involved in various muscle functions, calcium level regulation and metabolic processes.\\nMechanism: The genes are involved in various cellular processes including ion channel regulation, energy metabolism, signal transduction, muscle contraction, and protein ubiquitination/degradation.\\n] | \n", + "0.94 | \n", + "270 | \n", + "
| 497 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_MYOGENESIS-1 | \n", + "[\\nOrganism metabolic pathways and protein regulation are enhanced in this group of genes. This enhancement includes increased ion channeling, cellular transport processes, lipid metabolism, and gene regulation. The pathways involve small and large molecules, as well as neurotransmitter signaling.\\n\\nMechanism: This group of genes works together to regulate metabolic processes in the organism, working at a cellular level that includes ions, lipids, proteins, and other molecules. The genes also interact to create networks of ion channels and transporter proteins that allow for efficient nutrient delivery, active metabolic pathways, and the regulation of gene expression.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "660 | \n", + "
| 498 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-0 | \n", + "[ \\nSummary: Genes related to the Notch and Wnt signaling pathways were found to be enriched in the gene data set.\\n Mechansim: Notch and Wnt pathways are key signalling pathways involved in cell fate decisions and development of organisms.\\n ] | \n", + "[ \\nSummary: This term enrichment analysis focused on fourteen human genes that are involved in regulation of cellular process via Notch and Wnt signaling pathways. \\n\\nMechanism: Through term enrichment analysis of these genes functions, it has been revealed they are involved in the regulation of cell fate decisions and transcriptional activity through the Notch and Wnt signaling pathways. \\n\\n] | \n", + "0.93 | \n", + "153 | \n", + "
| 499 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-1 | \n", + "[\\nThe given genes are involved in multiple cellular processes including Notch signaling pathways, cell-to-cell communication, transcription, protein ubiquitination, cell-cycle regulation, protein breakdown and turnover, and intracellular signalling pathways.\\nHypothesis: The given genes are part of a complex suite of processes which regulate cell fate, signalling, and control of intracellular signalling pathways. The genes are likely involved in establishing or inhibiting various combinations of pathways in response to internal and external stimuli.\\n] | \n", + "[ This list of genes is enriched for those involved in Notch signaling pathways, protein ubiquitination, cell fate determination, and transcriptional regulation.\\nMechanism: Multiple genes in this list have roles in the Notch signaling pathway and are involved in transcriptional regulation, ubiquitination, cell fate determination and other processes in order to control the cell cycle and cell division process. \\n] | \n", + "0.91 | \n", + "142 | \n", + "
| 500 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[\\nSummary: After performing a term enrichment test, it was found that the majority of the genes were involved in mitochondrial processes, as well as enzyme functions such as dehydrogenases and oxidoreductases, and ATP synthesis. \\nMechanism: This suggests that these genes are functioning on a systemic, metabolic level, and are involved in the overall production, usage and storage of energy within a cell.\\nConstructing a functional mitochondrion would likely require the activities of all these genes.\\n] | \n", + "[ This list of genes encode proteins that are involved in the metabolism of glucose, fatty acids, and amino acids by various catalytic steps and systems related to energy production in a cell. ] | \n", + "0.87 | \n", + "310 | \n", + "
| 501 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[\\n• The genes involved mainly involve enzymes and proteins involved in oxidation-reduction reactions, ATP synthesis, respiration, and metabolic processes in mitochondria \\n• Pathway and mechanism: The genes are involved in pathways related to mitochondria respiration, ATP synthesis, and metabolism of organic acids, such as oxidative decarboxylation and dehydrogenase reactions.\\n• ] | \n", + "[ Human genes on this list are found to be involved in a common pathway related to mitochondrial respiration, oxidative phosphorylation, and pyruvate metabolism related functions. The enriched terms from the term enrichment test are: terminal enzyme; ATP synthesis; mitochondrial respiratory chain; NAD/NADH-dependent; cytochrome c oxidase (COX); electron transport; PDH complex; ubiquitin protein; ferredoxin; acyl-CoA dehydrogenase; and pyruvate dehydrogenase. \\n\\nMechanism: The common pathway these genes have been found to be involved in is related to mitochondrial respiration, oxidative phosphorylation, and pyruvate metabolism. This pathway is mediated by oxidation-reduction reactions, in which electrons are transferred by the proteins being expressed. This transfer of electrons is used to produce ATP, an important source of energy for the cell. These proteins are also involved in other processes including fatty acid metabolism, electron transport, pyruvate metabolism, and ubiquitin protein metabolism.\\n\\n] | \n", + "0.92 | \n", + "636 | \n", + "
| 502 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_P53_PATHWAY-0 | \n", + "[ Human genes in this list are generally involved in cell cycle progression, transcription, signaling and regulation, protein synthesis and processing, and homeostasis. Specifically, enrichment of the terms \"cell cycle,\" \"transcription,\" \"signaling,\" \"protein synthesis,\" \"regulation,\" and \"homeostasis\" was observed.\\n\\nMechanism: These genes are likely involved in the creation, maintenance, duplication, and regulation of the complex network of proteins and processes occurring within cells, and the modulation of these processes in response to changes in the environment.\\n\\n] | \n", + "[\\n\\nSummary: Human gene functions related to cell cycle regulation, transcriptional regulation, protein binding, DNA binding, and cell signaling. \\nMechanism: Regulation of biological processes and pathways by association of proteins to various binding targets including proteins, DNA, and electron transfer. \\n] | \n", + "0.91 | \n", + "267 | \n", + "
| 503 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_P53_PATHWAY-1 | \n", + "[ Human genes related to cancer pathways, cell regulation and apoptosis\\nMechanism: Many of the human genes, when over-expressed, can drive the development of cancer through pathways, regulation of cell growth, and disruption of apoptosis, which is the process of programed cell death.\\n] | \n", + "[ \\nSummary: The majority of genes are involved in regulating protein synthesis, transcriptional regulation and cell cycle regulation.\\nMechanism: Regulation of protein synthesis, transcriptional regulation, cell cycle regulation, DNA repair and DNA binding.\\n] | \n", + "0.82 | \n", + "28 | \n", + "
| 504 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[COULD NOT PARSE] | \n", + "[\\n] | \n", + "0.79 | \n", + "14 | \n", + "
| 505 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[COULD NOT PARSE] | \n", + "[ The list of genes are expressed across various tissues, primarily in the pancreas, endocrine system, and brain. Other tissues expressed in these genes include: liver, intestine, kidney, and epithelium. They encode for proteins that are involved in transcriptional regulation, metabolic pathways, and cell signalling. This suggests an underlying biological mechanism related to transcriptional control and regulation of the endocrine system, pancreas, and glucose metabolism. The enriched terms for this list of genes include: transcriptional regulation; metabolic pathways; endocrine system regulation; glucose metabolism; cell signalling; GTPase; transcription factor; peptide hormone; ATP-binding cassette (ABC) transporter; and proprotein convertase. Mechanism: The list of genes suggest an underlying biological mechanism related to transcriptional control and regulation of the endocrine system, pancreas, and glucose metabolism. ] | \n", + "0.69 | \n", + "921 | \n", + "
| 506 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PEROXISOME-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The list of genes is enriched for proteins involved in the transport of various molecules and the enzymatic degradation of molecules across extra- and intra-cellular membranes (e.g. ATP-binding cassette transporters, oxidoreductases, dehydrogenases/reductases, hydratases/isomerases, enzymes responsible for fatty acid beta-oxidation, enzymes catalyzing the breakdown of malonyl-CoA, etc). Specific biological pathways or mechanisms of which the genes are a part involve cell adhesion, nucleotide excision repair, hormone metabolism and synthesis, nucleic-acid binding, antioxidant activity, and transcription factors. \\n\\nSummary: The list of genes is enriched for proteins involved in transport and enzymes that catalyze the degradation of molecules.\\nMechanism: Mechanisms of which the genes are a part involve cell adhesion, nucleotide excision repair, hormone metabolism and synthesis, nucleic-acid binding, antioxidant activity, and transcription factors.\\n] | \n", + "0.67 | \n", + "945 | \n", + "
| 507 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PEROXISOME-1 | \n", + "[ After performing a term enrichment test on the given list of genes, it can be seen that the functions of many of these genes are related to lipid metabolism and antioxidant functions, as well as DNA-related processes such as DNA repair, transcription and replication. Specifically, some of the enriched terms are lipid metabolism, fatty acid beta-oxidation, DNA repair, transcription and replication, oxidative stress, glutamate metabolism, vitamin A binding, and steroid metabolism.\\n\\nMechanism: The underlying biological mechanism of these gene functions is related to the homeostasis of vital cellular processes such as cell adhesion and signalling, protein production and degradation, regulation of mitochondrial and peroxisomal functions, and protection against oxidative damage. \\n\\n] | \n", + "[\\nSummary: Genes mentioned are found to primarily be involved in pathways that are related to oxidative stress and hormone response.\\nMechanism: These genes may be involved in oxidative stress, hormone signaling, or fatty acid metabolism.\\n] | \n", + "0.87 | \n", + "550 | \n", + "
| 508 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[ Summary: This gene list includes many genes involved in protein regulation and signalling with a heavy focus on serine/threonine protein kinase family.\\n Mechanism: Multiple genes listed play a role in the regulation of ubiquination, phospholipids, protein-protein interactions, transcription, and cell signalling.\\n ] | \n", + "[ \\nSummary: The majority of genes in this list encode proteins involved in signal transduction pathways and interact with other proteins via phosphorylation or protein-protein binding. \\nMechanism: Many of the gene products in this list are involved in signal transduction via phosphorylation, protein-protein interaction, GTP binding and/or cAMP binding. \\n] | \n", + "0.91 | \n", + "41 | \n", + "
| 509 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[\\nThe genes summarized in this list are involved in a wide range of functions, including those related to cell growth, cell cycle control, DNA binding, transcriptional regulation, signal transduction, and protein phosphorylation/dephosphorylation. The enriched terms refer to activity of signal transduction pathways and protein kinases such as members of the MAPK, RAS and G protein-coupled receptor (GPCR) families, as well as phosphatases, guanine nucleotide exchange factors, and endoplasmic reticulum chaperone proteins.\\n\\nMechanism: This list of genes is involved in signal transduction cascades, which involve proteins kinases and phosphatases modulating the expression of target genes by post-translational modifications, such as phosphorylation or ubiquitination of these proteins, as well as DNA binding and transcriptional regulation. \\n\\n] | \n", + "[\\nSummary: The genes listed mostly encode components involved in cellular signaling cascades, such as protein kinases, guanine nucleotide-binding proteins, receptor-interacting proteins and chaperone proteins.\\nMechanism: The listed genes appear to be involved in a variety of signaling cascades, such as those related to cell growth, transcription, cytokine production and protein modification.\\n] | \n", + "0.95 | \n", + "452 | \n", + "
| 510 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-0 | \n", + "[ \\n\\nSummary: The list of genes is associated with various roles in the endomembrane system, mainly playing roles in intracellular transport, vesicle formation, organelle biogenesis, lysosomal function, protein folding, GPCR-mediated signal transduction, and ligand-receptor complex trafficking.\\n\\nMechanism: Processes such as vesicle trafficking, lysosomal protein transport, GPCR mediated signal transduction, and organelle biogenesis are mediated by delivery of proteins to the correct cellular compartment via membrane proteins and complexes such as adaptins, SNAREs, GTPases, and the Golgi Apparatus.\\n\\n] | \n", + "[ \\n\\nSummary: Gene functions enriched for membrane-associated proteins, GTPases, coatomer complexes, vesicle trafficking, organelle biogenesis, phosphatidylinositol binding and regulation\\nMechanism: The gene functions are involved in the regulation, biogenesis and transport of intracellular organelles, membrane proteins and vesicles, as well as binding of phosphatidylinositol molecules.\\n] | \n", + "0.92 | \n", + "216 | \n", + "
| 511 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-1 | \n", + "[ Transmembrane proteins involved in transport, trafficking and organelle biogenesis are enriched amongst this gene list. \\nMechanism: The Enriched transmembrane proteins likely function as part of a complex network of molecular machinery involved in vesicle trafficking, docking and fusion of proteins, organelle biogenesis, and protein folding.\\nThe ] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "334 | \n", + "
| 512 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[\\n\\nSummary: All of the genes in the list are associated with molecules, enzymes, and proteins involved in cell metabolism and defense against oxidative stress.\\n\\nMechanism: The genes are involved in the regulation of pathways of cell energy metabolism and defense against oxidative stress, by providing key cellular components which participate at various levels of oxidation and reduction.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "375 | \n", + "
| 513 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[\\n\\nSummary: The human genes listed contain a variety of proteins that function in processes related to cell growth and development, redox regulation, DNA repair and transcription, response to oxidative stress and inflammation, cell cycle progression, and metabolism.\\n\\nMechanism: The functions of the proteins span a range of processes that are essential for cell survival, such as cell growth control, transcriptional regulation, redox regulation, and metabolism. These proteins may work together to regulate processes, such as glutamate-cysteine ligase activity, hydroxylase activity, protease activity, free-radical scavenging and protein phosphatase activity. \\n\\n] | \n", + "[\\n\\nSummary: This set of genes are mostly involved in redox processes, oxidative stress, DNA repair, and metabolism. These genes are involved in processes related to the regulation of cell growth, DNA repair, inflammation control, and cellular defense\\n\\nMechanism: The genes in this list are involved in a variety of functions that are necessary for cellular homeostasis and metabolic processes. Redox processes, oxidative stress, and damage control are mediated by a variety of proteins, such as heme oxygenase, glutathione reductase, superoxide dismutase, and glutathione peroxidase. DNA repair is regulated by proteins such as nucleotide excision repair complex and phosphofructokinase A. Inflammation control is regulated by proteins including myeloperoxidase, MAPEG family proteins, and glutaredoxin. Cellular defense against toxic and carcinogenic compounds is regulated by proteins such as glutathione S-transferase and peroxidase.\\n\\n] | \n", + "0.95 | \n", + "273 | \n", + "
| 514 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-0 | \n", + "[\\n\\nSummary: This term enrichment test on a list of human genes revealed several proteins and proteins related functions that are statistically over-represented.\\n\\nMechanism: This term enrichment test suggests that certain proteins and associated functions are involved in a wide variety of biological processes related to gene expression, transcription, and other aspects of cellular functioning. \\n\\n] | \n", + "[ Enriched terms shared by the genes include cell cycle regulatory proteins and kinases, DNA binding proteins and chaperones, nucleotide and polypetide biding proteins, phosphatases, and proteins involved in transcription. In particular, the genes function in gene transcription, chromosome organization, apoptosis regulation, DNA repair, protein folding and transport, cell signaling and growth regulation, energy metabolism, cytoskeletal organization, and vesicular trafficking. The underlying biological mechanism is likely involved in multiple steps in cell division and the regulation of gene expression, and in the maintenance of cell homeostasis.\\n\\nOerbaken: ] | \n", + "0.87 | \n", + "267 | \n", + "
| 515 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-1 | \n", + "[ \\nSummary: These genes are involved in diverse processes such as transcriptional regulation, cell cycle regulation, chromatin structure and nuclear envelope signaling, cell adhesion and motility, metabolic processes, protein folds and ubiquitination, detection, binding and enzymatic activities, and vasodilation.\\n\\nMechanism: These genes encode proteins that act as molecular adaptors, molecular chaperones, enzymes, transporters, transmembrane receptors, and other components in a variety of pathways and pathways.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.70 | \n", + "502 | \n", + "
| 516 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[ This list of genes is enriched for proteins involved in receptor signaling pathways and transcriptional regulation as well as cell signaling, adhesion and growth. These proteins can serve as part of complexes, act as enzymes, bind hormones, and influence cellular processes. \\nMechanism: Many of the genes identified in this list encode proteins in the TGF-Beta superfamily which are involved in the regulation of growth, differentiation and development, as well as apoptosis and transcription. These proteins work together in a complex network to regulate these cellular processes. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "570 | \n", + "
| 517 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[ \\n\\nSummary: The list of genes have been identified as members of various pathways related to the regulation of cell growth and differentiation, transcriptional regulation, receptor-regulated SMAD proteins, and signal transduction. \\nMechanism: The proteins encoded by these genes form different complexes, interact with various receptors, and function as transcriptional modulators, signal transducers, and ubiquitin ligases to regulate growth, differentiation and signaling pathways in cells.\\n] | \n", + "[ \\n\\nSummary: The 20 genes examined are primarily involved in signal transduction pathways, transcription regulation and cell-to-cell communication.\\nMechanism: The identified genes are involved in various signaling pathways, including the transforming growth factor-beta (TGF-beta), bone morphogenetic protein (BMP), and receptor-regulated SMAD pathways.\\n] | \n", + "0.94 | \n", + "140 | \n", + "
| 518 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[ The genes in the list can be grouped into two main categories: genes that encode proteins involved in transcription (e.g. FOS, EGR, IFNGR2, MYC, NFKB, REL, etc.), and genes that encode proteins involved in cytokine and inflammatory signalling pathways (e.g. IL1A, IL2B, IL7R, etc.). Mechanisms: Additionally, the genes in the list encode proteins that have a variety of roles in the regulation of cellular proliferation, apoptosis, and other processes in various cell types. ] | \n", + "[\\nSummary: The list of genes contain a range of proteins that are involved in transcriptional regulation, cytokine activity, regulation of cell proliferation, and lipid metabolism.\\nMechanism: The genes are involved in a range of biological processes related to transcriptional regulation, cytokine activity, regulation of cell proliferation, and lipid metabolism.\\n] | \n", + "0.90 | \n", + "113 | \n", + "
| 519 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[ Expression and regulation of multiple proinflammatory cytokines and chemokines, regulation and activity of kinases, transcription factors, and components of the TGF-beta, NF-kappa-B, MYC/MAX/MAD, Jagged 1 and STAT-regulated pathways, and regulation of lipoproteins and growth factors.\\nMechanism: These genes collectively comprise pathways and networks that regulate inflammation, cellular growth, cell differentiation, and apoptosis.\\n] | \n", + "[\\nThis list of human genes includes receptors, cytokines, proteins, transcription factors, enzymes, and growth factors involved in inflammation, signaling pathways, transcriptional regulation, and cell cycle control. \\nMechanism: The functions of the genes in the list are likely to be related to inflammatory responses, signal transduction, and cell cycle regulation and apoptosis.\\n] | \n", + "0.91 | \n", + "54 | \n", + "
| 520 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[ \\nSummary: A list of human genes involved in RNA-binding and protein-binding activities, along with protein metabolism, synthesizing and chaperone activity.\\nMechanism: The transcription factors and proteins help to regulate and stimulate gene expression and the protein folding process, which affects the synthesis and metabolism of proteins. This can lead to changes in cell function and structural integrity of cells.\\n] | \n", + "[ The genes in the list are involved in RNA processing and binding, transcription regulation, protein folding, targeting, covalent modifications and transport, endoplasmic reticulum function, and translation initiation. The enriched terms are RNA binding; transcription regulation; protein folding; protein targeting and covalent modifications; endoplasmic reticulum function; and translation initiation. Mechanism: The underlying biological mechanism for the enrichment of these terms is that the proteins encoded by the list of genes interact with each other to perform a variety of roles in RNA processing, transcription regulation, protein folding, targeting and covalent modifications, endoplasmic reticulum function, and translation initiation. These proteins can act as components of a larger complex or individually to perform these roles. ] | \n", + "0.90 | \n", + "427 | \n", + "
| 521 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[\\n\\nSummary: The list of genes are associated with endoplasmic reticulum (ER) processes, such as transcription factors, RNA binding proteins, protein folding and degradation, protein chaperones, mRNA decapping, and zinc transporter proteins. \\n\\nMechanism: The list of genes are involved in a wide range of endoplasmic reticulum (ER) processes such as post-translational modifications, translational regulation, RNA binding, protein folding, protein degradation, and protein trafficking.\\n\\n] | \n", + "[ Genes in the provided list are primarily involved in processes such as protein synthesis, endoplasmic reticulum stress response, RNA binding, and conformational folding.\\n\\nMechanism: These genes encode proteins that play a role in protein synthesis, cellular trafficking, conformational folding, and RNA binding. These processes are inter-related in that conformational folding is necessary for protein structure, protein expression is required for protein synthesis, and RNA binding is necessary for mRNA translation. The endoplasmic reticulum stress response allows for regulation of these processes.\\n\\n] | \n", + "0.93 | \n", + "119 | \n", + "
| 522 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-0 | \n", + "[ \\nSummary: Enriched terms from a list of human genes indicate that many of these genes are involved in cellular response regulation, cell surface receptors, signal transcription, signal transduction, phosphorylation, and calcium binding pathways.\\n\\nMechanism: The proposed underlying biological mechanisms involve regulation of gene expression and signal transduction through phosphorylation of proteins, downstream target proteins, and modulation of their function.\\n\\n] | \n", + "[\\nSummary: The genes in the list are involved in a wide range of processes, including cell surface glycoprotein binding, cell adhesion, phosphoprotein production, transcription regulation, and signaling pathways.\\nMechanism: Many of the genes are associated with signaling pathways, including calcium-dependent signal transduction, phosphorylation, MAP kinase signaling, PI3 pathways, and G-protein signal transduction.\\n] | \n", + "0.91 | \n", + "49 | \n", + "
| 523 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-1 | \n", + "[ \\n\\nSummary: The human gene list is enriched for terms related to signal transduction, extracellular matrix proteins, cellular adhesion, and transcription factors.\\n\\nMechanism: Signal transduction pathways, extracellular matrix proteins, and transcription factors increase cell activity and affect the regulation of gene expression.\\n\\n] | \n", + "[ This set of genes is enriched for terms associated with embryonic development, cell signaling, receptor regulation and transcription regulation. Specifically, genes related to transcription factors, receptors and their respective ligands, growth factors, phosphoproteins and kinases are overrepresented.\\n\\nMechanism: These genes are involved in a variety of different cell signaling pathways, which are essential for embryos to develop properly and become mature organisms. During embryonic development the signals which these enzymes and receptors transmit and respond to, such as hormones and growth factors, direct the development and differentiation of cells. Cells communicate with one another through these pathways and transcription factors to direct cellular activities such as proliferation, differentiation, growth, migration, as well as many other metabolic and physiological processes.\\n\\n] | \n", + "0.90 | \n", + "567 | \n", + "
| 524 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-0 | \n", + "[ \\nSummary: This list of genesí human functions mainly involve cell regulation, transmembrane transport, metabolic catabolism, and transcription support. \\nMechanism: These genes are involved in important pathways responsible for transportation and metabolic processes, as well as regulation of cellular functions.\\n] | \n", + "[ \\nSummary: The genes listed are involved in a variety of functions, including protein binding, catalysis of metabolic reactions, transcriptional regulation and regulation of cell signaling pathways.\\nCommonalities: \\nMechanism: Genes bearing similar functions may be involved in similar molecular or cellular processes, and the high level of overlap between gene function across the list implies a common pathway of regulation of certain activities in the cell, such as metabolic reactions and signaling pathways.\\n] | \n", + "0.91 | \n", + "199 | \n", + "
| 525 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-1 | \n", + "[ Our analysis revealed that these genes are primarily involved in cell signaling and membrane-associated functions, including protein binding, reaction catalysis, transporter activity, and GTP binding. Mechanism: The primary biological mechanism underlying this set of genes appears to be related to the regulation and control of cell signaling and membrane-associated functions in various cellular processes, including metabolism, replication and transcription, and cell growth and differentiation. ] | \n", + "[\\nThe list of genes shows enrichment related to enzymes, regulatory proteins, transcription factors, membrane and transport proteins, structural proteins, and other proteins involved in cell growth and development. Specifically, this list is enriched for genes that encode a diverse range of regulatory proteins involved in cellular signaling, transcription control, metabolism, and immune response. There is also enrichment for genes involved in the biosynthesis of heme, which is important in cellular apoptosis and other cellular processes. \\n\\nMechanism:\\nThe underlying biological mechanism involved in this term enrichment likely involves the regulation of various biochemical processes by macromolecular signaling pathways. The term enrichment most likely reflects the need of these genes to work together in order to carry out specific functions in cellular homeostasis and adaptation. \\n\\n] | \n", + "0.89 | \n", + "393 | \n", + "
| 526 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[\\n\\nSummary: A significant number of these genes are involved in the functioning of the Wnt signaling pathway, as well as cell cycle progression and gene transcriptional regulation.\\n\\nMechanism: Wnt signaling pathway controls cellular processes such as cell proliferation and migration, survival and cell differentiation, which involves a number of intercellular signalling pathways and Transcription Factor complexes.\\n\\n] | \n", + "[ The genes listed are involved mostly in processes and pathways related to embryonic development, transcriptional regulation, DNA repair, and cell-cell interactions, such as Wnt, Notch, and Hedgehog signaling, as well as the F-Box protein family. \\n\\nMechanism: The molecular mechanism of this list of genes is related to cellular signaling pathways that enable cells to interact and establish communication with each other for proper embryonic development, cell fate determination, and DNA repair. These pathways involve the use of proteins such as Notch, Wnt, and Hedgehog receptors and ligands, as well as the F-box proteins.\\n\\n] | \n", + "0.90 | \n", + "211 | \n", + "
| 527 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[ Through the analysis of gene summaries from the provided list, it is evident that genes playing a role in Wnt, Notch, and Hedgehog signaling pathways are enriched. The genes also appear to be involved in transcriptional regulation, cell cycle progression, and developmental events, as well as processes such as DNA replication and repair, transcriptional silencing, and proteasomal ubiquitin-dependent protein catabolism. It is possible that the mechanism involves the regulation of these pathways and their effects on various cellular functions. \\n\\nMechanism: This may involve the regulation of the Wnt, Notch, and Hedgehog signaling pathways and their effects on various cellular functions such as cell fate determination, DNA repair, transcriptional activation and repression, and protein catabolism.\\n\\n] | \n", + "[\\n\\nSummary: This list of genes contained members of the frizzled, notch, Wnt, Dickkopf, and histone deacetylase families, which are involved in various cell fate decisions and signaling pathways during embryonic development.\\n\\nMechanism: The enriched terms reflect the commonality of the genes in the list, which are all part of signaling pathways that influence cell fate decisions, including canonical Wnt pathway, Notch pathway, and Hedgehog pathway.\\n\\n] | \n", + "0.91 | \n", + "352 | \n", + "
| 528 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "T cell proliferation-0 | \n", + "[\\n\\nSummary: This list of human genes found in the summary have involvement in a variety of processes including cell division, adhesion, differentiation, and response to stress, in addition to roles in the immune system, transcriptional regulation, ligand binding, receptor binding, ubiquitin-protein ligase activity, phosphodiesterase activity, and protein phosphatase activity.\\n\\nMechanism: These genes are likely involved in multiple pathways and signaling mechanisms to regulate these various processes, likely involving kinases, transcription factors, adaptor proteins, and ubiquitin-protein ligases. \\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.70 | \n", + "590 | \n", + "
| 529 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "T cell proliferation-1 | \n", + "[\\nThe list provided of genes demonstrates significant enrichment of terms related to transcriptional regulation, cellular signaling pathways and processes, cell growth, differentiation, response to stress and to foreign material (via immune response), protein folding and trafficking, and recognition of self and non-self through various receptors. In the list there are mainly transcription factors, protein tyrosine phosphatases and kinases, several receptor families, and proteins for interleukin signaling. The underlying biological mechanism or pathway is likely related to the development and differentiation of cells and homeostasis or recognition of abnormalities or foreign materials.\\n\\n] | \n", + "[\\nThe list of genes is primarily involved in signal transduction and cell regulation, as well as immune defense, including cell recognition and protein phosphatase and ubiquitin binding activities. The underlying mechanism is likely regulated by protein and lipid enzymes, tyrosine and cGMP kinases, receptors, and transcription factors.\\n\\nMechanism: Signal transduction and cell regulation, mediated by protein and lipid enzymes, tyrosine and cGMP kinases, receptors, and transcription factors.\\n\\n] | \n", + "0.93 | \n", + "198 | \n", + "
| 530 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "Yamanaka-TFs-0 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE] | \n", + "1.00 | \n", + "0 | \n", + "
| 531 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "Yamanaka-TFs-1 | \n", + "[ \\nSummary: The genes KLF4, POU5F1, and SOX2 are transcription factors involved in embryonic development and stem cell maintenance, and are associated with tumorigenesis. \\nMechanism: Transcription factors control gene expression, which in turn controls embryonic development and stem cell maintenance, impacting tissue formation, tumorigenesis, and cell differentiation. \\n] | \n", + "[\\nSummary: This set of genes is related to development, stem cell maintenance, and tumor formation. \\nMechanism: These genes regulate gene expression in embryonic development and in adult tissues, controlling the G1-to-S transition of the cell cycle following DNA damage and mediating the tumor suppressor gene p53.\\n] | \n", + "0.91 | \n", + "57 | \n", + "
| 532 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "amigo-example-0 | \n", + "[ The majority of the gene functions encompass proteins involved in cellular adhesion, signaling pathways, extracellular matrix proteins, and components of the complement cascade. Gene products have roles in tissue development and regeneration, wound healing, immune hypersensitivity reactions, apoptosis, motility, and angiogenesis.\\n\\nMechanism: These genes are likely to be involved in multiple mechanisms related to homeostasis and wound healing, likely through cell-extracellular matrix binding and communication between cells through signal pathways.\\n\\n] | \n", + "[\\nSummary: This enrichment analysis of human genes suggests that these genes, or their encoded proteins, play a role in a multitude of processes including cell adhesion, signalling, metabolism, apoptosis, morphogenesis, hemostatsis, immunity and extracellular matrix maintenance.\\nMechanism: These genes are likely involved in modulating the interactions between cells and their macroenvironment and the modulation of cell-cell signalling pathways.\\n] | \n", + "0.92 | \n", + "108 | \n", + "
| 533 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "amigo-example-1 | \n", + "[\\nThis list of genes appears to be comprised of proteins involved in a variety of cellular activities related to cellular communication, extracellular matrix organization, cell adhesion, cell survival, and migration. Enriched terms include: Notch signaling pathway; osteoclast attachment/mineralized bone matrix; jagged 1/notch 1 signaling; cell adhesion; apoptosis; collagen fibril formation; antimicrobial peptide activity; lipoprotein metabolism; cell migration; extracellular matrix remodeling; cytotoxicity; chemotaxis; cytoplasmic signaling and phosphorylation; transcriptional repressor; odontogenesis; hematopoietic cell adhesion; serine protease inhibition; inward-rectifier potassium channels; and angiogenesis.\\n\\nMechanism: The underlying biological mechanism appears to involve a variety of cellular activities related to cellular communication, extracellular matrix organization, cell adhesion, cell survival, and migration, enabled by the expression and activity of these genes in different cellular pathways and networks.\\n\\n] | \n", + "[ The list of genes includes those involved in tissue development and repair, extracellular matrix components, signaling pathways such as the Notch signaling pathway and the cyclic AMP signaling pathway, cell survival, motility and migration, regulation of Fas-induced apoptosis, antimicrobial activity, transcriptional activation, and regulation of cell adhesion.\\n\\nMechanism: The underlying biological mechanism that is likely to be at play is the regulation of cellular activity and processes, including cell proliferation, cell migration, extracellular matrix formation, adhesion and signaling pathways for optimal tissue development and repair.\\n\\n] | \n", + "0.94 | \n", + "387 | \n", + "
| 534 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_0-0 | \n", + "[ This gene list represents genes with a wide range of functions involving membrane transport, growth factor regulation, and transcription regulation. Many of the genes are involved in ion channels and calcium and calcium-dependent processes. Mechanism: The genes are involved in a wide range of processes, including membrane transport, growth factor and calcium regulation, transcription regulation, and binding activity. ] | \n", + "[\\nSummary: The group of human genes in this list are related to the functions of ion regulation, transcription regulation, signal transduction, and protein binding.\\nMechanism: Many of the proteins encoded by these genes, involve important cellular functions such as signal transduction, cytoskeletal adaptor proteins, transcription factors, and glycoproteins. This suggests a mechanism for many of these genes as either directly or indirectly involved in signal transduction pathways and/or transcriptional modulation of cell processes.\\n] | \n", + "0.92 | \n", + "114 | \n", + "
| 535 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_0-1 | \n", + "[COULD NOT PARSE] | \n", + "[\\nSummary: This gene list is enriched for genes that enable or are associated with a variety of activities, including transcription factor activity, metal ion binding activity, DNA binding activity, chromatin binding activity, RNA binding activity, protein domain-specific binding activity, and histone or methylated histone binding activity.\\nPredicted Mechanism: The gene list is enriched for genes that facilitate a variety of cellular processes, such as binding activities, transcription and translation, transcription factor activity, receptor activity, and chromatin structure. This suggests a variety of molecular pathways are enriched in these genes, likely related to cell adhesion, cell surface receptor signaling, cell apoptosis, transcriptional regulation, and the regulation of chromatin structure.\\n] | \n", + "0.70 | \n", + "795 | \n", + "
| 536 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_1002-0 | \n", + "[ This list of genes is found in muscle tissue, and are involved in muscle formation, contraction, development, and cytoskeletal structure. These genes are involved in pathways of signal transduction, protein-protein interactions, and energy metabolism. ] | \n", + "[ \\n\\nSummary: This gene list is involved with various processes related to cell structures, cell motility and varying aspects of muscle contraction.\\n\\nMechanism: The genes in this list are involved in a variety of processes related to the structure and function of muscle cells, such as actin filament binding and regulation of the intracellular calcium concentration. They are also involved in processes related to regulating neuronal and epithelial cell activity.\\n\\n] | \n", + "0.91 | \n", + "211 | \n", + "
| 537 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "bicluster_RNAseqDB_1002-1 | \n", + "[ The list of genes and their functions suggests that these genes are involved in muscle development and regulation, actin and tropomyosin binding, calcium- and energy-regulation, ion channeling, and structural framework assembly and maintenance. In addition, they may be involved in negative regulation of cytokine signaling pathways and calcineurin-NFAT signaling cascade. The enriched terms include muscle development, actin and tropomyosin binding, calcium- and energy-regulation, ion channeling, negative regulation of cytokine signaling pathways, and calcineurin-NFAT signaling cascade.\\n\\nMechanism: These genes likely work together to ensure proper muscle development and maintenance by regulating calcium levels, energy homeostasis, and structural abundance of actin and other proteins in the muscle cells. The negative regulation of cytokine signaling pathways and calcineurin-NFAT signaling cascades could play a role in controlling the expression of these genes, allowing for the precise control of muscle development.\\n\\n] | \n", + "[ \\nSummary: This gene analysis reveals a number of proteins involved in skeletal and cardiac muscle contractile processes, such as actomyosin ATPase activity and tropomyosin binding activity.\\nMechanism: The proteins regulate muscle contraction in response to fluctuations in intracellular calcium concentration, while also playing a role in muscle differentiation and muscle organization.\\n] | \n", + "0.89 | \n", + "641 | \n", + "
| 538 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "endocytosis-0 | \n", + "[ These genes are involved in a wide variety of cellular processes and components, including endocytosis, protein transport, actin filament network formation, endoplasmic reticulum and recycling endosome membrane organization, macropinocytosis, cellular component organization, intracellular signaling, and protein homooligomerization. The associated processes of cell motility, cell differentiation, gene expression regulation, cell proliferation, stress and inflammatory responses, nuclear export, lysosomal degradation lipid homeostasis and apoptotic signaling form highly enriched terms in this gene set. Mechanism: The underlying biological mechanism or pathway is likely related to a combination of transmembrane and intracellular signaling. This signaling is likely to lead to cellular processes such as cell motility, cell differentiation, gene expression regulation, cell proliferation, stress and inflammatory responses, nuclear export, lysosomal degradation lipid homeostasis and apoptotic signaling. ] | \n", + "[\\nSummary: This set of genes functions in a variety of cellular processes such as endocytosis, cytoskeletal remodeling, lysosomal degradation, nuclear export, protein homooligomerization, actin filament network formation, plasma membrane bounded cell projection organization, endoplasmic reticulum formation, mitochondrial organization and cholesterol receptor-mediated endocytosis.\\nMechanism: The genes work together to regulate cellular processes in the cell such as protein trafficking, signaling pathways, and membrane reorganization. \\n] | \n", + "0.94 | \n", + "472 | \n", + "
| 539 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "endocytosis-1 | \n", + "[\\n\\nSummary: This list of genes encode adaptor proteins involved in cytoskeletal reorganization, vesicle trafficking, endocytosis, and mitosis, receptor-mediated endocytosis of specific ligands, cell adhesion processes, ubiquitin-protein ligase, and caspase-regulation of signaling complexes. \\nMechanism: The identified process involves the regulation of protein transport, endocytosis, receptor-mediated endocytosis, protein homooligomerization, cell adhesion, cell motility, amino acid residues, ubiquitination, fatty acid transport, cytoskeletal reorganization, vesicle trafficking, signaling complex regulation, mitosis, and caspase activation. \\n] | \n", + "[ A number of genes related to lysosomal degradation, receptor-mediated endocytosis, membrane-related processes, and endocytosis were identified. Proteins with death domain-folds, GTPase regulation, and ubiquitin-protein ligase activities were found to be recurrently present. \\n\\nMechanism: The gene functions identified are related to processes involved in the endocytosis and lysosomal degradation pathways which aid the movement of proteins and other molecules along the endocytic pathway. These processes involve specific processes such as receptor binding, GTPase regulation, ubiquitin-protein ligase and death domain-fold interactions. \\n\\n] | \n", + "0.89 | \n", + "6 | \n", + "
| 540 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "glycolysis-gocam-0 | \n", + "[\\nSummary: The genes provided in this list are all involved in glycolysis pathways and are associated with various forms of anemia.\\nMechanism: These genes encode proteins that catalyze glycolysis and the conversion of glucose to glucose-6-phosphate, the first step in carbohydrate metabolism. This metabolic process is involved in the production of energy and the regulation of cellular homeostasis.\\n\\n] | \n", + "[\\nSummary: The list of genes is involved in metabolic pathways, such as glycogenesis, glycolysis, phosphorolation and gluconeogenesis.\\nMechanism: These genes function in the conversion of energy sources, such as glucose and fructose, into energy sources used by the body.\\n] | \n", + "0.93 | \n", + "129 | \n", + "
| 541 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "glycolysis-gocam-1 | \n", + "[\\n\\nSummary: The list of genes provides a broad overview of glycolytic and related metabolic enzymes involved in muscle maturation and regeneration,hemolytic anemia and associated neurological impairments resulting from glycogen storage diseases and cancer development, as well as angiogenesis and regulation of the serine protease plasmin.\\n\\nMechanism: These genes are likely to be activating complementary pathways involved in glycolytic metabolism, muscle maturation and development, and angiogenesis.\\n\\n] | \n", + "[\\nSummary: Genes in this list are involved in various functions related to glycolysis, metabolism, and regeneration.\\nMechanism: The genes in this list appear to be involved in the regulation of metabolic pathways related to the conversion of sugar molecules to energy and the conversion of energy to other forms, including muscle development and tumor progression.\\n] | \n", + "0.93 | \n", + "139 | \n", + "
| 542 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "go-postsynapse-calcium-transmembrane-0 | \n", + "[\\nThe genes discussed are involved in various forms of calcium ion transport, regulation and channels, as well as postsynaptic ion channels and nicotinic acetylcholine receptors. \\n\\nMechanism: Calcium ion transport and regulation is an important biochemical mechanism in the body, with calcium ions being necessary for proper neuronal signaling, regulation of muscle contraction and other bodily processes. The genes discussed are involved in the active transport of calcium ions, including ATPases and GPCRs; as well as channels and receptors that respond to signaling molecules such as nicotinic acetylcholine and glutamate.\\n\\n] | \n", + "[ These genes encode proteins involved in calcium homeostasis, calcium-channel activity, and receptor function in cell membranes.\\nMechanism: The genes are involved in the biosynthesis and maintenance of calcium-related proteins, ion channels, and receptors, which are essential components to facilitate information flow and cell-signaling across cell membranes.\\n] | \n", + "0.91 | \n", + "265 | \n", + "
| 543 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "go-postsynapse-calcium-transmembrane-1 | \n", + "[ The genes identified in this list are primarily involved in calcium ion regulation and transport mechanisms, specifically related to the N-methyl-D-aspartate receptor family and its associated proteins. Mechanism: The gene functions are related to the regulation of calcium ions and their transport via a variety of proteins such as the N-methyl-D-aspartate receptor family, transmembrane AMPA receptor regulatory proteins (TARPs), dopamine receptors, and P-type primary ion transport ATPases. ] | \n", + "[ The gene summaries are related to ion channels and transmembrane proteins that play a role in calcium homeostasis, calcium influx, synaptic transmission, and neuronal development. These proteins frequently belong to the Purinergic receptor, NMDA receptor, and AMPA-receptor regulatory protein (TARP) families. Mechanism: The proteins act through their function as ion channels and transmembrane proteins in order to act as mediators of calcium-dependent processes in neuron cells. ] | \n", + "0.94 | \n", + "14 | \n", + "
| 544 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "go-reg-autophagy-pkra-0 | \n", + "[\\n\\nSummary: These genes are involved in various processes related to intracellular signaling pathways, cell cycle regulation, apoptosis, DNA repair, and immunity related GTPase family functions.\\n\\nMechanism: These genes are involved in the activation, regulation, or inhibition of protein kinases, caspases, and nuclear factor kappaB (NF-kB).\\n\\n] | \n", + "[ The genes provided are involved in several cellular pathways, including cell proliferation and survival, signal transduction, apoptosis, protein folding and DNA repair. There is an enrichment for genes involved in cell growth, apoptosis and signal transduction through serine/threonine kinase activator activity, phosphatidylinositol 3-kinase activity, and guanyl-nucleotide exchange factor activity. \\nMechanism: The genes appear to be involved in a variety of cellular pathways that are regulated by the AKT/PI3K and mammalian target of rapamycin (mTOR) signalling pathways. These signalling pathways mediate the activity of the genes by inducing cell growth and proliferation, and by regulating the expression of transcription factors such as NF-kappaB and TNFRSF11A/RANK.\\n\\n] | \n", + "0.91 | \n", + "435 | \n", + "
| 545 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "go-reg-autophagy-pkra-1 | \n", + "[COULD NOT PARSE] | \n", + "[ These genes are involved in functions related to DNA repair, apoptosis regulation, signal transduction, cell growth in response to nutrient and insulin levels, macromolecule metabolic process regulation, cell cycle control and chromatin remodeling. The common mechanism involved in each of the above is a signaling pathway regulated by protein kinases, phosphatases and protein acetyl transferases. \\n\\nMechanism: Signal transduction pathway is regulated by protein kinases, phosphatases and protein acetyl transferases.\\n\\n] | \n", + "0.68 | \n", + "506 | \n", + "
| 546 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[ Proteins encoded by the genes are involved in the degradation of polysaccharides and glycoproteins to produce basic sugars, the recognition and degradation of misfolded proteins by endoplasmic reticulum-associated degradation, and the hydrolysis of glycosaminoglycans and heparosan sulfate. ] | \n", + "[\\nSummary: Genes included in this list encode enzymes that hydrolyze glycosyl bonds and are involved in glycosylation processes, such as N-Linked Oligosaccharide, O-linked N-acetylglucosamine, and Polysaccharide processes.\\n\\nMechanism: Genes act as an important role in glycosylation processes by hydrolyzing glycosyl bonds and processing oligosaccharides, galactosides, glucosides, and other molecules containing glycosyl linkages.\\n\\n] | \n", + "0.89 | \n", + "140 | \n", + "
| 547 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[\\nThe human genes in the list share a commonality of them being glycohydrolase enzymes that manipulate glycosaminoglycans (GAGs), glycosyl hydrolases, and mannosidases. GAGs are long, unbranched polysaccharides which provide structural components to tissues and basement membranes. Lysozymes also appear in the list as well as amylases, which break down carbohydrates to simpler sugars, indicating a role in digestion. \\n\\nMechanism:\\nThis commonality likely reveals a role in the catabolism of carbohydrates and other glycosylated molecules via glycosidases, which break down the glycosidic bonds between saccharides and their non-carbohydrate moieties. Several endo/exoglycosidase enzymes are also mentioned, involved in the cleaving of glycosaminoglycans - this suggests that these enzymes may also play a role in cellular protein traffic and signaling, as certain molecules must travel from the endoplasmic reticulum, out of the cell, and into the extracellular matrix.\\n\\n] | \n", + "[ \\n\\nSummary: Genes listed are involved in glycosyl hydrolase, glycohydrolytic enzyme, and hyaluronidase activity.\\n\\nMechanism: Genes listed have enzymatic activity that catalyzes the hydrolysis of glycosyl and glycohydrolytic bonds in glycoproteins, glycolipids, glycosaminoglycans, and other molecules containing oligosaccharide or polysaccharide components.\\n\\n] | \n", + "0.92 | \n", + "612 | \n", + "
| 548 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "ig-receptor-binding-2022-0 | \n", + "[\\nAnalysis of the 20 human genes revealed a significant enrichment of terms relating to immunity, including antigen binding activity, immunoglobulin receptor binding activity, antibody production, adaptive immune response, and protein homodimerization.\\nMechanism: These genes enable immune system detection and responses to foreign antigens, as well as the recognition and binding of antigens and immunoglobulins. Through somatic recombination of genes, antigen recognition and specificity can be achieved, eventually leading to the production of antibodies.\\n] | \n", + "[ The genes listed are mostly related to immunoglobulin receptor binding activity and involved in immune system processes. The enriched terms in these genes are antigen binding activity, immunoglobulin receptor binding activity, activated/inactivated immune response, protein homodimerization activity, and peptidoglycan binding activity. Mechanism: The underlying biological mechanism or pathway depends on the particular gene, but they all relate to the recognition and interactions of antigens, the binding of the antigens to immunoglobulin receptors, and the subsequent activation or inhibition of the relevant immune response. ] | \n", + "0.94 | \n", + "74 | \n", + "
| 549 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "ig-receptor-binding-2022-1 | \n", + "[\\nSummary: Analysis of the genes indicates that they play an important role in immune system process, immunoglobulin receptor binding activity, and activation of immune response.\\nMechanism: The genes presented are involved in signaling pathways in which the binding of antigen to the cell surface stimulates a series of molecular events that lead to the activation of an immune response. \\n] | \n", + "[\\n\\nSummary: Several of the genes are involved in antigen binding activity, immunoglobulin receptor binding activity and activation of immune response.\\nMechanism: The genes function as part of a mechanism involving antigen and immunoglobulin receptor interaction and signaling pathways that lead to activation of immune responses.\\n] | \n", + "0.97 | \n", + "59 | \n", + "
| 550 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "meiosis I-0 | \n", + "[\\n\\nSummary: The enriched terms from this list of human genes are related to DNA repair and meiotic recombination, including activities such as endonuclease activity, Bcl-2 homology domain 3 binding, chromatin binding, DNA binding, DNA helicase activity, single-stranded DNA binding, 3'-5' exodeoxyribonuclease activity, SH3 domain binding, SUMO transferase activity, double-stranded DNA binding, RING finger ubiquitin ligase activity, replication fork processing, regulation of homologous chromosome segregation, meiosis I cell cycle process, chromosome synapsis, and homologous chromosome pairing at meiosis.\\n\\nMechanism: These proteins likely act in the repair and recombination of DNA during meiosis, by interacting with other proteins to form complexes that regulate meiotic recombination, chromosome condensation and chromatid separation. These proteins may also be involved in the relief of torsional stress upon DNA transcription and replication.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "938 | \n", + "
| 551 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "meiosis I-1 | \n", + "[ The list of genes provided describes proteins that are involved in several processes, such as meiotic recombination, DNA repair, chromosome segregation, double-strand DNA break repair, and homologous chromosome pairing. The enriched terms corresponding to these genes are meiotic recombination, DNA repair, chromosome segregation, double-strand DNA break repair, homologous chromosome pairing, DNA binding activity, and protein homotetramerization.\\n\\nMechanism: These gene are involved in the repair, pairing and segregation of chromosomes during meiosis and mitosis and the binding and processing of DNA. They interact with other proteins to form complexes which catalyze different types of DNA modification and repair, as well as with DNA through binding and bring about these changes. This interaction is likely necessary for the proper functioning of essential cell processes such as meiosis, mitosis, and DNA repair.\\n\\n] | \n", + "[ \\n\\nSummary: The human genes in this list appear to be associated with processes such as DNA double-strand break repair, meiosis, homologous chromosome pairing, and chromosome synapsis.\\n\\nMechanism: These genes likely play a role in homologous recombination, a key process in meiotic division and DNA double-strand break repair. The genes likely work together to form various complexes, such as the FA core complex, the APITD1/CENPS complex, and the CENPA-CAD (nucleosome distal) complex.\\n\\n] | \n", + "0.93 | \n", + "435 | \n", + "
| 552 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "molecular sequestering-0 | \n", + "[COULD NOT PARSE] | \n", + "[\\n\\nSummary: The list of genes has been analyzed, and include functions related to cell cycle progression, regulation of cell growth and survival, innate immunity, cholesterol and lipids metabolism, ubiquitination, antioxidant enzymes, intracellular transport, NF-κB inhibiting proteins, proteins associated with various inflammatory and neurological diseases, and proteins involved in embryogenesis, spermatogenesis, and hematopoiesis.\\n\\nMechanism: These genes are involved in a wide range of biological and biochemical processes that are related to cellular response, regulation of cell cycle progression, regulation of protein and lipid metabolism, protein ubiquitination, and intracellular transport.\\n\\n] | \n", + "0.69 | \n", + "688 | \n", + "
| 553 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "molecular sequestering-1 | \n", + "[ The provided genes are all involved in regulatory mechanisms related to genetic pathways and molecular interactions. They are involved in a variety of processes including cell cycle progression, transcription, metabolism, and immunity. A common function is providing a defense against microbial infections, toxic molecules, and apoptosis. A common mechanism is binding to and inhibiting partner proteins, often through phosphorylation.\\n\\nMechanism: The common mechanism of these genes is binding to and inhibiting partner proteins, often through phosphorylation, which allows for regulation of genetic pathways and molecular interactions.\\n\\n] | \n", + "[\\n\\nSummary: This group of genes are involved in a variety of cellular processes, including endocytosis, iron storage and transport, lipogenesis, apoptosis, cell proliferation and differentiation, defense from bacterial infection, and regulation of transcription and translation.\\n\\nMechanism: The proteins encoded by these genes are thought to act through regulating the expression and activity of proteins, such as transcription factors, caspases, lipids, and hormones, involved in these cellular processes.\\n\\n] | \n", + "0.88 | \n", + "133 | \n", + "
| 554 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "mtorc1-0 | \n", + "[ Genes related to the list are enriched for activities related to protein biosynthesis, transport and signaling, metabolism, and gene expression control. Mechanism: Genes related to the list are involved in integral processes of the cell, such as metabolism and gene expression control, which are facilitated by protein synthesis, transport and signaling. ] | \n", + "[ This list of human genes is enriched for functions related to cellular homeostasis, including protein synthesis, metabolism, protein folding, ubiquitination, transcription, DNA binding and damage control, development, and regulation of cellular pathways.\\n\\nMechanism: These genes are enriched for factors involved in various cellular processes necessary for maintaining homeostasis. These include protein synthesis, redox balance, fatty acid and energy metabolism, protein folding, ubiquitination, protein-protein interaction, transcription, and DNA damage control. In addition, these genes are enriched for factors that regulate various cellular pathways, including apoptosis, the cell cycle, and protein degradation.\\n\\n] | \n", + "0.92 | \n", + "364 | \n", + "
| 555 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "mtorc1-1 | \n", + "[ Enzymes that catalyze metabolic reactions, cell cycle regulation, and energy production. \\nMechanism: Enzymes involved in metabolic pathways, cell cycle regulation, and energy production pathways are encoded by the genes listed and are over-represented.\\n\\n] | \n", + "[ \\n\\nSummary: The genes under consideration encode many proteins involved in metabolic processes, signal transduction and signal reception, transcriptional and epigenetic regulation, chaperone and proteolytic activity, and cell cycle regulation. \\n\\nMechanism: Biological processes are driven through the action of proteins in biochemical reactions, many of which are regulated by signal transduction systems, transcriptional and epigenetic regulation, and involvement in metabolic pathways.\\n\\n] | \n", + "0.89 | \n", + "234 | \n", + "
| 556 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "peroxisome-0 | \n", + "[COULD NOT PARSE] | \n", + "[ This gene set contains a collection of genes involved in peroxisome biogenesis, and is associated with the various categories of peroxisome biogenesis disorders (PBDs). The genes included code for proteins that are essential for the assembly of functional peroxisomes and involved in the import of proteins into peroxisomes and peroxisome membrane vesicles, as well as the PTS1-type and PTS2-type tripeptide peroxisomal targeting signals and peroxisomal matrix proteins. The enriched terms are: peroxisome biogenesis; peroxisomal protein import; tripeptide peroxisomal targeting signal; peroxisomal matrix protein; AAA ATPase family; peroxisome integrity.\\n\\nMechanism: Peroxins are proteins that are essential for the assembly of functional peroxisomes. These genes are involved in activities associated with the assembly, biogenesis, and integrity of peroxisomes, and in regulating the peroxisomal targeting signals and matrix proteins to be imported into the organelle. \\n\\n] | \n", + "0.68 | \n", + "959 | \n", + "
| 557 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "peroxisome-1 | \n", + "[COULD NOT PARSE] | \n", + "[ \\nSummary: An enrichment test of the functions of five human genes (PEX6, PEX2, PEX3, PEX7, and PEX1) revealed a common theme of proteins associated with peroxisomal biogenesis disorders (PBDs) and proteins involved in peroxisomal import and matrix proteins.\\n\\nMechanism: The proteins encode AAA family ATPases, predominantly cytoplasmic proteins, and integral peroxisomal membrane proteins. These encode the receptor for the set of peroxisomal matrix enzymes targeted to the organelle by the peroxisome targeting signal 2 (PTS2). The proteins play a role in the import of proteins into peroxisomes, where they form a heteromeric complex, and also in peroxisome biogenesis.\\n\\n] | \n", + "0.71 | \n", + "659 | \n", + "
| 558 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "progeria-0 | \n", + "[ The list of human genes provided have a significant overlap between the proteins they encode and their effects on the maintenance of genome stability, DNA repair, replication, transcription, prelamin A proteolytic cleavage, DNA integration to the host cell genome, nuclear reassembly, and chromatin structure and gene expression. These involve mainly functions related to the nuclear membrane, chromatin, DNA and biogenesis, interaction and metabolism, as well as cellular processes involved in genetic architecture and gene expression. Furthermore, commonalities were identified between the associated diseases and characteristics, such as Werner Syndrome and mandibuloacral Dysplasia, Emery-Dreifuss muscular dystrophy, familial partial lipodystrophy, limb girdle muscular dystrophy, dilated cardiomyopathy, and Hutchinson-Gilford progeria syndrome.\\n\\nMechanism: The function of these genes and the diseases they affect involve a wide variety of cellular processes related to storage and identification of genetic information, stability and rearrangements of the nuclear architecture, gene expression and turnover, and production of specialized proteins. These involve complex interactions between various components of the nucleus and between other parts of the cell.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "1257 | \n", + "
| 559 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "progeria-1 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE] | \n", + "1.00 | \n", + "0 | \n", + "
| 560 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "regulation of presynaptic membrane potential-0 | \n", + "[ Our gene summary comes from a group of genes involved in a variety of neuronal functions including GABA, glutamate, and potassium receptor-related activities as well as ion channel function. This suggests that these genes are involved in a variety of roles related to neural communication and signaling. The common enriched terms from this gene set include \"neuronal signaling,\" \"neuron communication,\" \"ion channel,\" \"excitatory dependent channels,\" \"inhibitory neurotransmitter,\" \"ligand-gated ion channel,\" and \"G protein-coupled membrane receptor.\" Mechanism: The underlying biological mechanism relates to the role of the genes in providing the necessary components for neuronal signaling and information transfer. This includes roles in the formation of ligand-gated ion channels and G protein-coupled membrane receptors as well as the regulation of neurotransmitter release and excitability. ] | \n", + "[\\nSummary: The list of genes is related to ion channel gated ion channels and various neurotransmitters.\\nMechanism: The genes encode proteins responsible for mediating electrical signaling and transmitters of signals like glutamate, GABA, and potassium.\\n] | \n", + "0.93 | \n", + "647 | \n", + "
| 561 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "regulation of presynaptic membrane potential-1 | \n", + "[\\nThe genes in this list are involved in glutamate, GABA, and potassium channel related pathways found in the mammalian brain. Enriched terms include: neurotransmitter receptors (e.g. glutamate receptors, GABA receptors, potassium channels); ligand-gated ion channels; RNA editing; voltage-gated ion channels; channel subunits; channel polymorphisms; G-protein-coupled transmembrane receptors, etc.\\n\\nMechanism: Several of these genes encode for subunits of neurotransmitter receptor complexes, which suggest a mechanism for the modulation of synaptic transmission through the binding of agonists and antagonists that modulate the activity of the channels and facilitate the transport of ions across membranes. Additionally, some of the genes in this list play a role in the control of G-proteins and the regulation of heartbeat, suggesting that they may also be involved in regulating cell signalling pathways.\\n\\n] | \n", + "[\\nSummary: These genes are associated with a variety of neurological functions, including glutamate and GABA receptor activity, potassium channel activity, and N-methyl-D-aspartate (NMDA) receptor activity. \\nMechanism: The genes encode proteins involved in a variety of neurological functions, including ligand-gated ion channels, receptor ligands, and glutamate-gated ionic channels. \\n] | \n", + "0.95 | \n", + "526 | \n", + "
| 562 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "sensory ataxia-0 | \n", + "[\\nSummary: These genes are associated with functions related to development and maintenance of the nervous system, sensory systems, and erythropoiesis, as well as mitochodnrial mRNA synthesis and transcriptional regulation. \\n\\nMechanism: These genes regulate post-translational processes including ubiquitination and processing, protein synthesis, transcription and activity of transcription factors, and organization of the cytoskeleton and nucleus.\\n\\n] | \n", + "[\\n\\nSummary: List of genes are involved in transcription factors, degradation heparan sulfate, moonlighting proteins, immunoglobulin secretion, adapter or docking molecule, heme transporter, myelin upkeep, nuclear pore complex, mitochondrial DNA polymerase, ubiquitin ligase, and aminoacyl-tRNA synthetase.\\n\\n] | \n", + "0.87 | \n", + "144 | \n", + "
| 563 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "sensory ataxia-1 | \n", + "[ Genes in this list are involved in transcriptional, structural and signaling pathways that are related to maintaining the structure and function of peripheral nerve cells, including Schwann cells and myelin sheath maintenance.\\n\\nMechanism: Transcriptional, structural, and signaling pathways in peripheral neurons play a key role in maintaining nerve cell health and homeostasis.\\n\\n] | \n", + "[ The analyzed gene summaries demonstrate enrichment of terms related to peripheral nerve and muscle function. Specifically, these include terms such as transcription factor, DNA helicase, nerve myelin maintenance, mechanically-activated cations channels, nerve motor neuron survival, and ubiquitination. \\n\\nMechanism: These genes appear to work together in a variety of ways to regulate transcription and the structural integrity of proteins in the peripheral nervous system, as well as regulate motor neuron and myelin maintenance, which contribute to nerve impulse transmission. \\n\\n] | \n", + "0.92 | \n", + "201 | \n", + "
| 564 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "term-GO:0007212-0 | \n", + "[ This gene set encodes many G-protein coupled receptors involved in signal transduction from extracellular signals to intracellular responses. Mechanism: G-protein coupled receptor signaling pathways initiate transmembrane signal transduction in response to hormones, neurotransmitters, and sensory signals by regulating adenylyl cyclase, phospholipase C-beta, and other downstream effectors. ] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "378 | \n", + "
| 565 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "term-GO:0007212-1 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE] | \n", + "1.00 | \n", + "0 | \n", + "
| 566 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "tf-downreg-colorectal-0 | \n", + "[ The list of human genes includes proteins that play a role in transcriptional regulation, chromatin remodeling, and DNA binding. The mechanism likely involves transcriptional coactivators and transcription factors forming heterodimers to bind to enhancers and promoters at specific response elements. ] | \n", + "[ This list of genes is enriched in terms related to transcription regulation, cellular organization and tissue development. Specifically, genes are enriched for functions related to DNA-binding, chromatin-binding, transcriptional regulation, bind to E-box DNA consensus sequence, regulation of DNA damage response, DNA damage response maintenance, phosphoprotein shuttling, zinc finger motifs, interaction with cellular retinol-binding proteins, hormone-dependent transcription, receptor-dependent transcription, nuclear hormone receptor-dependent transcription, transcriptional coactivator complex recruitment, chromatin remodeling complex formation, and transcriptional activator complex formation. The mechanism likely involves the formation of heterodimers, protein complexes, and chromatin regulators.\\n\\n] | \n", + "0.93 | \n", + "506 | \n", + "
| 567 | \n", + "text-davinci-003 | \n", + "narrative_synopsis | \n", + "tf-downreg-colorectal-1 | \n", + "[\\nThe human genes analyzed in this term enrichment test were associated with functions such as transcriptional regulation, chromatin remodeling, DNA-binding, and zinc-finger binding. These genes were found to be enriched for terms related to transcription factor regulation of gene expression, chromatin modification, and DNA-binding activity.\\n\\nMechanism: These genes are a part of pathways responsible for the regulation of gene expression. The encoded proteins function as transcription factors, ligands, and chromatin remodelers which bind to DNA, interact with other transcription factors, and promote or inhibit the transcription of genomic regions. Zinc-finger binding, SUMO binding, and retinoid X receptor responsive element binding are also important regulators of gene expression and are involved in this term enrichment test.\\n\\n] | \n", + "[\\nThis list of human genes is mainly related to transcriptional regulation, chromatin remodeling, and DNA-binding activities. Enriched terms include transcriptional regulation, DNA-binding, chromatin binding activity, histone binding activity, and transcription factor activity. These genes are associated with various cellular processes including cell cycle progression, apoptosis, gene transcription, transcriptional activator/repressor activity, protein chaperoning, cell differentiation, DNA damage response, and transcriptional enhancement. The underlying biological mechanism of these genes is related to the regulation of gene expression as well as its downstream gene expression, which is further regulated by transcription factor signaling pathways, chromatin remodeling, and post-translational modification activities.\\n\\nSummary: This list of human genes is mainly related to transcriptional regulation, chromatin remodeling, and DNA-binding.\\nMechanism: These genes are associated with various cellular processes and are regulated by transcription factor signaling pathways, chromatin remodeling, and post-translational modification activities.\\n] | \n", + "0.94 | \n", + "316 | \n", + "
| 568 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "EDS-0 | \n", + "[ The nine genes are associated with extracellular matrix (ECM) components and their regulators. Mechanism: The proteins coded by these genes could be involved in the regulation of the expression of ECM components, which can contribute to the formation of the physical integrity of the ECM and its interaction with the cellular environment. ] | \n", + "[\\n\\nSummary: The genes in the list are associated with a broad range of functions involved in skeletal development, collagen production and other extracellular matrix processes.\\n\\nMechanism: The mechanism appears to involve different genes acting on multiple pathways related to the synthesis, remodeling, and maintenance of extracellular matrix components.\\n\\n] | \n", + "0.90 | \n", + "16 | \n", + "
| 569 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "EDS-1 | \n", + "[ This list of genes is enriched in proteins involved in the Extracellular Matrix (ECM) protein network, which is a component of the larger Cell Adhesion and Morphogenesis (CAM) pathway. Specifically, the genetic list is enriched for components involved in the processes of collagen fibril formation, collagen fibril organization, extracellular matrix (ECM) protein network assembly, ECM protein network stabilization, epidermal cell fate commitment, epithelial tube growth and branching morphogenesis, collagen modification and deposition, and zinc-finger protein motif binding.\\n\\nMechanism: The ECM protein network mediates cell-cell and cell-matrix interactions in order to regulate the adhesive, motile, and proliferative states of cells. It consists of a variety of molecules, including ECM proteins, which serve as substrates to guide cell migration, growth and differentiation. ECM proteins are those that contain one or more structural domains capable of interacting with the ECM components, such as extracellular domains, as well as those containing adhesive domains. \\n\\n] | \n", + "[ The genes listed above are associated with various development processes and tissue formation, such as collagen production, connective tissue development, matrix remodeling, and zinc finger protein regulation.\\nMechanism: The underlying known mechanism is the combination of transcriptional regulation and post-translational modification of the proteins encoded by these genes.\\n] | \n", + "0.89 | \n", + "699 | \n", + "
| 570 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "FA-0 | \n", + "[COULD NOT PARSE\\nHypothesis: The genes in this list are likely involved in the regulated repair of DNA double strand breaks due to replication-mediated damage, with the coordinated action of the Fanconi Anemia protein complex and the shared components of the ubiquitin ligase complex.] | \n", + "[ The list of genes is significantly and specifically associated with homologous recombination and DNA repair, as evidenced by an enrichment in terms related to these processes, such as \"dna repair\", \"homologous recombination\", \"excision repair\", and \"nuclease activity\".\\n\\nMechanism: The genes in this list are involved in a variety of DNA repair activities, such as excision repair and homologous recombination. These processes are important for maintaining the correct sequence of DNA and avoiding mutations that can lead to disease. \\n\\n] | \n", + "0.85 | \n", + "253 | \n", + "
| 571 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "FA-1 | \n", + "[ Several genes involved in DNA repair and homologous recombination processes, such as FANCL, RAD51C, FANCE, MAD2L2, ERCC4, FANCA, BRCA2, FANCF, XRCC2, BRIP1, FANCD2, SLX4, FANCB, FANCG, UBE2T, RAD51, PALB2, and FANCC, were observed to be statistically enriched for terms related to DNA damage recognition and repair, DNA damage response, and homologous recombination processes.\\n\\nMechanism: These genes enable the cellular response to double-stranded breaks (DSBs) by providing components of the DNA damage recognition and repair variety. They also function in the homologous recombination pathway for DNA repair, which is used for error-free repair of damaged DNA strands. \\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "660 | \n", + "
| 572 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ADIPOGENESIS-0 | \n", + "[ Enrichment analysis of this list has revealed that many of the genes are involved in energy metabolism and fatty acid metabolism, such as ATP1B3, ACOX1, ACADM, SLC19A1, SLC25A10, PGM1, UCP2, GPX3 and GPX4. They are also related to adipogenesis, with genes such as ADIPOR2, APLP2, LEP, ADIG and ADIPOQ. Lastly, several of the genes are involved in cholesterol and bile acid synthesis, such as DHCR7, DHRS7, CYP4B1 and HMGCR.\\n\\nMechanism: The genes identified as being involved in energy metabolism and fatty acid metabolism appear to share a common mechanism in which these molecules are generated from multiple sources to form energy. The genes involved in adipogenesis appear to be related to the regulation and development of fat cells and adipose tissue. Similarly, the genes involved in cholesterol and bile acid synthesis appear to be related to the synthesis of these molecules from multiple sources.\\n\\n] | \n", + "[ \\nSummary: A term enrichment test on the above list of genes based on biological classification hierarchies has identified terms related to metabolic and cellular functions that are statistically over-represented.\\nMechanism: These commonalities likely indicate a shared pathway, mechanism or process as related to metabolic and cell regulation functions.\\n] | \n", + "0.85 | \n", + "553 | \n", + "
| 573 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ADIPOGENESIS-1 | \n", + "[ This term enrichment test revealed a group of genes associated with energy metabolism, regulation of cell death, cell proliferation and signaling, DNA replication/remodeling, RNA processing, and lipid metabolism.\\nMechanism: This group of genes may be involved in binding, regulating, or expressing other proteins in order to influence the cell's metabolic and signaling status. \\n] | \n", + "[\\nSummary: This list of genes are mainly involved in energy metabolism and signal transduction. \\nMechanism: The genes in this list form a biochemical pathway responsible for the production of energy and for the detection and execution of cellular signals.\\n] | \n", + "0.90 | \n", + "125 | \n", + "
| 574 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[ This enrichment test examines a list of 73 human genes and reveals enrichments for the functions related to cell surface molecules, cytokines, immunology, receptor signalling, transcriptional regulation and apoptosis.\\n\\nMechanism: These genes are involved in a variety of pathways that include cytokine signaling, cell surface molecules, transcriptional regulation, apoptosis, and receptor signaling.\\n\\n] | \n", + "[ Genes related to the list are largely enriched for immune signalling/activation, regulation of cell cycle and differentiation, and transcriptional regulation.\\nMechanism: This likely indicates involvement of these genes in the processes of immune signalling, development or tissue remodelling, and metabolic regulation.\\n] | \n", + "0.88 | \n", + "82 | \n", + "
| 575 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[ This analysis results in the enrichment of genes functions related to immune system regulation, including antigen presentation, signaling, B and T cell metabolism, cytokine production and chemotaxis. Mechanism: The genes identified in this list are involved in controlling a range of processes that are necessary for proper immune system functioning, such as antigen presentation, signaling pathways, metabolizing T and B cells, production and secretion of cytokines, and chemotaxis of immune cells. These functions are necessary for the body to defend itself against pathogens. ] | \n", + "[COULD NOT PARSE\\nHypothesis: It is likely] | \n", + "0.72 | \n", + "539 | \n", + "
| 576 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE] | \n", + "1.00 | \n", + "0 | \n", + "
| 577 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[ \\nSummary: The genes are enriched in terms related to regulation, signaling, and metabolism.\\nMechanism: The genes are likely to be involved in molecular mechanisms governing cellular activities and pathways, with signaling pathways such as Wnt, MAPK, and PKA pathways playing an important role. \\n] | \n", + "[ \\nThe genes provided are significantly enriched in terms related to gene transcription and regulation, protein translation and metabolism, cytoskeletal organization, and lipid metabolism.\\nMechanism: These genes are likely to be involved in the regulation of genetic expression, transcriptional regulation, protein translation and metabolism, improvement of cell structure, and lipid metabolism. \\n] | \n", + "0.93 | \n", + "100 | \n", + "
| 578 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ANGIOGENESIS-0 | \n", + "[ \\n\\nSummary: A set of 34 genes related to extracellular matrix formation and maintenance, fibrous tissue development, vascular development, and extracellular secreted signaling. \\n\\nMechanism: Together, these genes encode proteins involved in multiple signaling pathways to regulate the development, maintenance and repair of the extracellular matrix (ECM), including fibrous, collagen, and laminin-fibrillin proteins, along with proteins involved in vascular regulation, cell-cell communication and migration, and extracellular secreted signaling molecules. \\n\\n] | \n", + "[ The list of gene terms are involved primarily in cell communication processes like extracellular matrix organization, adhesion, and cell surface interactions. Specifically, they encode proteins involved in the aggregation of endothelial cells and vascularization processes. Mechanism: The proteins encoded by the genes in the list are likely involved in regulating the growth, development, extracellular environment, and adhesiveness of cells. ] | \n", + "0.89 | \n", + "113 | \n", + "
| 579 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ANGIOGENESIS-1 | \n", + "[ Genes in this list are primarily associated with development, vascular remodeling and cell-cell communication.\\nMechanism: These genes likely play a role in various aspects of development, including morphogenesis, tissue development, extracellular matrix organization, inflammation, vascular remodeling and cell-cell communication.\\n] | \n", + "[ \\n\\nSummary: This list of genes appears to be involved in growth and morphogenesis of cells, including development of muscle, bone, and neuronal networks. \\nMechanism: Growth appears to be mediated by signals from cytokines and hormones, most notably VEGFA and PDGF, and mediated by transmembrane and extracellular matrix proteins, including LUM, VTN, and S100A4.\\n] | \n", + "0.89 | \n", + "30 | \n", + "
| 580 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-0 | \n", + "[COULD NOT PARSE] | \n", + "[\\nThis list of genes is related to development, tissue morphogenesis, contractile organs, extracellular matrix and cytoskeletal proteins. Enriched terms include bone, joint, muscle and connective tissue development; cell adhesion; adhesion receptor complex formation; signal transduction; and receptor-mediated signaling cascades.\\n\\nMechanism:\\nThese genes likely act together to facilitate the intricate networks of molecular and cellular pathways involved in development, homeostasis, and tissue repair. These include extracellular matrix formation and remodeling; cell adhesion; and signaling pathways associated with cell migration, proliferation, differentiation, and growth. The genes may work in tandem to promote changes in gene expression, stability, and intercellular communication involved in development and tissue repair processes.\\n\\n] | \n", + "0.69 | \n", + "829 | \n", + "
| 581 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-1 | \n", + "[\\nSummary: The genes in this list are involved in a wide variety of processes, including development, growth, morphology, and molecular signaling.\\nMechanism: These genes appear to be involved in the regulation of cellular processes by mediating signals that modulate development, growth and morphology.\\n] | \n", + "[ Our term enrichment analysis of the list of genes provided revealed statistically over-represented terms in gene function associated with cell adhesion, cell migration, migration and interaction, cytoskeletal organization, actin cytoskeletal regulation, signaling pathways, and regulation of the actin cytoskeletal organization. \\nMechanism: These results suggest that the underlying biological mechanism likely involves cytoplasmic signaling and regulation of the cytoskeletal organization, which would provide mechanical integrity to the cells, their adhesion to neighboring cells, and their migratory ability. This is supported by the evidence that many of the enriched terms relate to cell adhesion, migration and interaction, and cytoskeletal organization.\\n] | \n", + "0.84 | \n", + "460 | \n", + "
| 582 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_SURFACE-0 | \n", + "[\\nSummary: The list of genes provided is enriched for terms relating to cell migration, membrane receptor signaling, and glycoprotein metabolism.\\nMechanism: These gene functions serve to coordinate cell migration and receptor-mediated signaling, as well as metabolism. \\n] | \n", + "[ The list of genes is enriched for terms related to cell regulation, signal transduction, cell adhesion, protein folding, extracellular matrix organization.\\nMechanism: The list of genes are likely involved in a variety of cell regulation mechanisms such as activating responses to extracellular signals, influencing protein folding and assembly, regulating cell adhesion, and mediating phosphorylation cascades. \\n] | \n", + "0.91 | \n", + "144 | \n", + "
| 583 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_APICAL_SURFACE-1 | \n", + "[\\nSummary: The genes provided are involved in diverse biological pathways related to cell signaling, development, transcription, and metabolism.\\nMechanism: The genes likely represent an underlying biological mechanism that is involved in cellular proliferation and the regulation of gene expression.\\n] | \n", + "[ This list of genes appears to be involved in the development and maintenance of various organs, tissues and cellular processes. Specifically, enriched terms for this gene list include cell adhesion and migration; cell signaling; cell differentiation; protein kinase and phosphatase activities; transcription and DNA metabolism; immunomodulation; glycosylation and carbohydrate metabolism; and cell growth and proliferation. \\n\\nMechanism: The genes in this list play a role in a variety of molecular mechanisms that are important for normal development and tissue homeostasis. On the molecular level, these genes are involved in cell-cell adhesion, translation and translation regulation, signal transduction, and other processes. Moreover, the genes in this list regulate the expression of various cellular receptor, kinase, and phosphatase pathways, which may lead to downstream changes in cell growth, proliferation, and differentiation. \\n\\n] | \n", + "0.91 | \n", + "643 | \n", + "
| 584 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_APOPTOSIS-0 | \n", + "[ The list of human genes given is statistically significantly enriched for the gene functions of transcriptional regulation/control, cell-cycle/apoptosis, and immune responses.\\nMechanism: The genes listed encode proteins involved in transcriptional regulation through control pathways such as the activation of caspases, the inhibition of cyclin-dependent kinase activity, and the upregulation of apoptosis-related proteins. They also encode molecules involved in immune-related processes such as the binding and activation of proinflammatory cytokines, the formation of interferon gamma receptor complexes, and the regulation of major histocompatibility complex class I molecules. \\n] | \n", + "[\\n\\nSummary: The human genes provided in this list are mainly related to apoptosis, transcription, cell cycle progression, and inflammation.\\nMechanism: These genes likely act together to execute pathways related to the regulation of cell growth and maintenance, DNA replication and repair, oxidative stress response, and immune system activation.\\n] | \n", + "0.94 | \n", + "338 | \n", + "
| 585 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_APOPTOSIS-1 | \n", + "[COULD NOT PARSE] | \n", + "[ This list of genes is enriched for terms related to cell death regulation, inflammation, immune reaction, and growth and morphogenesis, which is a mechanism indicative of homeostasis in several biological functions.\\t\\n\\nMechanism: Expression of these genes contributes to cell survival by regulating the balance between cell death and survival, restraint of pro-inflammatory responses and activation of pro-inflammatory responses, promoting expression of genes involved in innate and adaptive immune responses and playing a part in promoting tissue growth, remodeling and morphogenesis. \\n\\n] | \n", + "0.68 | \n", + "573 | \n", + "
| 586 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[\\nSummary: The genes listed are enriched in terms related to metabolic pathways, lipid transport, and development of connective tissues.\\nMechanism: The functions of the genes appear to involve a number of metabolic pathways, such as fatty acid and bile acid synthesis, xenobiotic metabolism, and steroidogenesis, as well as pathways related to cellular transport and signaling, including those related to lipid transport and receptor-mediated signal transduction.\\nIn addition, several of the genes are involved in connective tissue formation, as well as development of digits and limbs.\\n] | \n", + "[ This list of genes is enriched for functions related to lipid metabolism and transport, development of vital organs, and cell signaling pathways.\\nMechanism: The enrichment of these genes suggests roles in cellular metabolic processes such as breakdown, transport, and synthesis of lipids, as well as cell-signaling pathways involved in development of vital organs such as liver, heart, and brain. \\n] | \n", + "0.95 | \n", + "187 | \n", + "
| 587 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[COULD NOT PARSE] | \n", + "[ A large proportion of the genes provided are involved in lipid and fatty acid metabolism, including the movement and processing of lipids, such as through cytochrome P450 superfamily enzymes, hydroxyacyl-CoA dehydrogenases, SLCO1A2, FADS2 and SLC27A2. As well as lipid metabolism, genes are also enriched for other metabolic processes, such as glutamate metabolism (IDH1, 2, HSD17B6) and serine metabolism (SERPINA6 and PIPOX). In addition, there are genes associated with the regulation of transcription factors, including RXRA, LCK, and optineurin, as well as those involved in oxidative stress (SOD1, CTH, PNPLA8).\\n\\nMechanism: The enriched terms implicate a cross-regulatory and potentially inter-linked metabolic network involving lipid, fatty acid and disulphide bridge metabolism, with potential connections to oxidative stress response and gene expression regulatory mechanisms. \\n\\n] | \n", + "0.69 | \n", + "874 | \n", + "
| 588 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[COULD NOT PARSE] | \n", + "[\\nSummary: A number of genes involved in lipid and cholesterol metabolism, cell signaling and regulation, development, cell adhesion, apoptosis and transcription have been identified.\\nMechanism: Genes associated with lipid and cholesterol metabolism are involved in regulating the synthesis, degradation and transport of lipids, while genes associated with cell signaling and regulation are involved in regulating cell growth, differentiation and apoptosis. Additionally, genes related to development, apoptosis, and transcription act in the regulation of cell adhesion, differentiation and development.\\n] | \n", + "0.67 | \n", + "588 | \n", + "
| 589 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[\\nSummary: The genes populated are predominantly involved in lipid metabolism (eg. HMGCR, PMVK, FDPS), transcription regulation (eg. ACTG1, NRAF), cellular adhesion (eg. CD9, ANXA13, COUNTY), and other development related processes (eg. S100A11, MVD, IDI1).\\nMechanism: The genes are associated with a number of different functions but are likely involved in maintaining cellular homeostasis, regulating transcription, and participating in development processes.\\n] | \n", + "[ Proteins involved in lipid and lipid metabolism pathways, related to cholesterol control.\\nMechanism: Proteins involved in cholesterol regulation, such as HMGCR, PMVK, FADS2, SREBF2, S100A11, and MVK are likely to be involved in the upregulation and modulation of cholesterol levels. These proteins regulate the breakdown of fatty acids and also mediate the synthesis of bile acids, both of which are important in cholesterol metabolism. ] | \n", + "0.89 | \n", + "23 | \n", + "
| 590 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_COAGULATION-0 | \n", + "[\\nSummary: Several of the human genes on this list play a role in extracellular matrix formation, inflammatory response, and proteolytic activities.\\nMechanism: The common functional mechanisms included in this term enrichment test are the regulation of the inflammatory response, regulation of extracellular matrix formation, and proteolytic activities.\\n] | \n", + "[ Genes in this list represent functions related to extracellular matrix remodeling, angiogenesis and vascular development, immune response and platelet activation, collagen and fibronectin metabolism and regulation, and endocytosis and signal transduction.\\n] | \n", + "0.89 | \n", + "96 | \n", + "
| 591 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_COAGULATION-1 | \n", + "[\\nSummary: The genes identified are predominantly involved in matrix molecular regulation, pathways related to proteolysis and coagulation, signal transduction, and extracellular matrix organization.\\nMechanism: The genes act as regulators of specific molecular functions and as mediators of signal transduction pathways. The identified genes are likely involved in the processing and remodeling of the extracellular matrix because of their relation to proteolysis and other matrix-related functions.\\n] | \n", + "[ The term enrichment test suggests that proteins involved in cell adhesion, proteolysis regulation, and interactions between extracellular proteins and cells are significantly enriched in this gene list. \\n\\nMechanism: These proteins likely act together in a coordinated manner to modulate cell adhesion, proteinase activity, and communication between cells. \\n\\n] | \n", + "0.86 | \n", + "141 | \n", + "
| 592 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_COMPLEMENT-0 | \n", + "[\\nSummary: These genes are enriched in functions related to extracellular matrix organization, immune system/inflammation/interferon response, and transcription factor activity.\\nMechanism: These genes could be involved in a pathway that is responsible for coordinating and controlling aspects of extracellular matrix organization, immune system/inflammation/interferon response and the activity of transcription factors.\\n] | \n", + "[ Our term enrichment test suggests that the commonalities in function of these genes are related to the regulation of cell growth and development, signal transduction pathways, and immunity. Specifically enriched terms include development of tissue and organs; signal transduction; cell surface receptor binding; response to stimulus; immune system; immune response; and cytokine activities.\\n\\nMechanism: These functions likely occur through a combined mechanism of modulating transcription factors, receptor-ligand binding, cytokine release and signaling, and a balance of intracellular concentrations of proteins and lipids.\\n\\n] | \n", + "0.89 | \n", + "207 | \n", + "
| 593 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_COMPLEMENT-1 | \n", + "[ This enrichment test revealed several terms related to immune system functioning, cell adhesion and regulation, and extracellular matrix organization, which are likely the underlying mechanisms behind the commonalities among the listed genes. Enriched terms include: immunoglobulin like domains; B cell activation; T cell receptor signaling pathway; integrin mediated cell adhesion; apoptosis; regulation of transcription; signal transduction; receptor mediated endocytosis and exocytosis; extracellular matrix organization; and calcium mediated signaling. \\n\\nMechanism: These findings suggest that the genes involved in this test collectively contribute to a range of processes related to immune system functioning, cell adhesion, extracellular matrix organization, and intracellular communication. \\n\\n] | \n", + "[\\nThe list of genes provided is heavily enriched for functions related to cellular signalling, inflammatory responses, and cellular stress response.\\nMechanism: These genes are typically involved in regulating and mediating signalling pathways, activating and responding to the inflammatory response, activating and functioning in the cell stress response, and facilitating cell-cell interactions.\\n] | \n", + "0.87 | \n", + "406 | \n", + "
| 594 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_DNA_REPAIR-0 | \n", + "[ Gene functions related to DNA and RNA metabolism, protein synthesis, DNA damage repair, transcription, and chromatin organization are significantly over-represented.\\nMechanism: It is likely that many of these genes are involved in the same pathway related to the fundamental processes of DNA replication, transcription, and protein synthesis.\\n] | \n", + "[ The common functions for the human genes are involved in various developmental processes and DNA replication, with enrichment of terms such as \"developmental process\" and \"DNA replication\". \\n\\nMechanism: The genes act together to facilitate a variety of molecular processes in the cellular pathways to support embryonic and post-natal development, as well as DNA replication, transcription, and translation.\\n\\n] | \n", + "0.87 | \n", + "65 | \n", + "
| 595 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_DNA_REPAIR-1 | \n", + "[ \\nSummary: These genes are enriched for roles in DNA replication, transcription, translation and post-translational modifications.\\nMechanism: These genes are involved in various biological processes, including DNA replication, transcriptional regulation, translation, and post-translational modifications involved in gene expression. \\n] | \n", + "[\\nSummary: Our genes are primarily involved in nucleic acid metabolism, transcription, and post-transcriptional modifications.\\nMechanism: The proteins encoded by the genes in our list likely play roles in the various biochemical steps involved in transcription, such as chromatin remodelling, pre-mRNA splicing, DNA repair, RNA polymerization, mRNA processing, mRNA transport, and translation initiation.\\n] | \n", + "0.92 | \n", + "69 | \n", + "
| 596 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_E2F_TARGETS-0 | \n", + "[ Genes on the list are primarily involved in DNA cell cycle and replication, gene regulation, transcription and translation, chromatin modification, and DNA repair. \\n\\nMechanism: The genes are involved in the regulation of DNA replication and transcription, chromatin modification, and DNA repair processes during cell cycle progression. \\n\\n] | \n", + "[ The provided gene list is over-represented for transcriptional regulation, chromatin modification and mitotic division/cell cycle components.\\nMechanism: The underlying mechanism of this gene set is that the enrichments are involved in the regulation of transcription for gene expression, maintenance of chromatin and DNA structure and function, and regulation of mitotic division and cell cycle checkpoints.\\n] | \n", + "0.89 | \n", + "70 | \n", + "
| 597 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_E2F_TARGETS-1 | \n", + "[\\nSummary: The genes in the list are involved in diverse functions related to DNA replication, transcription, chromosome condensation and transcriptional regulation.\\nMechanism: These functions are likely related to canonical pathways and processes involved in coordinating and regulating DNA replication, the transcription of genetic information into proteins, and maintaining appropriate chromosome condensation states.\\n] | \n", + "[ This list of genes is enriched for functions related to DNA replication and repair, chromatin modification, transcriptional and translational regulation, network formation, spindle formation and kinesin and dynein motor proteins. Mechanism: These genes are likely to function as part of an interconnected cellular pathway and/or network that allows for the generation of daughter cells and the coordination of transcriptional activity and post-translational modifications. ] | \n", + "0.93 | \n", + "54 | \n", + "
| 598 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The list of genes provided show enrichment for terms relevant to extracellular matrix composition, cell adhesion and motility, cell-matrix interactions, growth factor and cytokine signaling, and matrix remodeling. \\n\\nMechanism: The mechanisms underlying the enrichment of these terms likely involve cell-matrix interactions, growth factor and cytokine signaling, and matrix remodeling.\\n\\n] | \n", + "0.67 | \n", + "372 | \n", + "
| 599 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[ Our enrichment test uncovered several terms related to extracellular matrix function, morphogenesis, and reproduction/growth. These terms include extracellular matrix organization; morphogenesis; collagen production; matrix metalloproteinase activity; glycoprotein metabolism; cytoskeletal component organization; regulation of growth and reproduction; and regulation of skin morphogenesis. Mechanism: The underlying biological mechanisms related to these genes likely involve the extracellular matrix (ECM), which provides structural and biochemical support to the cells and tissues. ECM components, such as collagen, can regulate activities such as cell signaling, structure formation and growth, and gene expression. Morphogenesis is likely modulated by ECM components, as well as by signaling pathways. ] | \n", + "[ The identified genes are enriched for terms related to skeletal morphogenesis, cell-cell adhesion and motility, extracellular matrix production and remodeling, development and differentiation of connective tissue, collagen production and turnover, and cytokine and chemokine signaling. \\n\\nMechanism: It is likely that these genes are involved in mechanisms that coordinate protein interactions during skeletal development and morphogenesis, cell adhesion and migration, and the maintenance of a healthy extracellular matrix. In addition, these genes likely contribute to the production and turnover of extracellular matrix components such as collagens and chemokines and cytokines involved in development and differentiation of connective tissue. \\n\\n] | \n", + "0.91 | \n", + "60 | \n", + "
| 600 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[\\nSummary: The list of genes identified are associated with cell morphology, homeostasis and regulation, innervation, and cellular metabolism.\\n] | \n", + "[\\nThis list of human genes was analysed in a term enrichment test. The test revealed that many of these genes were involved in a common pathway which supports normal cellular processes including DNA replication, transcription and gene expression, cell growth and differentiation, protein processing and trafficking. Furthermore, many of these genes were involved in bone morphogenesis and cancer-related pathways.\\n\\nMechanism:\\nThe underlying biological mechanism likely involves a number of distinct pathways, each with its own mechanism of action. Common processes shared by many of these genes include DNA replication, translation, and post-translational modification. Additionally, several of these genes are involved in cell-cell adhesion and the control of cellular migration and matrix remodeling, indicating roles in tissue morphogenesis. Furthermore, many of these genes are involved in intracellular signaling and signaling pathways that are essential for the processing and coordination of external and internal signals, which can ultimately result in cell growth, differentiation, and apoptosis.\\n\\n] | \n", + "0.87 | \n", + "964 | \n", + "
| 601 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[ Our analysis of the 34 human genes suggests an enrichment of gene functions related to cell signaling, regulation and morphology, including: immunological response; cell adhesion; transcription regulation; cell migration; development of epidermis, bones and muscle; transport of proteins between cellular compartments; and apoptosis. \\n\\nMechanism: These gene functions are likely related to the regulation of diverse mechanisms within the cell, such as protein-protein interactions, transcription signaling, and intracellular trafficking. \\n\\n] | \n", + "[ \\nSummary: The gene list includes genes involved in transcriptional regulation, signal transduction, membrane transport and lipid biosynthesis.\\nMechanism: The genes exhibit common patterns of transcriptional regulation and signal transduction, with a focus on protein-protein interactions and membrane transport.\\n] | \n", + "0.88 | \n", + "228 | \n", + "
| 602 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[\\nThe genes in the list are enriched for functions in the genomics and cytoskeletal processes, as well as immune response and extracellular modification.\\n\\nMechanism:\\nThe gene functions are implicated in various biological processes that are orchestrated by genetic control and/or regulation pathways. These pathways typically involve protein interactions and cellular processes. Additionally, these pathways often correlate to extracellular modification, immune response, and/or modulation of receptor signaling.\\n\\n] | \n", + "[ Genes related to extracellular matrix organization, cellular adhesion and migration, cell mobility and growth factor-mediated signaling pathways;\\nMechanism: This gene list suggests that extracellular matrix organization, adhesion and migration, cell motility, and growth factor signaling pathways are involved in gene expression in these genes. \\n] | \n", + "0.88 | \n", + "166 | \n", + "
| 603 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[COULD NOT PARSE] | \n", + "[ The genes are enriched for terms related to the structural organization of cells, transcriptional regulation, signal transduction, and immune responses.\\n\\nMechanism: These genes likely comprise a network that influences the physical and biochemical properties of the cell, including its membrane integrity, signal transduction pathways, gene expression, and immunomodulatory functions. \\n\\n] | \n", + "0.67 | \n", + "373 | \n", + "
| 604 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[ This list of genes is highly enriched for metabolic processes such as fatty acid metabolism and oxidation, cholesterol biosynthesis, glycogen metabolism, nucleotide metabolism and transport, and electron transport activity. This suggests that the list reflects a highly coordinated and interconnected network of metabolic processes to maintain the homeostasis of the cell. Enriched terms include: fatty acid metabolism; oxidation of lipids; cholesterol biosynthesis; glycogen metabolism; nucleotide metabolism; nucleotide transport; nucleotide biosynthesis; electron transport activity; enzyme regulation and regulation of metabolic pathways; and apoptosis. \\nMechanism: This set of genes likely acts through a number of interconnected pathways to maintain cellular homeostasis. Lipid metabolism is known to be important in cellular signaling, while other metabolic pathways interact with each other through enzyme regulation and regulation of metabolic pathways. Additionally, many of the genes are associated with cell death pathways, suggesting that these can also act in a coordinated way to respond to stress and maintain cellular homeostasis. \\n] | \n", + "[\\nSummary: The genes shown here are involved in a wide range of metabolic pathways and cellular functions, such as energy metabolism, lipid metabolism, amino acid metabolism, DNA damage repair, and cell signaling.\\n] | \n", + "0.91 | \n", + "937 | \n", + "
| 605 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[\\n\\nSummary: There is a strong enrichment of genes involved in metabolic processes, energy production and storage, lipid metabolism and transport, as well as acetyl-CoA biosynthesis and catalysis.\\n\\nMechanism: The identified genes likely influence the metabolic processes, energy production and storage, lipid metabolism and transport, as well as acetyl-CoA biosynthesis and catalysis by modulating cellular processes, protein and enzyme production, and functional metabolic pathways, such as oxidation and fatty acid metabolism.\\n\\n] | \n", + "[ Genes are enriched in roles associated with lipid metabolism and the cell cytoskeleton. Both pathways involve important signaling and metabolic roles. Mechanism: Lipid metabolism pathways involve synthesizing and degrading lipids, transporting lipids, and their oxidation. The cell cytoskeleton is involved in a variety of functions, including building of cell membranes, cell motility and traffic. ] | \n", + "0.90 | \n", + "128 | \n", + "
| 606 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-0 | \n", + "[\\nGene functions involved in cell cycle regulation, DNA replication, and chromatin remodeling are enriched among the provided list of genes. This could reflect a core pathway of regulation that has been conserved across multiple species.\\n\\nMechanism:\\nThe enriched terms suggest that this gene list could be involved in the G1/S transition of the cell cycle, DNA replication, and chromatin remodeling or modification. Specifically, cell cycle progression and DNA replication is likely driven by cyclin B-CDK1 activation, which is facilitated by Cks1b and Cdc25A mediated activation and either Wee1 or Cdc20-anaphase promoting complex-cyclosome (APC/C)-mediated inhibition. Chromatin modification is likely driven by histone H2A and H2B acetylation and lysine methylation, which involve various proteins, such as Hmga1, Hmgn2, H2az1, H2bc12, and Myc.\\n\\n] | \n", + "[ \\nSummary: This list of human genes are enriched for functions related to cell cycle and/or development, such as DNA replication and transcription, and may be involved in a variety of pathways and processes.\\nMechanism: These genes may be involved in pathways related to DNA replication, transcription and expression, and cell cycle regulation.\\n] | \n", + "0.92 | \n", + "504 | \n", + "
| 607 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-1 | \n", + "[ \\nSummary: This list of human genes are primarily involved in nuclear processes such as DNA replication, gene transcription, chromatin remodelling and cell cycle control.\\nMechanism: The genes may be involved in the regulation of a number of biological processes such as DNA repair, cell cycle regulation, gene expression, and gene regulation.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "328 | \n", + "
| 608 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_GLYCOLYSIS-0 | \n", + "[\\nSummary: Our term enrichment test shows that many of the genes on this list are involved in various aspects of developmental and morphogenic processes, including digit development, cell differentiation, angiogenesis, and metabolism.\\nMechanism: These genes are likely to be involved in biological pathways involving the development and maintenance of cellular structure, binding and transporting of molecules, energy metabolism and other metabolic processes, and cell signaling.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.71 | \n", + "464 | \n", + "
| 609 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_GLYCOLYSIS-1 | \n", + "[ The list of genes are primarily involved in essential metabolic functions in the cell. Specifically, they are involved in carbohydrate and energy metabolism, microtubule assembly, DNA binding and replication, actin cytoskeleton dynamics, ion channel regulation, transcriptional regulation, and cell adhesion. The mechanism is likely related to the coordination of these processes in order to maintain homeostasis and proper cell functioning.\\n\\nSummary: Genes mainly involved in metabolic processes. \\n\\nMechanism: Coordination of these processes to maintain cellular homeostasis.\\n\\n] | \n", + "[ \\nThis gene list is enriched for proteins involved in structural development and energy metabolism, such as structural proteins and enzymes of glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle. These terms are supported by evidence from gene ontologies (GO) assigned to the genes in the list.\\n\\nMechanism: \\nThe list of genes is involved in pathways which facilitate the efficient production and utilization of energy, such as glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle. They are also involved in the dynamic assembly of integral structures, such as the cytoskeleton, cell adhesion serve, proteoglycan synthesis, and extracellular matrix formation.\\n\\n] | \n", + "0.89 | \n", + "140 | \n", + "
| 610 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[\\nSummary: Many of the genes listed are involved in the development and morphogenesis of neurons and other cells. \\nMechanism: These genes are likely to work together to regulate cell and tissue shaping and differentiation, providing for the formation of specialized neuron structures and neural pathways. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "290 | \n", + "
| 611 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[\\n\\nSummary: This group of genes is commonly associated with morphogenesis, cell adhesion, development, and neuronal signaling\\nMechanism: The underlying biological mechanism is likely related to the regulation of cell proliferation, migration, differentiation, and neural plasticity during development. \\n] | \n", + "[ The genes appear to be involved in the development of various cell types, organs, and other growth processes, including neuron formation, cell adhesion and migration, signal transduction, tissue morphogenesis, and development of the nervous system. \\nMechanism: These genes likely act in a number of ways to promote and coordinate these processes, including recognizing and binding signaling molecules, relaying signals to other molecules, and affecting transcription of target genes. \\n] | \n", + "0.92 | \n", + "184 | \n", + "
| 612 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_HEME_METABOLISM-0 | \n", + "[\\nSummary: The genes in this list are highly enriched for functions related to membrane transport, energy metabolism, ribosomal proteins, and nucleic acid binding.\\nMechanism: The underlying biological mechanism or pathway may involve regulation and control of cellular functions and transcription activity, with multiple proteins interacting to ensure proper functioning of a variety of cellular pathways.\\n] | \n", + "[ The list of genes has a statistically significant enrichment of terms related to cellular metabolism, energy production and transport, cytoskeleton modification and remodelling, and cell adhesion. \\nMechanism: The molecular mechanisms involve the transfer of energy, metabolic pathways, and the coordination of cellular transport and reorganization.\\n\\n] | \n", + "0.91 | \n", + "54 | \n", + "
| 613 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_HEME_METABOLISM-1 | \n", + "[\\n\\nSummary: The human genes identified in this list are predominantly involved in cell development, gene expression, organogenesis and nucleic acid metabolism.\\n\\nMechanism: The human genes identified in this list are likely to be involved in processes that regulate cell development, including transcriptional regulation and organogenesis, as well as nucleic acid metabolism. \\n\\n] | \n", + "[ The enriched terms for this list of human genes suggest a common functional theme in organ development, morphogenesis and growth, immune system function, and transport processes. Enriched terms include: embryonic development; skeletal system development; organogenesis; morphogenesis; growth; immune system process; cell motility; steroid hormone receptor activity; receptor signaling pathway; transport; endocytosis; and cellular homeostasis.\\n\\nMechanism: The underlying biological mechanism suggested by the enriched gene functions is that these genes are involved in various organ and skeletal system development processes, in particular morphogenesis and growth, as well as immune system and transport processes. Specifically, these genes are involved in organogenesis, morphogenesis, growth, and cell motility through receptor signaling pathways, endocytosis, transport processes, and cellular homeostasis. Additionally, the genes are involved in steroid hormone receptor activity, further contributing to organ and skeletal system development.\\n\\n] | \n", + "0.88 | \n", + "675 | \n", + "
| 614 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_HYPOXIA-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The list of genes is involved in a variety of pathways and functions related to cell differentiation, metabolism, protein processing, and the regulation of gene expression. Specifically, this list was enriched for terms related to cell cycle, remodeling proteins, stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, transcription factors, chromatin-associated proteins, and kinases.\\n\\nMechanism: The overall mechanism of action of the genes appears to be related to the regulation of cellular processes via the modulation of expression of target genes, primarily through the regulation of epigenetic and transcriptional factors, in order to enable proper differentiation, metabolism, and protein processing. This is further supported by the enrichment of terms related to stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, transcription factors, chromatin-associated proteins, and kinases.\\n\\n] | \n", + "0.68 | \n", + "951 | \n", + "
| 615 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_HYPOXIA-1 | \n", + "[ \\nSummary: Genes related to cell development, cell metabolism, transcription, and regulation are enriched in this set.\\nMechanism: These genes regulate a variety of cellular processes such as cell cycle regulation, transcriptional regulation, and energy metabolism.\\n] | \n", + "[ Genes identified in this set are associated with several DNA/RNA binding and regulatory processes, including transcription and epigenetic modification. Statistically over-represented functions in these genes include development, cell structure and movement, cell cycle and division, signal transduction, transport, and energy production; proteins involved in these processes include transcription factors, kinases, histones, and other enzymes. Mechanism: This enrichment likely reflects the underlying biological pathways governing various aspects of gene expression and regulation. ] | \n", + "0.92 | \n", + "319 | \n", + "
| 616 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[ The gene set is enriched for genes involved in cell growth, cell detection/regulation, and immunity. Mechanism: These genes are likely involved in a number of pathways that contribute to cell and tissue development, growth, and regulation, as well as regulation of the immune system. ] | \n", + "[\\nSummary: These genes are predominantly related to immunological functions, actin cytoskeleton organization, cell surface receptors, and pro-inflammatory regulation.\\nMechanism: The genes listed appear to be involved in the immune response, actin cytoskeleton organization, cell surface receptor-mediated signaling, and pro-inflammatory regulation.\\n] | \n", + "0.88 | \n", + "63 | \n", + "
| 617 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[COULD NOT PARSE] | \n", + "[ The list of human genes provided are enriched for terms related to immunity, inflammatory response, cell growth, differentiation and development, and signaling pathways.\\n\\nMechanism: This underlying biological mechanism could involve proteins interacting with each other and coordinating pathways to govern immune response, inflammatory response, cell growth, differentiation, and development, as well as other cellular processes.\\n\\n] | \n", + "0.69 | \n", + "417 | \n", + "
| 618 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[ Genes in the list are enriched for the Cellular Processes of Pain Sensing and Signal Transduction; Chemotaxis; Cytokine-mediated Signaling Pathway; Leukocyte Transendothelial Migration; Immune Response; and Platelet Activation. There is a potential mechanism for the underlying biological pathway whereby these genes interact in signal transduction to facilitate pain sensing and immune response, including ligand-receptor interactions, signal transduction of cytokines, and the actions of transcription factors, such as those encoded by JUN, REG1A, STAT1, STAT2, STAT3 and TLR2.\\n\\n] | \n", + "[ This list of genes is enriched in terms related to cell signaling, cytokine production and regulation, regulation of gene expression and transcription, and cell adhesion.\\nMechanism: This list of genes promotes the core pathways of cell signaling, cytokine production and regulation, regulation of gene expression and transcription, and cell adhesion. This enables the body to respond to a variety of external signals, to recognize and respond to inflammation and stress, to produce the necessary molecules for the body to function correctly, and to hold the cell together so that it may adhere to corresponding cells and fulfill its role within the network of cells.\\n] | \n", + "0.90 | \n", + "86 | \n", + "
| 619 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[\\nSummary: The list of genes are significantly enriched for functions of immunity, signaling, and transcription regulation\\nMechanism: These genes are likely involved in the coordination of immune responses and the regulation of pathways for signal transduction and transcription.\\n] | \n", + "[ Increased expression of cytokines, chemokines, and interleukins; increased expression of developmental, signal transduction, and immune system pathways involved in cellular differentiation, cell motility and adhesion, signal transduction, and inflammation. \\nMechanism: The genes listed all appear to be involved in immune system, signal transduction and intercellular communication pathways. Through the identification of commonalities between the gene functions, inference can be made that these genes are involved in up-regulation of cytokines, chemokines, and interleukins involved in cellular differentiation, cell motility, adhesion, signal transduction and inflammation. \\n] | \n", + "0.89 | \n", + "400 | \n", + "
| 620 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[ Genes associated with human immunity, inflammation and signalling pathways are enriched.\\n\\nMechanism: These genes are likely involved in pathways related to human immunity, inflammation and signalling, either directly or through regulation of transcription and translation activity.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.67 | \n", + "269 | \n", + "
| 621 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[ The list of genes is significantly enriched for terms related to immune cell signaling, cell movement, and cell surface receptor activity. \\nMechanism: These genes are likely involved in the regulation of pathways involved in initiating and responding to inflammation, cell migration, cell–cell interactions, and immune cell receptor-mediated signaling.\\n] | \n", + "[ The list of genes is enriched in functions related to the immune system, especially mediation of inflammatory response and cytokine production and signalling.\\nMechanism: The genes are involved in a variety of functions related to immune cell activation and cellular signaling, including cell adhesion, G-protein and receptor-coupled pathways, transcriptional regulation, cytokine and cytokine receptor binding, and lipid metabolism. \\n] | \n", + "0.93 | \n", + "81 | \n", + "
| 622 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[ Our analysis of the list of human genes have revealed a set of enriched terms related to the activation and inhibition of immune signaling pathways, and their functions in regulating inflammation. Specifically, we observed an increased prevalence of molecules and proteins involved in mechanism activating or inhibiting the Nuclear Factor Kappa B (NF-κB), Interferon Regulatory Factor (IRF) as well as JAK-STAT pathways. Terms such as \"inflammatory response\", \"neutrophilic activation and degranulation\", \"T-Cell receptor signaling pathway\", \"Toll-Like Receptor Cascade\", \"Type I Interferon Signaling\", and \"Inflammatory Regulation\" were enriched in this gene set.\\n\\nMechanism: The genes in this list are involved in multiple pathways that are related to the modulation of inflammatory responses and can be broadly summarized as either regulating cytokine production or modulating the inflammatory response by inhibiting the NF-κB, IRF and JAK-STAT pathways. While there is significant overlap of these genes with the NF-κB pathway, the IRF and JAK-STAT pathways are also significant contributors, as evidenced by the enriched terms. \\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.70 | \n", + "1122 | \n", + "
| 623 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[ This group of genes is significantly enriched for functions related to immune system regulation, interferon response, apoptosis, and cell membrane regulation.\\n\\nMechanism: This list of genes is likely involved in both innate and adaptive immune responses, functioning to modulate the level of inflammation and cytokine production, as well as to induce cell death and regulate cell membrane composition. Specific terms enriched that pertain to these functions include interferon signalling pathways, interferon gamma activity, interferon regulatory factor activity, status response to interferon, apoptosis, lipid binding, calcium ion binding, and neutrophil mediated immunity. \\n\\n] | \n", + "[ Genes listed appear to be primarily involved in the regulation of interferon response pathways and the transcriptional control of interferon-stimulated genes. The genes appear enriched for the cellular pathways of immune response, inflammation, and cytokine signaling.\\n \\nMechanisms: The interferon response pathways activated in this population of genes modulate the expression of cytokines, chemokines, and antimicrobial and antiviral proteins, in order to activate an innate immune response to virus and bacteria. \\n\\n] | \n", + "0.93 | \n", + "160 | \n", + "
| 624 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[\\nSummary: A majority of the genes were found to be involved in important immune response and cell signaling pathways.\\nMechanism: The immune response and cell signaling pathways are likely to be regulated by cytokines and transcription factors such as those related to interferon responses and nuclear factor kappaB-dependent transcriptional regulation.\\n] | \n", + "[ In this gene set, there are multiple genes that are enriched for functions related to immunology, such as antigen presentation, inflammatory responses, chemokine signaling, cell adhesion, and cytokine interactions. \\nMechanism: One hypothesis is that these genes are involved in an immune-mediated response related to their roles in antigen-presentation, inflammatory responses, the regulation of chemokines, and cell adhesion. \\n] | \n", + "0.88 | \n", + "78 | \n", + "
| 625 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[\\nSummary: The enriched terms among the list of genes includes pathways involved in immunity, interleukin regulation, transcriptional regulation, inflammation, cell signaling, and apoptosis.\\nMechanism: Signaling and pathways involving these genes are likely to regulate these biological processes.\\n] | \n", + "[ This list of genes is enriched in terms related to cell signaling, transcription regulation, and immune system regulation. Specifically, genes are enriched in pathways related to: interferon signaling; antigen processing, presentation, and recognition; cytokine signaling; cell cycle and DNA damage response; and apoptosis.\\n\\nMechanism: It appears that the genes identified in this list are functionally connected and may be involved in a larger underlying biological mechanism or pathway. The proteins associated with each gene are known to interact with one another and repress/activate various genes leading to the regulation of cell signaling, transcription, and immune system functions. This molecular regulation process is essential in the control of cellular functions and physiological behavior. \\n\\n] | \n", + "0.95 | \n", + "509 | \n", + "
| 626 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[ Genes in this term enrichment test were found to be enriched for terms related to the development of bones, morphogenesis, growth and maintenance, cell-cell signaling and communication, protein modification, and transport.\\nMechanism: It is likely that the genes identified in this term enrichment test make up a biological pathway that is involved in the development of bones, growth and morphogenesis, and other processes related to regulating cell-cell signaling and communication, protein modification, and transport.\\n] | \n", + "[ The analysis of the list of human genes reveals that these genes are related to development, regulation, and signaling mechanisms within the cell. Specifically, the terms associated with development, such as digit development, neural development, immune system development and transcriptional regulation, are enriched. Additionally, terms related to signal transduction, such as G-protein coupled receptors, protein kinases, and guanine nucleotide exchange factors, are also enriched.\\n\\nMechanism:The mechanism underlying the term enrichment of the list of human genes is likely related to the fact that these genes play a role in a wide range of essential cellular processes. It is likely that signaling molecules and transcription signals coordinate these processes to enable proper development and homeostasis.\\n\\n] | \n", + "0.92 | \n", + "293 | \n", + "
| 627 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[\\nSummary: The list of genes are found to be significantly associated with physiological processes related to morphogenesis, cell-cell communication and development, and hormone regulation.\\nMechanism: The genes are likely to be involved in a variety of biological mechanisms, such as cell-signalling, cellular differentiation and cell-cycle, as well as hormone mediated processes.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "365 | \n", + "
| 628 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[ Genes in this list are predominantly involved in signal transduction pathways and morphogenesis; specific terms enriched include signal transduction, cell morphogenesis, response to stimulus, angiogenesis, regulation of molecular function, and extracellular matrix organization.\\nMechanism: The list of genes are likely to be involved in signaling pathways involving kinases, growth factors and receptors, as well as involvement in morphogenesis processes such as cell-cell adhesion, cellular movement and cell differentiation.\\n] | \n", + "[ This list of gene names is enriched for genes involved in signal transduction, cell cycle control, and cell-to-cell adhesion.\\nMechanism: The enrichment of these genes indicates a shared biological pathway in which cellular communication, pathways, and networks are regulated by controlling the production of proteins and other molecules. This can lead to changes in other intracellular activities, such as cell cycle progression and adhesion. \\n] | \n", + "0.93 | \n", + "83 | \n", + "
| 629 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[\\nSummary: This set of genes appears to be involved in a variety of cellular processes, including morphogenesis and tissue development, cell signaling, and immune regulation.\\nMechanism: These genes appear to be involved in transcription modulation, signal transduction pathways, and regulation of cell adhesion and migration.\\n] | \n", + "[\\nSummary: This list of genes is enriched for terms related to cell adhesion and signal transduction, including terms such as integrin, chemokine receptor, protein kinase and G-protein-coupled receptor.\\nMechanism: These genes are involved in pathways important for cell adhesion, such as integrin and chemokine receptor-mediated interactions, as well as signal transduction pathways which include protein kinases, G-protein-coupled receptors and other associated proteins.\\n] | \n", + "0.90 | \n", + "147 | \n", + "
| 630 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[COULD NOT PARSE] | \n", + "[\\n\\nSummary: The list of human genes have diverse enrichment in the functions of cell cycle control, cell adhesion, and cytoskeletal organization.\\nMechanism: These genes enable cells to interact with their environment and complete the cell cycle by organizing components, regulating activities, and controlling signaling pathways.\\n] | \n", + "0.68 | \n", + "314 | \n", + "
| 631 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[ Enriched terms show a commonality among these genes for processes related to cytoskeletal organization and migration of the cell, cell division, DNA replication and repair, and targeting proteins to the correct place in the cell.\\nMechanism: The proteins represented by these genes likely play a role, either directly or indirectly, in the regulation of a number of vital cell processes including cell division, DNA replication and repair, and targeting proteins to the right place in the cell.\\n] | \n", + "[ \\nSummary: The genes that were provided are statistically enriched for terms related to cell division, protein phosphorylation, chromatin remodeling, and microtubule binding and organization.\\nMechanism: These genes likely function in biological pathways related to spindle assembly, chromosome segregation and movement, cell-cycle control, and other processes related to mitosis. \\n] | \n", + "0.92 | \n", + "114 | \n", + "
| 632 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-0 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE] | \n", + "1.00 | \n", + "0 | \n", + "
| 633 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-1 | \n", + "[ The list of genes is enriched in functions related to protein synthesis, energy metabolism, cellular transport, and immune response.\\nMechanism: It is likely that these genes are co-regulated in networks that are responsible for cellular energy production and regulation, protein synthesis and degradation, and immune response.\\n] | \n", + "[\\nSummary: This list of genes is involved in a variety of pathways related to cell growth and development, including morphogenesis, transcription, and protein synthesis.\\nMechanism: The physiological processes induced by these genes likely work in concert to mediate a variety of cellular processes including cellular translation, metabolism, and signalling.\\n] | \n", + "0.88 | \n", + "29 | \n", + "
| 634 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-0 | \n", + "[ The genes appear to be involved in processes related to RNA and protein synthesis, ATP-related processes, cytoskeleton organization and assembly, transcription, and chromatin remodeling.\\n\\nMechanism: The genes likely play a role in regulating various cellular processes, such as gene expression, signal transduction, and translation, via multiple pathways that are related to RNA processing, translation initiation, mRNA stability, and DNA replication.\\n\\n] | \n", + "[\\nThe list of genes are involved in a variety of processes including, but not limited to, protein synthesis and modification, DNA replication, cell cycle regulation, and transcription regulation.\\nThis suggests that these genes may be involved in a co-dependent pathway or pathways that regulate cell growth, development, and gene expression.\\n] | \n", + "0.91 | \n", + "113 | \n", + "
| 635 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-1 | \n", + "[ Genes from this list are mainly involved in translation, transcription, and post-transcriptional modification processes. Specifically, these genes are involved in mRNA splicing, mRNA transport, mRNA stability, protein synthesis, ribosome biogenesis, RNA interference, and chromatin remodeling. Mechanism: These genes likely operate according to the canonical mechanisms of gene expression, by which genes are transcribed, spliced, and translated into proteins. These processes are tightly regulated and involve a complex network of interacting proteins, RNAs, and other molecules. ] | \n", + "[\\nSummary: This list of genes have overlapping functions in development, energy production, and regulation.\\nMechanism: There may be a pathway involved in controlling energy production, protein synthesis, and structural maintenance of cell components in development.\\n] | \n", + "0.88 | \n", + "317 | \n", + "
| 636 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The enrichment test identified a set of genes related to protein and nucleic acid metabolism and cell cycle regulation. Specifically, genes involved in protein post-translational modifications, phosphorylation, transcription, translation, and ribosome biogenesis were enriched.\\n\\nMechanism: These gene functions are likely related to the underlying biological mechanism or pathway, since genes related to these processes have an essential role in regulatory activities and cell cycle control. ] | \n", + "0.69 | \n", + "478 | \n", + "
| 637 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-1 | \n", + "[\\nSummary: The gene set is enriched for terms related to cell activation and proliferation, as well as DNA replication and replication-associated processes such as transcription and translation.\\n] | \n", + "[ \\nSummary: Many of the genes listed appear to be related to chromatin and transcriptional regulation.\\nMechanism: Regulation of gene expression and chromatin structure via transcription factors and nucleosome remodeling enzymes. \\n] | \n", + "0.86 | \n", + "35 | \n", + "
| 638 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MYOGENESIS-0 | \n", + "[ Gene expression and structure, cytoskeletal structure and dynamics, calcium regulation and signaling, cell adhesion and migration, cell death biochemistry, and metabolic regulation are all enriched terms based on the genes provided that are common to these roles in humans.\\n\\nMechanism: The underlying biological mechanism for the enriched terms observed in this list of genes is likely related to the wide range of regulatory roles these genes and gene products have in maintaining cellular health and enabling proper physiological functions and development at the cellular level. \\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "569 | \n", + "
| 639 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_MYOGENESIS-1 | \n", + "[ The list of genes show an enrichment for terms related to the extracellular matrix, cytoskeleton, muscle structure and development, neuromuscular structure, ion channels, and ion transport. \\nMechanism: These genes appear to be involved in various intra- and extracellular pathways and mechanisms related to the formation and maintenance of the cytoskeleton, neuromuscular structure, and muscle formation, as well as ion transport and channel proteins serving as important mediators of electrical and chemical signals in cells. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.67 | \n", + "514 | \n", + "
| 640 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-0 | \n", + "[\\nThe list of genes are involved primarily in aspects of embryonic development, regulation of cell cycle, and calcium signaling.\\nMechanism: The genes function primarily in regulating various aspects of cell signaling and cycle regulation during embryonic development, such as down-regulation of Notch signaling, regulation of Wnt signaling and Hedgehog signaling pathways, cell morphogenesis, and calcium signaling.\\n] | \n", + "[ These genes are associated with Notch receptor, transcription factor, and Wnt pathway signaling, which are involved in tissue and organ development.\\nMechanism: Notch receptor, Wnt, and transcription factor signaling pathways leads to a variety of processes such as morphogenesis, organogenesis, tissue development, cell fate determination, and cell interaction. \\n] | \n", + "0.89 | \n", + "51 | \n", + "
| 641 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-1 | \n", + "[COULD NOT PARSE] | \n", + "[\\nSummary: The genes in this list are associated with cell proliferation, morphogenesis and development, nerve system differentiation, and regulation of transcription.\\nMechanism: The genes likely function in pathways involved in the WNT and Notch signalling pathways, which have numerous roles in development and differentiation of different tissue types. \\n] | \n", + "0.69 | \n", + "341 | \n", + "
| 642 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[\\n\\nSummary: This list of genes is enriched for terms related to mitochondrial activity, electron transport chain, oxidative phosphorylation, and metabolic regulation/activation.\\nMechanism: This list of genes are likely to be involved in the various steps of mitochondrial activity, electron transport chain, oxidative phosphorylation, and metabolic regulation/activation. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "357 | \n", + "
| 643 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[\\nSummary: The list of genes is predominantly involved in cellular respiration and metabolism, as evidenced by the enriched terms related to mitochondrial bioenergetics, ion transport and metabolite-binding proteins.\\nMechanism: The commonality amongst the genes likely contributes to the normal functioning of mitochondria, and is involved in the bioenergetic processes that involve ATP synthesis, as well as maintaining electron transfer and transporter function.\\n] | \n", + "[ Genes in this list are mainly associated with mitochondrial bioenergetics and associated pathways. Specifically, the terms \"mitochondrial electron transport chain complex activity\"; \"mitochondrial electron transport, NADH to ubiquinone\"; \"mitochondrial respiratory chain complex I activity\"; \"respiratory chain complex I assembly\"; \"respiratory chain complex III activity\"; and \"respiratory chain complex IV activity\" are found to be enriched in this gene set.\\n\\nMechanism: Mitochondria are dynamic organelles that are responsible for many of the metabolic pathways, including cellular respiration. A variety of mitochondrial electron transport complexes are involved in the production of energy, including complex I (NADH:ubiquinone oxidoreductase), complex III (ubiquinone:cytochrome c oxidoreductase), complex IV (cytochrome c oxidase), and complex V (ATP synthase). As these genes are associated with mitochondrial functions, it is possible that there is an underlying mechanism related to metabolic pathways and energy production within the mitochondria. \\n\\n] | \n", + "0.91 | \n", + "598 | \n", + "
| 644 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_P53_PATHWAY-0 | \n", + "[ Analysis of this gene list revealed a significant enrichment of terms in functions related to cytoskeleton alteration, calcium homeostasis modulation, ubiquitin-proteasome pathway activation, cell cycle control, and transcriptional and post-transcriptional regulation.\\n\\nMechanism: These functions likely act in concert to mediate the regulation of cellular growth, differentiation, and survival.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "383 | \n", + "
| 645 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_P53_PATHWAY-1 | \n", + "[ Genes in this list are associated with regulation of the cell cycle, DNA damage repair, cell signaling and processes involved in cell growth, apoptosis, and immune modulation. The genes are enriched for functions related to transcription, chromatin dynamics, cell adhesion molecules, and cytokines. \\nMechanism: The regulation of these genes (directly or indirectly) is likely to be part of a complex network of pathways, signaling molecules, and protein-protein interactions. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.67 | \n", + "463 | \n", + "
| 646 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[\\nSummary: This gene set is enriched in functions related to pancreas development, glucose metabolism, cell motility, and neural development. \\nMechanism: It is hypothesized that these genes function in a network to control developmental processes relevant to pancreas development, glucose metabolism, cell motility and neural development.\\n] | \n", + "[ Genes play diverse roles in the development of the pancreas, nervous system, and musculoskeletal system. Major term enrichment was found for pancreas development, nervous system development, development of neural structures, organogenesis, and transcriptional regulation. \\nMechanism: These genes are likely involved in a variety of biological mechanisms including, the regulation of morphogenesis, cell-to-cell adhesion, and protein synthesis pathways, as well as hormonal metabolism and signaling.\\n] | \n", + "0.90 | \n", + "162 | \n", + "
| 647 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[\\nSummary: This term enrichment test identified gene functions related to morphogenesis, neural development, signal transduction, insulin hormone secretion, transcription regulation, and transcription factor activity.\\nMechanism: These genes likely work together to facilitate the development of body organs, neuronal function and pathways, insulin secretion, and transcription factor activity.\\n] | \n", + "[ Analysis of these genes revealed common pathways related to metabolic regulation, neural development, and transcription/translation control. The terms enriched by these genes are neurogenesis; metabolism; transcriptional control; translation; morphogenesis; body patterning and organization; neurological system development; and cell differentiation.\\n\\nMechanism: Signaling pathways involved in neural development will have an influence on neurogenesis, while metabolic pathways will be involved in pathways that regulate glucose and lipid metabolism. Additionally, transcription and translation pathways are essential for regulating gene expression but also cell differentiation and morphogenesis. Finally, body patterning and organization rely on genes that control cell fate and cellular migration. \\n\\n] | \n", + "0.90 | \n", + "411 | \n", + "
| 648 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PEROXISOME-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The human genes given in the list are involved in metabolic biochemical pathways associated with lipid metabolism, stress response, mRNA transcription, DNA repair, skeletal and cartilage development, and cell migration. \\nMechanism: Metabolic enzymes and transport proteins appear to regulate these pathways, allowing for the synthesis and degradation of cellular compounds, as well as transporting molecules into and out of the cell to maintain physiological homeostasis.\\n] | \n", + "0.68 | \n", + "459 | \n", + "
| 649 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PEROXISOME-1 | \n", + "[ Genes involved in the list are associated with lipid metabolism, lipid storage and transport, steroid metabolism, regulation of transcription and, importantly, regulation of the cell cycle. \\nMechanism: An enrichment of pathways associated with lipid, steroid and transcriptional metabolism, as well as regulation of the cell cycle.\\n] | \n", + "[\\nSummary: Genes in this list are associated with a wide array of terms, including metabolism, transcription, regulation, transport and signaling.\\nMechanism: These genes likely play a role in a broad biological mechanism involving various metabolic pathways, transport, and regulatory functions.\\n] | \n", + "0.90 | \n", + "38 | \n", + "
| 650 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[ Gene expression, DNA repair and maintenance, growth factors, cellular signaling pathways and lipid metabolism \\nMechanism: Regulation of gene expression through the activation of transcription and DNA repair and maintenance pathways is likely involved. The enriched terms related to growth factors suggests that the list of genes may be involved in cell proliferation and differentiation. Signaling pathways and lipid metabolism may be involved in cell-cell communication and energy-related processes, respectively.\\n] | \n", + "[ The list of genes is enriched for terms related to signal transduction pathways and development, such as morphogenesis and cell differentiation.\\nMechanism: Signal transduction pathways are likely involved in the regulation of the gene functions, with particular importance of tyrosine kinase activity and modulation of relevant receptor activities.\\nHypothesis: The genes may be involved in the regulation of tissue development and cell differentiation.\\n] | \n", + "0.90 | \n", + "62 | \n", + "
| 651 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[ The list of genes given are involved in cell cycle regulation, gene transcription, transcription factor activation and signal transduction pathways.\\nMechanism: The genes included in this list are involved in various mechanisms of cell cycle regulation, gene transcription, transcription factor activation and signal transduction pathways. These involve the regulation of cell cycle progresses such as synthesis, growth, proliferation and differentiation, as well as the operations of protein kinases, transcription factors, receptor proteins and other essential molecules. \\n] | \n", + "[ \\n\\nSummary: This gene list covers a broad range of functions, including cell signaling, growth and survival, protein and lipid metabolism, transcription regulation, and cell cycle control.\\nMechanism: The genes in this list are likely involved in a variety of pathways that facilitate or regulate various cellular activities, such as receptor signaling, protein glycosylation, kinase activity, apoptosis, and G-protein interactions.\\n] | \n", + "0.93 | \n", + "143 | \n", + "
| 652 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-0 | \n", + "[COULD NOT PARSE] | \n", + "[ Genes listed are associated with vesicular transport, trafficking, and membrane fusion in the cell.\\nMechanism: Vesicular transport involves the formation of vesicles from the host membrane, trafficking of these vesicles through the cell and organelles, and fusion of the vesicles with host membranes for which these genes are responsible.\\n] | \n", + "0.67 | \n", + "325 | \n", + "
| 653 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-1 | \n", + "[COULD NOT PARSE] | \n", + "[ Enrichment test on a given list of human genes resulted in the identification of several enriched terms, which have important roles in post-translational modification, protein folding, protein synthesis, endocytosis, oligosaccharide metabolism, and lysosomal trafficking.\\n\\nMechanism: The mechanism behind this enrichment pattern is likely related to the various mechanisms regulated by these genes, such as the regulation of PTMs, protein folding, protein synthesis, endocytosis, oligosaccharide metabolism, and lysosomal trafficking.\\n\\n] | \n", + "0.69 | \n", + "522 | \n", + "
| 654 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[\\nSummary: This list of genes is enriched for terms involving redox regulation, antioxidant defense and detoxification of reactive oxygen species, peroxisomal and mitochondrial biogenesis, and cell metabolism.\\nMechanism: The underlying biological mechanism involves the production and regulation of reactive oxygen species, adaptation to oxidative stress and related forms of damage, and the maintenance of redox homeostasis.\\n] | \n", + "[\\nSummary: The list of genes is associated primarily with metabolic processes, defense against oxidative damage and DNA repair.\\nMechanism: These processes are likely related to cellular level metabolic regulation, protection against oxidative damage, and DNA damage repair.\\n] | \n", + "0.93 | \n", + "152 | \n", + "
| 655 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[ \\nSummary: 13 genes are enriched for functions associated with redox regulation, metabolism, cell cycle regulation, and transcriptional regulation.\\nMechanism: These genes likely play a role in the regulation of a cell's redox balance, metabolism, cell cycle progression and gene expression.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "276 | \n", + "
| 656 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-0 | \n", + "[\\nThe gene list is enriched for functions related to cell signaling, protein regulation, and cell cycle control, as well as complex development processes such as morphogenesis, organogenesis and cytoskeletal regulation.\\nMechanism: A wide range of mechanims are at work here, which involve the transcription and translation of genes to encode proteins and the regulation of their functions to mediate both common and specific biological processes.\\n] | \n", + "[ Genes associated with this list indicate enrichment for a variety of cell cycle control and chromatin remodeling processes, as well as protein ubiquitination, regulation of DNA replication, spindle assembly, and nuclear organization.\\n\\nMechanism: The enriched terms suggest that these genes are involved in a variety of related functions related to the regulation and maintenance of the cell cycle, chromatin remodeling, DNA replication, spindle assembly and nuclear organization.\\n\\n] | \n", + "0.89 | \n", + "36 | \n", + "
| 657 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-1 | \n", + "[ Genes related to organ development, morphogenesis, cytoskeletal proteins, signal transduction.\\nMechanism: Proteins from the list are likely used as part of a unified pathway for organ/tissue development and morphogenesis, and involved in cell cycle checkpoint regulation and signal transduction.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "282 | \n", + "
| 658 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[ The list of genes analyzed in this term enrichment test is related to pathways associated with cell growth and development, such as MAPK, TGF-β, Wnt/β-catenin, Hippo and transcriptional regulations. Specifically, pathway enrichment of genes included muscle and tissue morphogenesis, regulator of G-protein signaling and inflammatory response pathway.\\n\\nMechanism: The general mechanism is that the genes are involved in signaling pathways for cell processes such as growth, differentiation and apoptosis. These signals modulate the expression of downstream genes and ultimately lead to changes in cell shape and other cellular activities.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "625 | \n", + "
| 659 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[COULD NOT PARSE] | \n", + "[ Our term enrichment analysis of these genes reveals an overrepresented pattern of general cellular processes related to the development and proliferation of cells, as well as homeostasis, cell division, and migration. Specifically, genes related to transcriptional regulation, signal transduction, cell cycle regulation, protein kinase pathways, and translation were enriched.\\n\\nMechanism: These overrepresented functions suggest a complex coordination of biochemical pathways contributing to cell development and proliferation, junctions, and cytoskeletal organization.\\n\\n] | \n", + "0.69 | \n", + "558 | \n", + "
| 660 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[ These genes are mainly involved in developmental processes, inflammation, immunomodulation, inflammation, cell signalling and metabolic pathways.\\nMechanism: These genes are likely to be involved in pathways leading to the regulation of morphogenesis and tissue development, control of cell proliferation and apoptosis, regulation of immune system immune response, regulation of inflammation and activation of metabolic pathways.\\n] | \n", + "[ The genes in the given list are predominantly involved in the TLR signaling pathway, development, inflammation and immune-response regulation.\\nMechanism: The TLR signaling pathway consists of an intricate set of reactions starting with the recognition of a pathogen-associated molecular pattern (PAMP) by the TLR receptor, leading to the activation of various transcription factors, such as NFKB and MAPK, which work to activate a cascade of gene expression and ultimately the secreting of pro-inflammatory molecules.\\n\\n] | \n", + "0.90 | \n", + "90 | \n", + "
| 661 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[\\nSummary: The genes are enriched for terms related to gene transcription, cytoskeleton formation, and signal transduction. \\nMechanism: The genes are likely involved in a wide range of processes, including transcriptional regulation, actin cytoskeleton organization, cytokine receptor signaling and NF-kB signaling pathways.\\n] | \n", + "[ Gene functions related to inflammation and immunity appear to be enriched when analyzing the list of genes provided, including cytokine-mediated signaling, antigen-receptor mediated signaling, B-cell proliferation, cytokine expression and release, immunoregulatory interactions, NF-kappaB (NF-κB) activation, and interferon (IFN) signaling.\\n\\nMechanism: These genes are likely involved in an inflammatory response in which cytokines are released and induce receptor activation, which leads to NF-κB activation and transcription of genes that produce cytokines and other signaling molecules, as well as triggering an IFN response. This ultimately leads to B-cell proliferation and immunoregulatory interactions in order to mount a response to the any pathogens. \\n\\n] | \n", + "0.87 | \n", + "439 | \n", + "
| 662 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[ The genes in the list may be generally involved in processes such as mRNA transcription, ribosome biogenesis and protein folding, as well as nucleolar and spliceosomal activity. \\nMechanism: These genes likely regulate cellular processes such as protein production and transport, RNA processing, and cell cycle control. \\n] | \n", + "[\\nSummary: A significant enrichment of genes involved in translation and protein folding is found in the gene list, indicating a common pathway for these genes.\\nMechanism: The genes in this list are likely all involved in the same pathway, centered around translation and protein folding.\\n] | \n", + "0.91 | \n", + "33 | \n", + "
| 663 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[\\nSummary: The enrichment analysis on the list of genes revealed a common theme of gene functions related to metabolism, protein synthesis, and post-translational modifications.\\nMechanism: The observed gene functions suggest a pathway of metabolic and protein regulatory processes that involve the synthesis of proteins, post-translational modifications such as phosphorylation, and other processes related to metabolism and folding.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.70 | \n", + "418 | \n", + "
| 664 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-0 | \n", + "[ The genes identified are associated with protein kinases, cellular signaling pathways, and development of skeletal and extracellular matrix components.\\nMechanism: These identified genes may be involved in complex regulation and signaling pathways, focusing on post-translational phosphorylation and transcriptional regulation, as well as the control of growth, development and remodeling of skeletal structures.\\n] | \n", + "[ This enrichment test demonstrates over-representation of the genes involved in cell signaling, structural and enzymatic proteins, and morphogenesis. Mechanism: The mechanisms underlying this enrichment are likely related to the roles of these proteins in regulating the mechanism of intercellular signaling associated with cell development, adhesion, migration, metabolism, skeletal growth, and cell death. ] | \n", + "0.88 | \n", + "5 | \n", + "
| 665 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-1 | \n", + "[ Many of the genes are clustered around those involved in structure, development and regulation. They are involved in processes such as mitotic regulation, bone morphogenesis, morphogenesis of specific organs and tissues, regulation of signaling pathways, regulation of transcription, regulation of cell proliferation, cellular responses to external stimuli, protein phosphorylation and DNA binding.\\n\\nMechanism: These genes are likely to be involved in the regulation and development of several different processes, including the regulation of cell proliferation, transcription, morphogenesis of organs and tissues, and mitotic regulation. These mechanisms are likely to be controlled by the interactions among gene products, signaling pathways and regulatory components such as transcription factors.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.67 | \n", + "788 | \n", + "
| 666 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-0 | \n", + "[ Proteins involved in development, cell growth, gene transcription, and metabolism are enriched.\\nMechanism: These proteins are involved in a variety of biological processes that underlie development and cell growth, as well as affecting gene transcription and metabolism.\\n] | \n", + "[\\n\\nSummary: The enriched terms from the list of genes suggest a commonality in roles related to protein and organelle trafficking, DNA methylation, transcription and binding, chromatin remodeling, cell cycle regulation and metabolism. \\n\\nMechanism: The proposed mechanism is that these processes are essential components of pathways that regulate cell development, growth, and the response to internal and external stimuli.\\n\\n] | \n", + "0.90 | \n", + "151 | \n", + "
| 667 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-1 | \n", + "[ Genes in this list are mainly involved in cell growth, morphogenesis, regulation of transcription, signal transduction of receptors, DNA/protein activity and metabolism. More specifically, the terms enriched in this list of genes are cell proliferation, cell cycle regulation, DNA replication and repair, signal transduction, calcium signaling, apoptosis, lipid metabolism and oxygen pathway.\\n\\nMechanism: The genes in this list mainly participate in the regulation of various biological processes through their encoding for proteins that act as transcription factors, receptors, and enzymes. These proteins are activated by a variety of signals including DNA damage, growth factors and hormones to induce changes in gene expression and cellular behavior. They also control cell growth, differentiation and metabolism by regulating DNA, protein, lipid and oxygen pathways, ultimately resulting in morphogenesis and cell proliferation. \\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.67 | \n", + "922 | \n", + "
| 668 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE] | \n", + "1.00 | \n", + "0 | \n", + "
| 669 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[\\nSummary: The gene list appears to mostly contain genes involved in Wnt signaling, Notch signaling, transcription regulation and cell cycle regulation processes.\\nMechanism: The underlying biological mechanism appears to be the regulation of processes such as transcription, cell cycle, and Wnt and Notch signaling that may in turn affect the morphogenesis and development of various organs and tissues.\\n] | \n", + "[ Genes highly enriched in the provided list have functions related to cell signaling and regulation, including morphogenesis, transcription, and development. Specifically, genes involved in Wnt, Notch, and Hedgehog pathways, transcription factors, and cell cycle genes such as Axin, β-catenin, HDAC2, and CUL1 are all significantly enriched in the list.\\n\\nMechanism: Many of the genes involved in these pathways are responsible for controlling cell fate and regulating morphogenesis and development. The Wnt pathway, a key regulator in embryonic development, is involved in axial patterning, tissue organization and differentiation, and cell-fate decisions. The Notch and Hedgehog pathways are also important for stem cell maintenance and development in early development, as well as tissue patterning, morphogenesis, and organogenesis in adulthood. The transcription factors, such as LEF1, TCF7, and NKD1, drive gene expression in response to these signaling molecules. Lastly, genes such as ADAM17, DKK1, PSEN2, and AXIN2 are involved in cell-cycle regulation and apoptosis. \\n\\n] | \n", + "0.93 | \n", + "675 | \n", + "
| 670 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "T cell proliferation-0 | \n", + "[ \\nSummary: The genes in the list are found to be involved primarily in cell signalling, development, and immunity processes.\\nMechanism: The numerous genes with enriched terms are involved in coordinating both intra- and extracellular activity through signal transduction pathways and receptor-mediated signaling, with downstream effects on cellular growth, differentiation, and function within various organs and systems in the body.\\n] | \n", + "[\\nSummary: This list of genes are enriched for terms related to cell development and signaling, specifically those involved in receptor-mediated signaling and the regulation of cell morphology. \\nMechanism: These genes likely act through regulating cell development and receptor-mediated signaling pathways to their respective functions, such as morphogenesis and gene expression.\\n] | \n", + "0.94 | \n", + "55 | \n", + "
| 671 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "T cell proliferation-1 | \n", + "[ The enrichment test found that the genes listed have common functions associated with cell signaling and immune regulation, such as signal transduction, growth factor production and response, immune response and modulation, calcium homeostasis, transcription factors, development and differentiation, receptor binding, and cytokine production.\\n\\nMechanism: The enrichment test suggests that these genes may contribute to signal transduction pathways that facilitate cell proliferation, differentiation, and survival; growth factor production and signal transduction; immune response and modulation; calcium homeostasis; transcription factor activity including regulation of gene expression; development and differentiation; receptor binding and signal transduction; and cytokine production.\\n\\n] | \n", + "[ \\nThis sample of genes are mainly involved in regulation of the immune system, cell signaling, cytoplasmic transport, and apoptosis. Specifically, the genes are enriched for terms such as cytokine receptor binding; cell adhesion; immunoreceptor-antigen complex binding; regulation of the ubiquitin-proteasome pathway; transcription factor regulator activity; GTP-binding protein binding; cell differentiation; T-cell receptor binding; antigen presentation; and immune system process.\\n\\nMechanism: This list of genes likely act in concert to regulate the immune system. They perform a variety of functions, including binding and processing cytokines, receptor-antigen complexes, and other molecules involved in the binding or processing of molecules, such as transcription factors, that are involved in regulating gene expression. Additionally, these genes may be involved in cell differentiation, antigen presentation, and other processes involved in the regulation of the immune system. \\n\\n] | \n", + "0.91 | \n", + "197 | \n", + "
| 672 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "Yamanaka-TFs-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The genes provided are related to transcription factor activity, as they are associated with embryonic stem cell differentiation and pluripotency.\\n] | \n", + "0.67 | \n", + "133 | \n", + "
| 673 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "Yamanaka-TFs-1 | \n", + "[\\nThe list of genes provided encode transcription factors associated with early development of embryonic stem cells.\\nMechanism: Transcriptional regulation via these transcription factors control the expression of other genes related to embryogenesis and stem cell development.\\n] | \n", + "[ The given list of genes is involved in the regulation of cell differentiation and development, specifically in the formation of stem cells, by regulating the expression of developmental proteins. ] | \n", + "0.90 | \n", + "79 | \n", + "
| 674 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "amigo-example-0 | \n", + "[\\nSummary: This term enrichment test on the list of human genes shows enrichment for terms related to extracellular matrix organization and cell adhesion, morphogenesis and morphological changes, and cell signaling. \\nMechanism: The underlying biological mechanisms may involve a combination of protein-protein interactions, transcriptional regulation and extracellular matrix modifications.\\n] | \n", + "[ The genes included in this list are related to cell proliferation, tissue morphogenesis, motility regulation, vascular development, bone growth, and the immune system. The mechanism is the transcription of gene products that cause expression of varied proteins that mediate these functions.\\n\\nMechanism: Transcription of gene products inducing the expression of varied proteins that mediate cell proliferation, tissue morphogenesis, motility regulation, vascular development, bone growth, and the immune system.\\n\\n] | \n", + "0.85 | \n", + "124 | \n", + "
| 675 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "amigo-example-1 | \n", + "[COULD NOT PARSE] | \n", + "[ This list of genes are all involved in the development and maintenance of the vascular system. Specifically, these genes play a role in angiogenesis, cell proliferation and migration, matrix remodeling, and tissue remodeling. The genes are implicated in processes such as Jagged-mediated signaling, transcriptional regulation, platelet activation and aggregation, immune regulation, and extracellular matrix formation.\\n\\nMechanism: These genes are involved in a variety of pathways that are responsible for the formation and maintenance of the vascular system. Specifically, the Jagged and Notch pathways are implicated in the control of endothelial cell proliferation and migration, while the TGF-β and Wnt/β-Catenin pathways are involved in matrix remodeling. Additionally, these pathways are also involved in platelet activation and aggregation and the formation of extracellular matrix components.\\n\\n] | \n", + "0.68 | \n", + "888 | \n", + "
| 676 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_0-0 | \n", + "[\\nSummary: The list of genes are involved in morphogenesis, development, transcription regulation, cellular signalling and ion transport.\\nMechanism: The genes are likely to be involved in a variety of biochemical and molecular pathways pertaining to the specified functions.\\n] | \n", + "[ Genes associated with this list are enriched for functions related to development and signaling, including cell growth, differentiation, and migration; chromatin modulation; transcription regulation; cytoskeletal organization; intracellular trafficking and adhesion; signal transduction; and DNA/RNA metabolic processes.\\nMechanism: The genes are likely to be involved in multiple biological mechanisms and pathways, including processes related to healing, morphogenesis, angiogenesis, and muscle growth and development.\\n] | \n", + "0.92 | \n", + "247 | \n", + "
| 677 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_0-1 | \n", + "[ These genes are primarily involved in development and signaling pathways, particularly morphogenesis, neuronal growth, and neuronal system development. Mechanism: These genes facilitate cell-cell communication and signaling, allowing for cells to coordinate their functions together and form efficiently organized tissues and organs. ] | \n", + "[ This analysis identified a number of genes involved in various cellular processes such as chromatin regulation, cell development, protein translation, and ion transport.\\nMechanism: The underlying biological mechanism likely involves regulation of gene expression through the actions of transcription factors, the post-translational modifications of proteins, and the transport of ions across cell membranes.\\n] | \n", + "0.87 | \n", + "74 | \n", + "
| 678 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_1002-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The human genes listed are involved in skeletal muscle structure and contractility. The genes are enriched for processes such as myofibrillogenesis, actin filament organization, and muscle contraction.\\n\\nMechanism: The genes likely act to regulate processes involved in myofibrillogenesis, such as Z-disc formation and maintenance, nuclear positioning, and muscle fiber organization. They also may act to modulate ion channel influx/efflux, thereby influencing muscle contraction and force. \\n\\n] | \n", + "0.66 | \n", + "478 | \n", + "
| 679 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "bicluster_RNAseqDB_1002-1 | \n", + "[ The genes listed were significantly over-represented for processes related to muscle formation and human body structure, such as muscle and skeletal development, skeletogenesis, and myogenesis. \\n\\nMechanism: The set of genes is involved in multiple pathways related to muscle formation and structure in the human body, such as muscle and skeletal development, skeletogenesis, and myogenesis. These pathways likely involve the regulation of protein synthesis and biosynthesis, as well as processes related to muscle contraction and relaxation. \\n\\n] | \n", + "[\\nSummary: Genes in this set are involved in muscle structures and processes.\\n] | \n", + "0.90 | \n", + "468 | \n", + "
| 680 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "endocytosis-0 | \n", + "[ These genes are involved in signaling pathways, vesicle/lipid trafficking, and cellular adhesion related processes.\\nMechanism: These genes act as regulators of nutrients, cell metabolism, and cytoskeletal organization. They are also involved in endocytosis, exocytosis, and the regulation of intercellular adhesion and motility.\\n] | \n", + "[\\nSummary: These genes are related to lipid metabolism, cell signaling pathways, and cell cycling.\\nMechanism: These genes are thought to have a role in regulating lipid metabolism, cell signaling pathways and cell cycling. \\n] | \n", + "0.91 | \n", + "107 | \n", + "
| 681 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "endocytosis-1 | \n", + "[\\nSummary: The genes in this list are associated with processes related to membrane trafficking, receptor signaling, protein proteolysis, and lipid metabolism. \\nMechanism: The underlying biological mechanism is likely regulation of membrane trafficking, receptor signaling, protein proteolysis, and lipid metabolism. \\n] | \n", + "[\\nSummary: The genes in this list are predominantly involved in endocytosis and intracellular signaling.\\nMechanism: The genes in this list interact to form a molecular pathway that is involved in endocytosis and intracellular signaling. Endocytosis allows receptors and newly synthesized molecules to be moved cellular compartments and can result in changes in cell signaling.\\n] | \n", + "0.92 | \n", + "59 | \n", + "
| 682 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "glycolysis-gocam-0 | \n", + "[ An analysis of gene functions in these 10 genes shows an enrichment of terms associated with metabolism, including glycolysis, aerobic glycolysis, and gluconeogenesis.\\n\\nMechanism: This suggests a possible underlying biological mechanism in which glycolysis and gluconeogenesis pathways are deployed by cells in order to provide sufficient energy to cope with various metabolic demands.\\n\\n] | \n", + "[\\nBased on the list of genes provided, common terms enriched amongst the genes include ATP synthesis, glycolysis, energy metabolism, and metabolic pathways.\\n\\nMechanism: \\nThe underlying biological mechanisms involve ATP synthesis by way of glycolysis and energy metabolism pathways, which produce necessary energy required for a variety of cellular activities.\\n\\n] | \n", + "0.93 | \n", + "28 | \n", + "
| 683 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "glycolysis-gocam-1 | \n", + "[ The human genes provided in this list are enriched for metabolic functions involved in glycolysis and pentose phosphate pathways.\\nMechanism: The mechanism likely involves the direct or indirect control of enzymatic activities through the coordinated activity of multiple genes.\\n] | \n", + "[ The genes identified are related to glycolysis, the metabolic pathway that produces ATP from glucose and other carbohydrates. \\nMechanism: Glycolysis involves the series pathways in which a compound molecule of glucose is broken down into two molecules of pyruvic acid, which are further converted into ATP. \\n] | \n", + "0.89 | \n", + "30 | \n", + "
| 684 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "go-postsynapse-calcium-transmembrane-0 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE] | \n", + "1.00 | \n", + "0 | \n", + "
| 685 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "go-postsynapse-calcium-transmembrane-1 | \n", + "[COULD NOT PARSE] | \n", + "[\\nSummary: This gene set is primarily involved in neuronal functional regulation, including ion transport, membrane potential regulation and neurotransmission.\\nMechanism: These genes are involved in the regulation of neuronal activity, likely through the regulation of a number of ion channels, neurotransmitter receptors, and calcium/potassium regulators.\\n] | \n", + "0.69 | \n", + "341 | \n", + "
| 686 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "go-reg-autophagy-pkra-0 | \n", + "[\\n \\nSummary: The genes in this list are involved in various aspects of biological processes, ranging from cell growth and development to immune response and proteolysis.\\n \\nMechanism: The genes interact in multiple overlapping pathways to influence cellular processes such as immune response and protein degradation. \\n \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "303 | \n", + "
| 687 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "go-reg-autophagy-pkra-1 | \n", + "[ Several pathways related to cellular signaling and signalling transduction are enriched among this set of human genes. Specifically, phosphatidylinositol signalling, vascular endothelial growth factor receptor signalling, progesterone-mediated oocyte maturation, NF-kB signaling and neuroprotection are all enriched with five or more genes represented in the set, suggesting that the underlying biological mechanism could be related to these pathways.\\n\\nMechanism: Several pathways related to cellular signaling and signalling transduction.\\n\\n] | \n", + "[\\nThe genes provided are all involved in cell regulation and signaling pathways. Specifically, they all have roles in the activation of transcription factors, and in the activation, regulation and inhibition of signaling proteins such as Ras, Akt and calcium associated kinases.\\nMechanism: \\nThe genes all act together in order to affect the expression of various genes and proteins. They function by either upregulating or downregulating the expression of transcription factors and signaling proteins, as well as by modulating the phosphorylation state of these proteins, thus controlling their activity.\\n] | \n", + "0.89 | \n", + "62 | \n", + "
| 688 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[ These human genes are involved in cellular functions related to glycosaminoglycan metabolism, lysosomal and catabolic pathways, as well as digit and skeletal development. The genes are enriched for functions in carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomal, peroxisomal, and catabolic processes; and digit, skeletal, and limb morphogenesis. \\nMechanism: The genes likely act by providing enzymes, carriers, and structural proteins that together play essential roles in the transport and metabolism of carbohydrates, as well as help form and shape the skeleton and digits during embryonic development. \\n] | \n", + "[ These genes are apparently associated with lysozymes, mucins, glycosyltransferases, and hyaluronidases, enzymes and proteins with roles in the breakdown and regulation of glycosylation.\\nMechanism: The mechanism behind this gene cluster's biological role seems to be in the regulation of cell processes related to glycosylation, such as enzyme production and its breakdown.\\n] | \n", + "0.88 | \n", + "272 | \n", + "
| 689 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[ The human genes in this list are mostly related to glycoside hydrolase (GH) activity, but also include proteins involved in chitin and mucin biosynthesis, as well as cysteine protease and lysosomal activities. Most of the genes have either a glycoside hydrolase activator or a lysosomal enzyme function. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "291 | \n", + "
| 690 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "ig-receptor-binding-2022-0 | \n", + "[COULD NOT PARSE] | \n", + "[\\nSummary: The genetic pathways enriched in these genes involves immunoglobulin heavy/light chain combination, antigen specific receptors, J-chain, and T-lymphocyte receptors. \\nMechanism: These genes mainly play a role in immune response, specifically the regulation of the combination of immunoglobulin heavy and light chains to form antigen-specific receptors, the formation of J-chain, the production of T-lymphocyte receptors, and the regulation of immune function.\\n] | \n", + "0.68 | \n", + "454 | \n", + "
| 691 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "ig-receptor-binding-2022-1 | \n", + "[\\nSummary: These genes are mainly involved in Immunoglobulin Function and Blood Coagulation. \\nMechanism: The terms enriched for these genes are related to the immune system and blood clotting pathways, specifically those related to Immunoglobulins, B Cell Receptors, and Fibrinogen-related proteins. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "285 | \n", + "
| 692 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "meiosis I-0 | \n", + "[ \\nSummary: Genes involved in DNA damage repair and meiotic recombination processes\\nMechanism: Genes in the list are involved in DNA damage recognition, DNA double-strand break repair, meiotic recombination, and chromosome segregation.\\n] | \n", + "[ This list of genes is enriched for functions related to DNA replication, repair, and replication fidelity. Mechanism: The list of genes is likely to be involved in simulating DNA synthesis, prioritizing DNA strands for replication, ensuring proper repair of damaged DNA strands, and ensuring that high-fidelity replication is taking place during the cell cycle. ] | \n", + "0.90 | \n", + "128 | \n", + "
| 693 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "meiosis I-1 | \n", + "[ Enrichment test revealed that genes are related to DNA repair, replication, and splicing.\\n\\nMechanism: The commonalities in the function of the genes revealed in the enrichment test suggest that there may be a biological pathway that is responsible for creating and maintaining a stable genetic system. This may involve DNA repair to combat mutation and damage, replication to create new copies, and splicing for the proper expression of genes.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "431 | \n", + "
| 694 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "molecular sequestering-0 | \n", + "[ This enrichment test indicates that the listed genes are involved in multiple pathways that are involved in cell proliferation, apoptosis, and molecular transport in diverse cell types. Specifically, some of the enriched terms associated with these genes include mechanisms involved in cell cycle checkpoints, cell adhesion/motility complexes, transcriptional complexes, protein modifications, and RNA processing complexes. \\nMechanism: These pathways likely affect cell proliferation, apoptosis, and molecular transport by responding to a variety of environmental stimuli, including calcium-based signaling, growth factor-mediated signaling, and oxidative stress. \\n] | \n", + "[ 17 of the genes in the list are related to functions involving calcium homeostasis, including calcium signaling, regulation of calcification, and regulation of calcium ion transport. Mechanism: The genes identified are involved in the regulation of calcium homeostasis and signaling, along with functions related to calcification, calcium buffering and transport, protection against calcium overload, and calcium-v influx/efflux. ] | \n", + "0.85 | \n", + "235 | \n", + "
| 695 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "molecular sequestering-1 | \n", + "[ The analysed genes are mostly involved in calcium binding, apoptotic regulation, and immune modulation, all of which are important mechanisms for a variety of biologic processes.\\n\\nMechanism: The mechanism is likely related to the genes' ability to modulate calcium and apoptotic pathways as well as reduce oxidative stress and influence immune effectors.\\n\\n] | \n", + "[\\nSummary: Our list of human genes suggests pathways involved in cell structure regulation and metabolism.\\nMechanism: These genes are likely involved in the regulation of cell morphology, metabolic processes and apoptosis.\\n] | \n", + "0.87 | \n", + "135 | \n", + "
| 696 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "mtorc1-0 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE] | \n", + "1.00 | \n", + "0 | \n", + "
| 697 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "mtorc1-1 | \n", + "[ Analysis of the genes provided shows that the genes are enriched for functions relating to energy production and metabolism, protein biosynthesis and folds, cell regulation, growth and development, and protein turnover. \\n\\nMechanism: The likely underlying biological mechanism behind these functions is likely related to the regulation, management and production of energy and metabolites to carry out processes such as cell growth and to synthesize proteins which are essential for the functioning of the cell, cell signaling and related pathway activities.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "545 | \n", + "
| 698 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "peroxisome-0 | \n", + "[ PEX proteins are involved in peroxisome biogenesis and formation. \\nMechanism: PEX proteins play a role in driving the biogenesis of peroxisomes, a type of organelle that plays a role in various metabolic functions. \\n] | \n", + "[\\nThis list of genes is enriched for terms related to protein homeostasis and peroxisome biogenesis. The genes are likely to have roles in maintaining and regulating the levels of specific proteins, as well as helping to form and breakdown peroxisomes in the cell.\\n\\nMechanism: The mechanism underlying these functions appears to involve forming, maintaining and regulating the levels of specific proteins, as well as assisting in the formation and breakdown of peroxisomes in the cell. \\n\\n] | \n", + "0.86 | \n", + "270 | \n", + "
| 699 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "peroxisome-1 | \n", + "[ The provided genes are all peroxisomal biogenesis factor genes and are associated with peroxisomal biogenesis, protein transport, and oxidative damage resistance.\\n\\nMechanism: These factors regulate the assembly of the peroxisome, a subcellular organelle involved in fatty acid metabolism, carbohydrate metabolism, and oxidative damage resistance.\\n\\n] | \n", + "[ The genes provided are all related to Peroxisomal Biogenesis, an important cellular process. \\nMechanism: Peroxisomal biogenesis requires the coordinated expression of multiple genes in order for the peroxisome to be expressed and maintained in cells. \\n] | \n", + "0.90 | \n", + "96 | \n", + "
| 700 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "progeria-0 | \n", + "[ The genes in this list are all associated with a cellular carboxyl-methyl transferases, a type of protein involved in RNA and DNA metabolism. The proteins are associated with development and growth, particularly that of cell structural elements such as gene transcription and transcriptional regulation. \\nMechanism: The mechanism involves carboxyl-methyl transferase proteins that modulate gene expression and the communication between transcription factors and the DNA strand.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "464 | \n", + "
| 701 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "progeria-1 | \n", + "[ These genes are involved in a number of processes related to DNA replication and repair, including DNA replication and repair, nucleosome assembly, telomere maintenance, and transcriptional regulation.\\n \\nMechanism: Genes LMNA, WRN, and BANF1 are all involved in several mechanism related to the general processes of DNA replication, repair, and transcriptional regulation through the assembly and maintenance of the different levels of chromatin structure. LMNA is involved in the assembly and disassembly of the nuclear lamina, a type of intermediate filament that helps to anchor chromosomal proteins to the nuclear envelope. WRN is involved in telomere maintenance, which is critical for accurate chromosomal replication and stability. Finally, BANF1 is involved in a number of DNA repair processes, including translesion DNA synthesis, homologous recombination, and non-homologous end joining. These processes are essential for the accurate repair and replication of DNA molecules, and all require an understanding of, and proper interactions between, transcription and chromatin structure. \\n\\n] | \n", + "[ Shortly, these genes are involved in a range of functions including transcriptional regulation, DNA repair, cell cycle regulation, and cell differentiation. \\nMechanism: These genes all have common functions related to the transcription, repair, and/or regulation of DNA, which suggests that they all play a role in the response to cellular damage or stress, which in turn can influence the downstream processes of cell cycle, differentiation, and growth.\\n] | \n", + "0.85 | \n", + "642 | \n", + "
| 702 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "regulation of presynaptic membrane potential-0 | \n", + "[\\n\\nSummary: This term enrichment test identified genes involved in signal transduction, ion transport, and regulation of neurotransmitter release.\\nMechanism: This is likely related to the regulation of excitatory and inhibitory signal transmission, potentially mediated by ion channels and signal transduction pathways associated with the G-protein coupled receptors, voltage-gated K+ and Na+ channels, and ligand-gated ion channels.\\n] | \n", + "[ Through a term enrichment test on this list of genes, we see that they are over-represented in terms related to ion conductivity and neural excitability, including ion channels, membrane proteins, and synapse formation.\\n\\nMechanism: These genes likely play a role in neural excitability, leading to the formation of specific ion channels that can conduct ions and help form synapses between neurons.\\n\\n] | \n", + "0.90 | \n", + "32 | \n", + "
| 703 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "regulation of presynaptic membrane potential-1 | \n", + "[COULD NOT PARSE] | \n", + "[ This group of genes is enriched for terms related to ion-channel function, neuron excitability, and synaptic transmission.\\nMechanism: This group of genes suggested the underlying molecular pathway involves communication between neurons via ion-channel mediated synaptic transmission.\\n] | \n", + "0.68 | \n", + "270 | \n", + "
| 704 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "sensory ataxia-0 | \n", + "[ This list of genes is related to muscle, central and peripheral nervous system development, as well as protein and lipid transport and metabolism. \\nMechanism: The genes appear to be involved in regulatory pathways for growth and development of the skeletal and nervous systems via coordination of morphology, protein and lipid synthesis, and transport.\\n] | \n", + "[ These genes are mainly involved in protein synthesis, metabolism, ion channel transport, and muscle contraction or development.\\n\\nMechanism: These genes function as transcriptional regulators, enzymes in metabolic pathways, ion channels, or as key mediators of neuromuscular development and contraction.\\n\\n] | \n", + "0.91 | \n", + "49 | \n", + "
| 705 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "sensory ataxia-1 | \n", + "[\\n\\nSummary: Analysis of the genes yielded significant enrichment of terms related to protein transport, development of the central nervous system, skeletal structure and muscle formation.\\n\\nMechanism: The function of these genes likely reflects the underlying biological pathways for the development and maintenance of different organ systems, including the central nervous system, muscular system, and skeletal structure. \\n\\n] | \n", + "[ This list of genes encodes many proteins which are involved in nucleic acid metabolism, binding, and transport. Terms enriched in these genes include: Nucleic Acid Metabolism; Nucleic Acid Binding; Nucleic Acid Transport; Protein Metabolism; Protein Binding; and Protein Transport.\\n\\nMechanism: The proteins encoded by these genes are likely to be involved in nucleic acid metabolism and other related downstream processes. These proteins are likely involved in mRNA transcription, mRNA processing and/or mRNA translation. The proteins could also be involved in processes like RNA editing, DNA replication, DNA repair, and DNA recombination. These proteins are likely to be involved in the regulation of gene expression and other pathways related to this process.\\n\\n] | \n", + "0.87 | \n", + "342 | \n", + "
| 706 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "term-GO:0007212-0 | \n", + "[ This list of genes is enriched for terms related to signal transmission and transduction, specifically the G Protein-Coupled Receptor (GPCR) family, which is associated with cell-signaling pathways and regulation of receptor activities. The specific terms enriched include G alpha subunit signaling, related GPCR activation and signaling, G Protein-Coupled Receptor (GPCR) function, and dimerization. \\n\\nMechanism: This set of genes is involved in pathways that involve the G protein-coupled receptor (GPCR) family. GPCRs can bind to extracellular molecules, such as hormones and neurotransmitters, and then activate signaling pathways inside the cell, leading to the activation of intracellular proteins, including G proteins. The G proteins then facilitate the exchange of proteins such as cAMP, DAG, and calcium ions into the cell, in order to create a signal cascade and ultimately effect changes to the cell’s behavior.\\n\\n] | \n", + "[ This gene list is enriched for terms related to G-Protein Coupled Receptors (GPCRs), G-protein subunits, adenylate cyclase, calcium channels, and kinases.\\n\\nMechanism: The GPCRs and G protein-coupled subunits are involved in signal transduction pathways that regulate a variety of cellular activities. They activate adenylate cyclases, which catalyze the synthesis of the secondary messenger cAMP. This acts downstream to activate pathways and processes such as G-protein mediated second messenger systems and cation channels. Kinases are involved in the regulation of the G-protein by phosphorylating the Gα subunits and other associated components, leading to changes in their activity, and ultimately, signaling cascades.\\n\\n] | \n", + "0.96 | \n", + "200 | \n", + "
| 707 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "term-GO:0007212-1 | \n", + "[\\nSummary: The list of genes is involved in the regulation cellular signaling and development of the nervous system.\\nMechanism: The list of genes is likely transmitting signals through G proteins, phosphorylation cascade, and calcium signaling pathways to regulate the development of the nervous system, including alterations in the nervous system structure, indoleamine metabolism, and neurotransmission.\\n] | \n", + "[\\n\\nSummary: The enriched terms from these genes suggest a correlation with signaling pathways, cellular growth and differentiation, organization of the cytoskeleton, regulation of endocrine systems, and transcriptional regulation. \\n\\n] | \n", + "0.88 | \n", + "173 | \n", + "
| 708 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "tf-downreg-colorectal-0 | \n", + "[ The gene list includes members of the nuclear receptor superfamily, molecules involved in transcription regulation, epigenetic regulation, cell cycle regulation, DNA binding and chromatin remodeling, developmental processes and cell signaling pathways, and components of the nuclear lamina and nuclear matrix.\\n\\nMechanism: The enriched terms suggest a molecular pathway underlying gene regulation, where transcription factors and chromatin reorganization molecules interact with nuclear receptors and other molecular mechanisms in order to regulate gene expression. Moreover, the gene list may represent a mechanism involved in the regulation of cell growth, differentiation and development.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.67 | \n", + "678 | \n", + "
| 709 | \n", + "text-davinci-003 | \n", + "no_synopsis | \n", + "tf-downreg-colorectal-1 | \n", + "[ The genes provided are involved in developmental pathways and functions, such as transcriptional regulation, chromatin modification, morphogenesis, cardiovascular development and differentiation.\\nMechanism: These genes are associated with a wide range of cellular processes, primarily related to embryonic development, including fetal growth and development, stem cell differentiation, and postnatal growth. \\n] | \n", + "[ The enriched terms for this list of genes are cellular growth, transcriptional regulation, and chromatin remodeling. These genes are generally involved in the regulation of transcription, chromatin modifications, and cell cycle regulation. These terms are statistically over-represented compared to the gene list provided.\\n\\nMechanism: The likely underlying biological mechanism for these genes is that they are involved in multiple pathways like transcription, chromatin modifications, and cell cycle regulation. These pathways control essential processes such as cell growth and differentiation in the body. Through these mechanisms, the genes may help to regulate embryonic development and maintain tissue homeostasis in adults. \\n\\n] | \n", + "0.91 | \n", + "324 | \n", + "
| 710 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "EDS-0 | \n", + "[ These genes are mostly involved in collagen metabolic processes and extracellular matrix organization (ECM) - processes mediated by metalloendopeptidase activity, chondroitin sulfate biosynthesis, and galactosyltransferase activity, as well as by platelet derived growth factor, calcium ion, and zinc ion binding activities. Genes which affect ECM organization and/or collagen metabolic processes are implicated in symptoms of Ehlers-Danlos Syndrome.\\n\\nMechanism: The mechanism for these metabolic processes and ECM organization is likely to include the generation of specific proteins, peptides, and/or peptide modifications which affect the activity, binding, and/or interactions of collagen molecules and potential substrates of collagen.\\n\\n] | \n", + "[ \\nSummary: The list of genes are found to be associated with proteins involved in collagen and extracellular matrix related activities and the control of transcription.\\nMechanism: These proteins are involved in various processes, such as collagen fibril organization, connective tissue development, extracellular matrix organization, glycosaminoglycan biosynthetic process, negative regulation of transcription by RNA polymerase II, positive regulation of transcription by RNA polymerase II, proteoglycan biosynthetic process, Rho protein signal transduction, skin morphogenesis, and zymogen activation.\\n] | \n", + "0.89 | \n", + "139 | \n", + "
| 711 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "EDS-1 | \n", + "[ These human genes enable functions related to collagen fibril organization, extracellular matrix organization, collagen biosynthetic processes, glycosaminoglycan biosynthetic processes, peptidyl-prolyl cis-trans isomerase activity, epidermal cell differentiation, and wound healing.\\n\\nMechanism: The genes involved likely work towards a common mechanism involving the integration of extracellular matrix and collagen assembly and remodeling, as well as supporting cellular processes such as wound healing, epidermal cell differentiation, and collagen fibril organization.\\n\\n] | \n", + "[\\nSummary: The genes in this list are associated with extracellular matrix organization, collagen fibril organization, collagen biosynthesis, proteoglycan biosynthesis, and glycosaminoglycan biosynthesis.\\nMechanism: These genes are likely to be involved in the organization of extracellular matrix, the formation of collagen fibrils, and the synthesis of proteoglycans and glycosaminoglycans. \\n] | \n", + "0.92 | \n", + "180 | \n", + "
| 712 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "FA-0 | \n", + "[COULD NOT PARSE] | \n", + "[ Genes are involved in processes related to DNA repair and protein monoubiquitination, part of Fanconi anaemia nuclear complex, and located in multiple cellular components including chromatin, nucleus and cytosol. Hypothesis: These genes work in concert to coordinate the repair of DNA damage, likely with monoubiquitination acting as a signal for protein binding activities related to DNA repair. ] | \n", + "0.69 | \n", + "383 | \n", + "
| 713 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "FA-1 | \n", + "[COULD NOT PARSE] | \n", + "[\\nSummary: Members of the Fanconi Anemia Nuclear Complex are involved in protein monoubiquitination and DNA repair processes.\\nMechanism: Members of the Fanconi Anemia Nuclear Complex act in a coordinated fashion to catalyse monoubiquitination of proteins, regulate cell cycle, and repair damaged DNA.\\n] | \n", + "0.69 | \n", + "285 | \n", + "
| 714 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ADIPOGENESIS-0 | \n", + "[ The genes listed are enriched for functions related to protein binding, protein homodimerization, ATP binding, and DNA binding activities, as well as functions related to enzyme and receptor activities, GTPase and phosphorylation activities, and metal ion and lipid bindings.\\n\\nAdditionally, several of the genes are enriched for functions related to metabolic processes, including NADH dehydrogenase and glycerophosphocholine O-acyltransferase activities, as well as carboxylic ester hydrolase, aldehyde dehydrogenase, ubiquitin protein ligase, and 2'-3'-cyclic GMP-AMP binding activities.\\n\\nMechanism:The proteins encoded by these genes are likely involved in a variety of biological processes, such as processes related to metabolism, signaling, and cell regulation, which requires their involvement in protein-protein or protein-DNA interactions, as well as protein homodimerization, ATP binding, and chemical and lipid bindings. The proteins also likely participate in various enzyme activities, such as cyclic GMP-AMP binding and GTPase activities. \\n\\n] | \n", + "[ The terms found to be enriched in the gene summaries include “protein binding activity”, “NAD(P)H oxidase activity”, “ATP binding activity”, “GTP binding activity”, “transmembrane transporter activity”, “DNA binding activity”, “receptor binding activity”, “cysteine-type endopeptidase inhibitor activity”, “caspase binding activity” and “RNA binding activity”. \\n\\nMechanism: These genes likely contribute to or are part of a variety of processes involving cellular signaling pathways, tissue development and repair, immune system modulation, and metabolic pathways.\\n\\n] | \n", + "0.94 | \n", + "489 | \n", + "
| 715 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ADIPOGENESIS-1 | \n", + "[ Processes related to protein function, binding, regulation, transportation, metabolism, and receptor activity are enriched in this list of genes, as evidenced by the high frequency of activities such as protein homodimerization, enzyme binding, ATPase activity, and receptor binding. The underlying biological mechanism likely involves a complex network of proteins that interact with and regulate each other for a variety of cellular processes. \\n] | \n", + "[ \\nSummary: These genes are largely involved in protein binding activities and enzyme activities.\\nMechanism: Enzyme activities and protein binding activities allow for the regulation of cell processes, cell signaling and energy production. \\n] | \n", + "0.92 | \n", + "208 | \n", + "
| 716 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[ This list of genes, describe a variety of functions related to cellular communication, regulation, and response. This includes binding, receptor activity, signaling, enzyme and protein binding activity, transcription, cytokines activity, chemical and peptide binding, as well as receptor and protein complex binding activity.\\n\\nMechanism: These genes likely serve as part of a complex molecular network involved in regulating immune responses and regulating other cellular functions. The enriched terms indicate that these genes play a role in various stages of the communication process including receptor binding, signaling, and transcription, as well as other functions such as chemical and peptide binding.\\n\\n] | \n", + "[\\nThis list of genes is involved in a broad range of biological processes, including growth factor and cytokine activities; enzyme binding, activating and regulating activities; transcription activator, receptor and factor binding activities; and other activities related to binding and signaling. These genes are primarily involved in protein homodimerization, protein heterodimerization, and identical protein binding activities, as well as protein kinase, DNA-binding and RNA-binding activities.\\n\\nMechanism:\\nThese processes are mostly facilitated by the interactions between various domain specific proteins and pathways, including SH3 domain binding, C-X-C chemokine binding, heparin binding, ubiquitin-protein ligase binding, calmodulin binding, ICAM-3 receptor activity, TAP complex binding activity, MHC class II protein complex binding, interleukin-12 receptor binding, and Toll-like receptor 2 binding activity.\\n\\n] | \n", + "0.91 | \n", + "209 | \n", + "
| 717 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[ \\nThe list of genes show enrichment for terms related to binding activity (enzyme binding, RNA-binding, protein binding, chemokine receptor binding, DNA-binding), protein kinase binding (protein serine/threonine/tyrosine kinase), and cytokine activity (growth factor activity, interleukin binding, etc).\\n\\nMechanism: These genes are involved in various cellular pathways involving binding and signaling. The binding activity of these genes can lead to the formation of enzyme-substrate/protein-protein complex which is necessary for a variety of physiological processes. The cytokine activity of these genes are likely to involve their roles in regulating cellular growth, differentiation, and the physiological responses to external stimuli.\\n\\n] | \n", + "[ This enrichment test reveals genes associated with extra- and intra-cellular biological processes and functions, specifically related to cell adhesion, receptor binding and signaling, transcription regulatory region sequence-specific DNA binding, chemokine related activities, and enzymatic, growth factor and cytokine related activities. Mechanism: This enrichment test demonstrates the involvement of specific genes in biological pathways related to cell adhesion, receptor binding and signaling, transcription regulatory region sequence-specific DNA binding, chemokine related activities, and enzymatic, growth factor and cytokine related pathways. ] | \n", + "0.91 | \n", + "90 | \n", + "
| 718 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[ The list of human genes demonstrated a significant enrichment of terms related to binding activities and activities involving enzymes, as well as some terms related to cell differentiation and cell cycle progression, suggesting that these genes are involved in diverse cellular processes such as transduction and transition of signals, physiological activities, and structural peptide modifications.\\n\\nMechanism: This list of human genes likely contribute to cellular events by participating in interactions with other molecules such as DNA or proteins, and by catalyzing biochemical modifications.\\n\\n] | \n", + "[ These genes are involved in a variety of functions, including transporter activity, protein binding, protein kinase binding, receptor activity, transcription, cellular metabolism, DNA damage response, and cytoskeleton organization. The commonalities between the gene functions include transport activity, protein binding, DNA binding, hydrolase activity, metal ion binding, GTPase activity, receptor activity, and transcription. The underlying biological mechanism or pathway involves cell organization, signal transduction, cell adhesion, cell cycle progression, and differentiation. \\n\\nMechanism: Cell organization, signal transduction, cell adhesion, cell cycle progression, and differentiation. \\n\\n] | \n", + "0.90 | \n", + "101 | \n", + "
| 719 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[ This gene list provides evidence for the involvement of a variety of protein activities, including binding, kinase activity, transcription, receptor activity, and enzymatic activities, in a variety of metabolic, signaling, and structural processes. The mechanism underlying these processes is likely the regulation of various cellular proteins and pathways, such as phosphorylation, cyclin-dependent protein kinase activity, DNA binding and transcription, and postsynaptic organization.\\n\\nMechanism: Regulation of various cellular proteins and pathways, such as phosphorylation, cyclin-dependent protein kinase activity, DNA binding and transcription, and postsynaptic organization.\\n\\n] | \n", + "[\\nSummary: The given list of genes includes proteins with DNA-binding, transcription, ubiquitin-binding, phosphatase, kinase, and other activities, which are associated with a wide range of cellular processes and pathways.\\n\\nMechanism: The molecules associated with the given genes function as protein regulators to control the expression of specific target genes and regulate intracellular processes.\\n\\n] | \n", + "0.93 | \n", + "283 | \n", + "
| 720 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ANGIOGENESIS-0 | \n", + "[\\nThe list of genes is enriched with functions related to the extracellular matrix and cell-cell/cell-matrix adhesion. These functions include extracellular matrix structural constituent conferring compression resistance, collagen binding activity, integrin binding activity, molecular adaptor activity, identical protein binding activity, fibronectin binding activity, protein dimerization activity, heparan sulfate proteoglycan binding activity, cell-matrix adhesion, and regulation of cell-substrate adhesion. \\nMechanism: The underlying biological mechanism is focused on processes related to extracellular matrix organization, cell-matrix/cell-cell adhesion, and modulation of signaling pathways involved in development, immune response and homeostasis. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "743 | \n", + "
| 721 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ANGIOGENESIS-1 | \n", + "[\\nThis term enrichment test reveals that a majority of these genes are involved in cellular processes such as protein binding activity, signaling receptor binding activity, phospholipid binding activity, positive regulation of intracellular signal transduction, protease binding activity, and positive regulation of macromolecule metabolic process. A majority of these genes are also part of several cellular components, such as chromatin, the plasma membrane, the Golgi apparatus, the endoplasmic reticulum-Golgi intermediate compartment, and the extracellular matrix. \\n\\nMechanism:\\nThe enriched terms indicate that the genes are likely in involved in a variety of transmembrane and extracellular transport processes and in processes related to cellular signaling and metabolism. One possible underlying mechanism is that the genes interact with specific proteins and receptors to alter the phosphorylation of target proteins and regulate the downstream activities, such as the formation of the complex cellular structures and the metabolic activities of cells.\\n\\n] | \n", + "[ \\n\\nSummary: Genes in this list are involved in a variety of functions, including collagen binding, fibroblast growth factor binding, phosphatase binding, integrin binding, calcium ion binding, signaling receptor binding and lipase activity. \\n\\nMechanism: These genes are likely involved in cellular processes and cellular component organization.\\n\\n] | \n", + "0.88 | \n", + "716 | \n", + "
| 722 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-0 | \n", + "[ The list of genes functions is found to be significantly enriched in the following terms: cell-cell adhesion, agonist binding activity, cytoplasmic matrix binding, protein homodimerization and signaling receptor binding, which are involved in cellular adhesive processes and signal transduction. \\nMechanism: The functions of these genes likely work in concert to mediate multiple adhesive processes, as well as signal transduction pathways. \\n] | \n", + "[\\nSummary: The enriched term list includes cell adhesion, integrin binding, GTP binding activity, collagen binding activity, ATP binding activity, phospholipase binding activity, cell-matrix adhesion, cell adhesion molecule binding, and SH3 domain binding. \\nMechanism: The biological mechanism underlying the enrichment includes cell signalling pathways, actin filament binding and cell-to-cell adhesion, as well as cytoskeletal protein binding and receptor binding activities.\\n] | \n", + "0.89 | \n", + "34 | \n", + "
| 723 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_JUNCTION-1 | \n", + "[ The list of genes are associated with a variety of functions, including binding activities (i.e. ion binding, cell adhesion molecule binding, identical protein binding, signaling receptor binding, etc.), catalytic activities (i.e. ATPase activity, GTPase activity, acetyl CoA oxidase activity, nucleotide-exchange activity, etc.), involvement in processes (i.e. T cell activation, cell-matrix adhesion, cell-cell adhesion, extracellular matrix formation, etc.), and structural roles (i.e. extracellular matrix structuring, ankyrin binding, etc.). The enriched terms associated with this set of genes are binding activities, catalytic activities, involvement in biological processes, and structural roles. \\n\\nMechanism: Most of the genes in the list are associated with catalytic activities that, when taken together, provide insights into the underlying biological mechanisms and pathways. These functionalities lead to different types of cell-cell and cell-matrix adhesion, structuring of extracellular matrix, signaling pathways, and many other cellular activities.\\n\\n] | \n", + "[ This set of genes is associated with extracellular matrix structures, adhesion and binding activities, signal transduction/receptors, and cytoskeleton support/stabilization; all necessary for cell-cell and cell-matrix communication and coordination.\\n\\nMechanism: These genes likely contribute to a diverse set of signaling pathways, involved in cell-cell communication and between the cell and the extracellular environment, mediated by binding with substrate molecules, interactions of receptor molecules, and the formation and stabilization of mRNA structure.\\n\\n] | \n", + "0.91 | \n", + "506 | \n", + "
| 724 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_SURFACE-0 | \n", + "[ \\n\\nSummary: The genes listed support a wide range of processes, including membrane and protein organization, protein modification and transport, endocytosis, signal transduction, and apoptosis. \\n\\nMechanism: These genes act at many levels, but the overall result is to help regulate the organization and modifications of protein structures and the movement of proteins (in trafficking and transport) across the membrane.\\n\\n] | \n", + "[ Human genes involved in processes associated with cytosolic transports, membrane transports, and cellular extravasations, in addition to processes involved in the defense response and the positive regulation of macromolecule metabolism, appear to be enriched.\\n\\nMechanism: These processes impact the responses of cells in two ways: by allowing the transport of molecules between cells and by modulating the production of proteins which also modulate cellular activity. Furthermore, the signaling pathways regulated by these proteins impact a wide variety of downstream processes to regulate gene expression, cell motility, and cell adhesion.\\n\\n] | \n", + "0.91 | \n", + "222 | \n", + "
| 725 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_APICAL_SURFACE-1 | \n", + "[ The list of gene descriptions is related to pathways and processes related to cellular adhesion; protein folding and regulation; cytoplasmic ion homeostasis; and regulation of gene expression. The enriched terms that underlie all the genes and their functions include cell adhesion, protein folding and regulation, ion homeostasis, and gene expression regulation.\\n\\nMechanism: Cell adhesion and protein folding are essential processes that enable cells to interact with the extracellular environment and to form and maintain a functional structure. These processes are regulated by cell surface receptors that transmit signals to the cell and regulate gene expression, involved in the regulation of multiple cellular pathways. Ion homeostasis is also an important process, wherein cells maintain adequate balance of various ions in the cytoplasm and regulate various functions, such as cell differentiation, proliferation, and metabolism. Lastly, gene expression is regulated by a variety of transcription factors and signaling pathways, allowing cells to respond to external stimuli and adapt to changes in the cellular environment.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "1120 | \n", + "
| 726 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_APOPTOSIS-0 | \n", + "[\\nSummary: This list of human genes is involved in numerous functions, including enzyme, protein and nucleic acid binding activities, transcription factor, cysteine-type endopeptidase and calcium ion binding activities, oxidation and NAD+ binding activities, among others.\\nThe enriched terms are DNA binding activity; protein binding activity; enzyme binding activity; cysteine-type endopeptidase activity; identical protein binding activity; signaling receptor binding activity; calcium ion binding activity; protein kinase binding activity; transcription factor activity; and BH3 domain binding activity. \\nMechanism: The underlying biological mechanism is likely related to the regulation of various cellular processes, including DNA replication, transcription, apoptosis and cell adhesion. \\n] | \n", + "[\\nSummary: A set of human genes involved in a variety of biological functions, including binding activities and enzyme activities, are enriched for functions such as DNA binding activity, protein dimerization activity, protein binding activity, and enzyme activity.\\n\\nMechanism: These genes are likely to be involved in the control of cellular processes, such as cell proliferation, apoptosis, and signal transduction pathways.\\n\\n] | \n", + "0.94 | \n", + "366 | \n", + "
| 727 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_APOPTOSIS-1 | \n", + "[ The genes listed are primarily involved in apoptosis, cell signaling pathways, the response to UV, and immunological processes. Furthermore, the enriched terms found include calcium ion binding activity, protein binding activity, and identical protein binding activity.\\n\\nMechanism: These genes are likely involved in a variety of pathways, such as apoptosis, cell signaling, cellular response to UV, and immunological processes. Specifically, their activity is likely to be regulated by calcium ions, binding to specific proteins, as well as other molecules or chemical compounds. It is also possible that some of these genes are involved in regulating the transcription of certain genes.\\n\\n] | \n", + "[ Genes in this list are involved in a variety of functions related to immune response, apoptosis, protein folding and expression, cytoskeletal structure and regulation, extracellular matrix structural constituents, transcription/translation regulation, angiogenesis/neovascularization, calcium/potassium ion binding and transport, cell signaling, and other cellular processes. Overrepresented terms include: protein binding activity; identical protein binding activity; enzyme binding activity; DNA-binding transcription factor activity; RNA polymerase II-specific transcriptional activity; cysteine-type endopeptidase activity; and cytokine receptor activity. \\n\\nMechanism: These genes are involved in a wide variety of complex functions that help form, maintain, and shape the immune response, cell structure and cytoskeletal integrity, cell signaling pathways, and inflammatory processes. They work by binding to and regulating a variety of molecules, hormones, and proteins throughout the body and at the cellular level.\\n\\n] | \n", + "0.93 | \n", + "334 | \n", + "
| 728 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[\\n\\n\\nSummary: Genes in this list are primarily involved in metabolic and transporter activities, signaling activities, and protein binding activities.\\n\\nMechanism: The genes primarily have roles in transferring small molecules across membrane boundaries, binding small molecules, and regulating processes such as metabolism and protein interactions.\\n\\n] | \n", + "[ This analysis shows a statistically significant over-representation of genes related to ATP processing/binding activities, cholesterol binding, transmembrane transport, protein heterodimerization, DNA binding, and enzyme/oxidoreductase activity. Mechanism: The underlying biological mechanism of these processes likely involves the maintenance of ATP and cholesterol levels and other metabolic processes, as well as regulation of transcription and cellular signaling via domains such as the SH2 domain or through DNA binding or various ligase activities. ] | \n", + "0.90 | \n", + "208 | \n", + "
| 729 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[ \\nSummary: The listed genes are part of various metabolic pathways, involved in a variety of functions, including DNA binding, ATP hydrolysis, protein homodimerization, peptidase activity, and other enzyme binding and regulatory activities. \\nMechanism: Enzymatic activity and protein binding are key components of the pathways involved, which help to catalyze, catalyze and regulate further metabolic activity. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "397 | \n", + "
| 730 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[ \\nSummary: This term enrichment test reveals an overlap of gene functions related to lipid metabolism, cholesterol homeostasis, and protein regulation.\\nMechanism: The terms enriched suggest that these genes help to maintain proper levels of cholesterol, regulate lipid metabolism and synthesis, and regulate protein expression, localization, and response. \\n] | \n", + "[\\n\\nSummary: These human genes are associated with processes relating to cholesterol biosynthesis, cell adhesion, cell structure and organization, signaling, and apoptosis.\\n\\nMechanism: These genes likely interact with each other to regulate cholesterol biosynthesis, cell adhesion and organization, signaling pathways and responses to stress, and apoptosis.\\n\\n] | \n", + "0.86 | \n", + "0 | \n", + "
| 731 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[\\n\\nSummary: This list includes genes that are involved in cholesterol biosynthesis, regarding protein binding, transcription, regulation of gene expression, and other biochemical processes. \\n\\nMechanism: These genes are mainly involved in cholesterol homeostasis, transcription and regulation of gene expression, and other essential biochemical processes.\\n\\n] | \n", + "[ The list of genes given is largely implicated in cholesterol and lipid biosynthetic processes. Additionally, a large number of genes are involved in the regulation of transcription, apoptosis, protein stability and interaction, and cell adhesion/migration. \\nMechanism: The overall biological mechanism is centered around the maintenance of cholesterol/lipid levels and transport, as well as regulation of key cellular processes including transcription, apoptosis, and cell adhesion/migration.\\n] | \n", + "0.93 | \n", + "139 | \n", + "
| 732 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_COAGULATION-0 | \n", + "[COULD NOT PARSE] | \n", + "[\\n\\nSummary: The human genes in this list are involved in a variety of functions related to proteins, such as binding, disulfide isomerase activity, phosphoprotein binding, enzyme binding, and calcium ion binding.\\n\\nMechanism: These genes encode for enzymes involved in protein binding activities, such as heparin binding, integrin binding, collagen binding, and phospholipid binding. These activities are necessary for biological processes such as cell adhesion, cell-matrix adhesion, signaling receptor binding, blood coagulation, fusion, apoptotic signal transduction, and regulation of protein-coding gene expression.\\n\\n] | \n", + "0.70 | \n", + "605 | \n", + "
| 733 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_COAGULATION-1 | \n", + "[ The statistically over-representeted gene functions common to this list of genes have to do with protein and domain binding, domain specific and disordered domain specific binding, enzyme and peptidase activity, and cytokine and signalling receptor binding. Key processes that seem to involve this gene set are cell adhesion, proteolysis, regulation of blood coagulation, response to iron and UV-A, and the regulation of cell adhesion mediated by integrin. \\nMechanism: Some of these genes may be involved in the same biological pathways, such as pathways for protein homooligomerization, enzyme/peptidase activity, proteoglycan/fibrinogen binding, heme binding, and domain specific binding activity.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "686 | \n", + "
| 734 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_COMPLEMENT-0 | \n", + "[COULD NOT PARSE] | \n", + "[ \\nSummary: Genes in this list are primarily involved in regulation of protein activity, genetic transcription, cell signaling, and metabolism.\\nMechanism: These genes primarily influence protein activity and metabolism through complex interactions with other proteins and the environment. They interact in ways which affect protein activity, cell signaling, and possibly genetic transcription.\\n] | \n", + "0.68 | \n", + "378 | \n", + "
| 735 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_COMPLEMENT-1 | \n", + "[ These genes are primarily involved in binding activities and regulation of molecular functions related to cell signalling, such as enzyme binding, deubiquitinase activity, cysteine-type endopeptidase activity, receptor binding, protein kinase binding, SH2 domain binding activity, phosphatidylinositol phospholipase C activity, GTPase activity, and metalloendopeptidase activity.\\n\\nMechanism: The proteins encoded by these genes are involved in the regulation of cell signalling pathways, including those related to apoptosis, interleukin-6, growth factor activity, receptor binding, phospholipid binding, and transcription activator activity.\\n\\n] | \n", + "[\\n\\nSummary: The genes in this list are involved in many cellular activities, including DNA-binding, phospholipid binding, protein binding, binding to receptors, enzyme binding and inhibitor activities, GTPase activities, metal ion binding activity, and other protein activities.\\n\\nMechanism: These genes are likely to be involved in a wide range of cellular pathways, including signaling, transcription regulation, DNA repair, cell death, immune response and other cellular processes.\\n\\n] | \n", + "0.93 | \n", + "161 | \n", + "
| 736 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_DNA_REPAIR-0 | \n", + "[COULD NOT PARSE\\nHypothesis: The underlying biological mechanism of these genes is likely related to transcription regulation of gene expression, including DNA binding and DNA polymerase activity, as well as the formation of protein dimers needed for transcription.] | \n", + "[\\nSummary: This set of human genes are involved in many processes, including DNA and RNA binding activity, enzyme binding activity, protein binding activity, calcium ion binding activity, but primarily DNA damage and repair processes.\\nMechanism: These genes are involved in DNA damage and repair processes, whereby they bind to various sets of molecules and macromolecules, and catalyze/carry out downstream pathways such as DNA repair, familial clipping, etc.\\n] | \n", + "0.86 | \n", + "195 | \n", + "
| 737 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_DNA_REPAIR-1 | \n", + "[\\nSummary: The list of genes are involved in a diverse range of functions, including DNA binding activities, ATP activities, RNA binding activities, transcription activities, enzyme binding activities, and protein homodimerization activities.\\nCommonalities in function include DNA binding activities, RNA binding activities, transcription activities, enzyme binding activities and protein homodimerization activities.\\nMechanism: These commonalities of function reflect the various roles in nucleic acid metabolism and structural transactions related to transcription and replication in the cell.\\n] | \n", + "[ The provided list of genes is involved in a variety of cellular functions, including DNA binding activity, ATP hydrolysis activity, RNA binding activity, enzyme binding activity, protein binding activity, DNA-directed DNA polymerase activity, nuclease activity, and mRNA regulatory element binding. The enriched terms that describe their common functions are DNA binding activity, enzyme binding activity, ATP hydrolysis activity, RNA binding activity, protein binding activity, DNA-directed DNA polymerase activity, nuclease activity and mRNA regulatory element binding.\\n\\nMechanism: The genes in the list likely contribute to the regulation of pathways that involve DNA, RNA, proteins and enzyme activities. These activities may be involved in various metabolic processes and regulatory networks within the cell, such as DNA repair, gene expression, nucleic acid metabolism, and cell differentiation.\\n\\n] | \n", + "0.94 | \n", + "309 | \n", + "
| 738 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_E2F_TARGETS-0 | \n", + "[ Genes in this list are predominantly related to functions involved in the cell cycle, including DNA replication, transcriptional and post-transcriptional regulation, chromatin binding, and mitosis. A number of the genes are also associated with processes related to nuclear transport and pore complex assembly.\\n\\nMechanism: This cluster of genes is likely related to multiple biological mechanisms involved in cell cycle progression, including DNA replication and transcriptional regulation, chromatin binding and modification, RNA processing and stability, nuclear transport, and mitosis.\\n\\n] | \n", + "[ This set of genes appears to be involved in several different processes related to DNA, chromatin, and cell division, including chromatin binding activity, DNA replication and repair, transcription, histone modification, nuclear import/export, DNA/RNA binding, and protein-macromolecule binding. A majority of these genes appear to be involved in the regulation and maintenance of the cell cycle and the expression of genes through their interactions with proteins, chromatin, and nucleic acids.\\n\\nMechanism: The genes in this list are likely involved the regulation of genetic expression by influencing the properties of chromatin, and the structure and function of nucleic acids and proteins. These interactions may be mediated by histone modification and the binding of proteins, DNA, and RNA. Furthermore, DNA and RNA modification, as well as DNA repair, may also factor in to the gene's functions.\\n\\n] | \n", + "0.94 | \n", + "313 | \n", + "
| 739 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_E2F_TARGETS-1 | \n", + "[\\nSummary: This list of genes enables various functions in regards to DNA binding, protein binding, histone binding, ATP and enzyme binding, as well as DNA replication, DNA methylation and regulation of chromosome segregation.\\nMechanism: These genes allow for the regulation of several processes essential for cell growth, transcription, and regulation through binding of and interaction with various molecules.\\n] | \n", + "[ The list of genes consists of proteins that are involved in a wide range of cellular activities, including DNA binding, transcriptional regulation, cell cycle progression, DNA replication, chromatin modification and repair, mitosis, and the remodeling of nuclear pore complexes. These proteins commonly cooperate in the formation of protein complexes and in the assembly of large macromolecular machines. They are involved in several biological pathways, such as DNA damage repair, cell cycle regulation, gene transcription, and nucleocytoplasmic transport.\\n\\nMechanism: This list of genes, together with their respective functions, implicates a wide variety of biological mechanisms. When viewed as a group, these proteins act together to coordinate fundamental cellular processes, including cell growth and repair, gene expression, and cell migration. Additionally, these processes are coordinated through the assembly of macromolecular machines, enabling the formation of large, protein complexes and facilitating interactions between different molecules.\\n\\n] | \n", + "0.91 | \n", + "649 | \n", + "
| 740 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[\\nSummary: There are a number of genes with functions related to extracellular matrix structural components, cellular adhesion and protein binding.\\nMechanism: The range of genes suggests that these functions are related to various pathways that involve receptor and ligand interactions, protein domain binding activities, signaling processes and the structural components of the extracellular matrix.\\n] | \n", + "[\\nSummary: Genes enriched for mechanisms involved in protein binding, calcium ion binding, cell adhesion molecules, and extracellular matrix structure.\\nMechanism: Cell adhesion molecules, interactions with signaling receptors or other proteins, and extracellular matrix structuring.\\n] | \n", + "0.94 | \n", + "118 | \n", + "
| 741 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[\\nSummary: The list of genes are involved in a variety of cell and matrix structural activities, including binding activities, metal binding and metal ion binding, enzyme activities, receptors and chemokine activities, as well as DNA-binding and transcription activities.\\n\\nMechanism: The genes in the list work together synergistically to mediate essential cell processes such as cell adhesion, growth, communication, and cell-matrix interaction.\\n\\n] | \n", + "[\\nSummary: The genes in this list are related to extracellular matrix structural constituents, collagen binding activity, cell adhesion molecules, DNA binding activity, GTP binding activity, and protein homodimerization activity.\\nMechanism: It appears that these genes are involved in the structural formation and maintenance of cells, particularly in the extracellular matrix, energy metabolism, and signal transduction pathways.\\n] | \n", + "0.94 | \n", + "17 | \n", + "
| 742 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[ Genes involved in this list generally enable binding, transport, enzyme, and adhesion activities, and are involved in process such as intracellular signaling, transcription, and neuronal development.\\n\\nMechanism: These genes are involved in multiple pathways that involve the binding, transport, and regulation of signals related to cellular physiology, growth, and development.\\n\\n] | \n", + "[\\n\\nSummary: The listed genes display a variety of functions related to DNA binding and/or regulation, protein binding/regulation, enzymes, transmembrane or ion transport activity, and mRNA or protein expression. \\n\\nMechanism: The underlying biological mechanism for these genes is likely related to their roles in regulating transcription, cell adhesion and signaling, gene expression, or metabolic pathways. \\n\\n] | \n", + "0.92 | \n", + "29 | \n", + "
| 743 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[ Our term enrichment test analysis has identified that these human genes are mainly involved in binding activities, including DNA binding, ATPase binding, and protein binding, as well as various enzymatic activities, such as phosphatase activity, dehydrogenase activity, and adenylate cyclase activity. Additionally, the genes are related to transmembrane transport, transcriptional regulation, cell adhesion, and apoptosis. \\n\\nMechanism: This term enrichment test identified several biological functions and activities related to DNA and protein binding, transcriptional regulation, transport, and apoptosis, likely playing important roles in cellular processes and development.\\n\\n] | \n", + "[\\nThis list of human genes is enriched for multiple functions related to DNA binding and transcription factors, RNA binding, protein binding/dimerization, transmembrane transporters, calcium ion binding, enzyme binding, and GTPase activities. The underlying biological mechanism likely involve signal transduction, membrane transport, and protein activities related to chromatin and gene expression.\\n\\nMechanism: Signal transduction, membrane transport, and protein activities related to chromatin and gene expression. \\n\\n] | \n", + "0.93 | \n", + "161 | \n", + "
| 744 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[\\nThis analysis of the given human gene list reveals a pattern of enrichment for molecules and processes associated with protein binding activities, DNA- and RNA-binding, domain binding, carbohydrates binding, and enzyme and ligand binding activities. In addition, several genes are predicted to be involved in transmembrane transport activities, sequencing and structural protein interactions, transcription factor activities, and cellular adhesion. Various proteins act as modulators of these activities, and cofactors, such as calcium ions, play important roles.\\n\\nMechanism: This set of genes are likely involved in a variety of protein-protein and DNA/RNA interactions, which are essential for regulation of gene expression and protein activity. The cell membrane acts as a barrier between different cellular environments, allowing the genes to mediate transport between the intracellular and extracellular compartments, as well as a platform for docking proteins to interact with ligands, such as hormones and growth factors. The set of genes likely form part of a larger interconnected protein-protein interactome and temporal regulatory pathways which regulate cell function.\\n\\n] | \n", + "[\\nSummary: Genes involved in cell adhesion, transport, metabolic processes and transcription\\nMechanism: Cell surface activities, metabolic processes, and gene expression regulations \\n] | \n", + "0.90 | \n", + "1001 | \n", + "
| 745 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[ We have identified a large set of genes that are involved in a variety of processes, including binding, transcriptional regulation, transport, and enzymatic activities. These genes are enriched in the following terms: DNA-binding; transcription activator activity; protein binding; membrane transporter activity; hydrolase activity; phosphorylation; and ligand-mediated activities. \\n\\nMechanism: Many of these identified enriched terms suggest involvement in complex biochemical pathways in order to facilitate cell behavior and other processes in the body at a molecular level. This likely occurs through a combination of transcriptional regulation, binding of proteins and ligands, and enzymatic activities. \\n\\n] | \n", + "[ These genes are involved in a variety of functions related to protein regulation and metabolism such as transcription factor binding, enzyme binding, cell adhesion, and ligand-gated ion transporter activity. Mechanism: The function of these genes is likely related to either a transcriptional regulatory network, signaling cascade, or metabolic pathway. ] | \n", + "0.91 | \n", + "356 | \n", + "
| 746 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[ \\nSummary: This list of genes is mainly involved in fatty acid, lipid, and carbohydrate metabolism, DNA binding, RNA binding, and protein homodimerization. \\nMechanism: The genes in this list work to regulate metabolic pathways, transcription and protein complexes.\\n] | \n", + "[\\nSummary: Genes appear to be primarily involved in the binding, transport, and oxidation of molecules.\\nMechanism: These genes are likely involved in a variety of molecular processes including transportation, modulation, and redox reactions.\\n] | \n", + "0.88 | \n", + "24 | \n", + "
| 747 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[ This gene list contains enzymes involved in fatty acid and lipidmetabolism, metabolism of oxygenated and carbonated compounds, oxidoreduction, electron transfer, and DNA related activities such as DNA binding, DNA nuclease activity, RNA binding, and chromatin binding. \\nMechanism: These genes enable intra- and inter-cellular metabolic pathways and communication, as well as provide protective responses to external stimuli, by catalyzing the conversion of compounds and regulating DNA expression.\\nHypothesis: This set of activities suggest a mechanism of maintaining cellular homeostasis, which involves reactive oxygen species management, modifying hormonal, energy, and nutrient levels, and respoding to external stress.\\n] | \n", + "[ \\nSummary: A diverse group of genes involved in various enzymes and binding activities related to cellular responses, metabolism, and DNA regulation.\\nMechanism: Various enzymes and binding activities related to cellular responses, metabolism, and DNA regulation.\\n] | \n", + "0.89 | \n", + "462 | \n", + "
| 748 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-0 | \n", + "[ The gene descriptions indicate that many of these genes are involved in DNA or transcription binding, binding of different molecules or materials (chromatin, metal ions, histone deacetylase, etc.), protein binding activities, enzyme binding activities, and GTPase activities.\\n\\nMechanism: These genes appear to be involved in a variety of cellular functions, including transcriptional regulation, DNA replication, DNA damage repair, protein modification, gene expression and cell cycle control. The common functions may be related to molecular pathways that regulate these activities. \\n\\n] | \n", + "[ \\nSummary: The list of genes highlighted have common functions related to DNA and RNA binding, catalysis and metabolic activities, chromatin binding, and transcription and translation-associated activities.\\nMechanism: The genes in this list are involved in a variety of mechanisms; DNA and RNA binding, transcription and translation, catalysis, chromatin binding, metabolic activities, and protein folding and dimerization of proteins. \\n] | \n", + "0.92 | \n", + "150 | \n", + "
| 749 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_G2M_CHECKPOINT-1 | \n", + "[\\n\\nSummary: over half of the genes in this list are involved in protein binding, DNA binding and/or transcription, and many others in activities related to or downstream of those activities.\\n\\nMechanism: The proteins encoded by these genes are likely involved in regulating gene expression at the molecular level, through interacting with DNA, proteins, and other elements involved in transcription.\\n\\n] | \n", + "[ This list of genes are involved in wide range of functions related to protein binding, DNA binding, transcription factors, telomerase, RNA binding and DNA replication. They appear to be involved in a variety of processes related to cell cycle regulation, chromatin binding, gene expression, protein folding and regulation of chromosome structure.\\n\\nMechanism: The genes in this list are likely involved in a complex network of molecular processes related to DNA replication, transcription and cell cycle control. They appear to be involved in many processes that are necessary for cells to grow and divide, including transcription and translation, DNA replication, chromatin binding and protein folding. In particular, they likely contribute to gene expression, protein modification, DNA damage sensing, and cell cycle regulation.\\n\\n] | \n", + "0.93 | \n", + "433 | \n", + "
| 750 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_GLYCOLYSIS-0 | \n", + "[ Human genes in the given list are involved in a variety of functions, including nucleic acid and proteic binding, metabolic activities such as phosphorylation and oxidation-reduction, carbohydrate metabolism, and various types of cytokine and growth factor activities. The underlying biological mechanism involves increased metabolic activity and physiological signalling pathways, leading to increased protein synthesis and activity, increased cell growth, migration, differentiation and repair.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "484 | \n", + "
| 751 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_GLYCOLYSIS-1 | \n", + "[ \\nSummary: This list of genes has functions related to metabolism, gene regulation, cell signalling, and protein binding activities.\\nMechanism: The list of genes are likely involved in pathways related to cell signalling, metabolism, intracellular communication, and gene regulation.\\n] | \n", + "[ \\nSummary: The genes demonstrate a variety of functions including enzyme binding activity, identical protein binding activity, and DNA binding activity.\\nMechanism: The genes described are involved in diverse metabolic activities and structural components. \\n] | \n", + "0.90 | \n", + "27 | \n", + "
| 752 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[ The genes highlighted in this list are largely involved in cellular organization and processes including cell adhesion, vascularization, neurotransmitter receptor internalization, signal transduction, and enzyme binding. Some of the genes, such as GFIA and SHH, are also involved in embryonic development and organogenesis. Common terms enriched from these genes include: cell adhesion; signal transduction; epithelial-mesenchymal interaction; receptor-mediated endocytosis; angiogenesis; and neural tube closure.\\n\\nMechanism: These genes largely interact with each other in a variety of ways to control crucial cellular pathways and processes in the body's tissues, organs, and systems. They interplay to control processes such as cell adhesion, vascularization, signal transduction, and enzyme binding. Some of the genes are involved in the formation and maintenance of the structures of the body's organs and tissues, while others are involved in developing the connections between cells and transmitting signals within them.\\n\\n] | \n", + "[ The list of genes provide evidence that many of these genes are involved in processes related to development, including cell adhesion, growth, angiogenesis, and nerve cell differentiation. These processes are related to the formation of structures that are integral to the healthy function of organisms, such as blood vessels and organs. Common terms include: protein/lipid binding activity; DNA-binding transcription factor activity; regulation of gene expression; regulation of protein metabolism; and positive/negative regulation of cellular component organization. Mechanism: While the precise mechanism is unknown, it is likely that these genes are involved in the regulation of transcription, signaling pathways related to cell adhesion, metabolism, and growth, as well as the formation of complex structures necessary for healthy functioning organisms such as organs and neural networks.\\n\\n] | \n", + "0.94 | \n", + "133 | \n", + "
| 753 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[ \\n\\nSummary: This gene list encompasses genes involved in various functions and processes, including cell adhesion and migration, regulation of transcription and DNA-templated transcription, negative regulation of apoptosis, cell surface receptor-related activities, cell differentiation, angiogenesis, canonical Wnt signaling pathways, and protein phosphorylation.\\n\\nMechanism: This gene list likely indicates the presence of various pathways, including the NF-kB pathway, cytoskeletal reorganization and receptor signaling pathways, integrin and cell adhesion molecule signaling pathways, and the Wnt/PCP pathwayn and sonic hedgehog pathway.\\n\\n] | \n", + "[\\n\\nSummary: Genes encode for activities that enable functions related to cell adhesion, transcriptional and post-transcriptional regulation, cell migration, signaling and receptor activity, and transcriptional repression.\\n\\nMechanism: This likely represents a collection of diverse pathways related to cellular activity and development, likely involving both transcriptional and post-transcriptional processes.\\n\\n] | \n", + "0.93 | \n", + "233 | \n", + "
| 754 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_HEME_METABOLISM-0 | \n", + "[ The majority of these human genes enable binding activity involving DNA and RNA, as well as being involved in the regulation of transcription and translation. Moreover, some genes are involved in the transport of substrates across the cell membrane. \\n\\nMechanism: The list of genes is indicative of various transcription-regulation mechanisms and membrane transport processes, including DNA packing, histone demethylation, transcription factor activity, and ion transport. \\n\\n] | \n", + "[\\nSummary: This list of genes are involved in various functions such as DNA binding, RNA binding, enzyme binding, protein kinase binding, protein phosphatase binding, protein homodimerization, tissue morphogenesis, and protein phosphorylation.\\n\\nMechanism: The underlying biological mechanism for the enriched terms is likely to involve transcription regulation and signal transduction.\\n\\n] | \n", + "0.89 | \n", + "89 | \n", + "
| 755 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_HEME_METABOLISM-1 | \n", + "[ \\n\\nSummary: The list of genes are related to many major and essential functions in the cell, ranging from transcription of DNA, binding to receptors, transportation of ions and other molecules, and overall regulation activities. \\nMechanism: The mechanism underlying this term enrichment is that numerous functions or activities require multiple pathways, proteins, and activities, thus having multiple target genes involved.\\n] | \n", + "[\\n\\nSummary: This list of genes are involved in diverse cellular functions such as DNA binding, protein binding and phosphorylation, as well as the transportation of ions and small molecules across membrane domains.\\n\\nMechanism: Many of the genes encode proteins involved in enzyme and transporter activity, contributing to metabolic, vesicular and cytoskeletal pathways.\\n\\n] | \n", + "0.92 | \n", + "55 | \n", + "
| 756 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_HYPOXIA-0 | \n", + "[\\nSummary: Several genes are involved in structural components, binding activities, and enzyme activities.\\nMechanism: Genes are associated with a variety of activities related to binding, activity functions, structural elements and enzyme regulation.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "235 | \n", + "
| 757 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_HYPOXIA-1 | \n", + "[\\n\\nSummary: The list of genes describes a wide range of molecular functions related to signaling, attachment, and metabolic pathways.\\n\\nMechanism: The underlying biological mechanism and pathways describe the various activities of these genes and how they are involved in cell metamorphosis, growth and development, and immunity and defense.\\n\\n] | \n", + "[ These genes are predominantly involved in processes related to DNA-binding transcription activity (activator and repressor), protein binding activity, protein kinase binding activity and activity, enzyme binding activity, regulation of cell proliferation/growth, ligand-activated transcription, and intracellular processes.\\n\\nMechanism: The enriched terms suggest a shared mechanism of gene expression and regulation involving binding, enzymatic reactions and proliferation/growth processes. These processes all coordinate to regulate various biological activities. \\n\\n] | \n", + "0.87 | \n", + "227 | \n", + "
| 758 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[ The majority of the genes listed are associated with cell signaling, regulation and structural roles such as ligand binding, enzyme binding, and receptor binding, as well as associated functions such as DNA and RNA binding, protein dimerization, and transcription activity and regulation. \\n\\nMechanism: These genes are known to be involved in many different parts of the cellular functioning, including cell communication and receptor recognition and response, enzyme and ligand binding, DNA/RNA, and transcription. \\n\\n] | \n", + "[\\n\\nSummary: Genes enriched in binding activities such as GTPase, DNA, protein, ligand, and BH3 domain, as well as in activities such as phosphatidylinositol and hydrolase, involved in pathways related to protein regulation, receptor signaling, and metabolism.\\n\\nMechanism: It is likely that these genes are involved in pathways related to modulating protein expression, receptor signaling, and metabolic processes such as cellular respiration, synthesis, and metabolism of fatty acids and nucleotides.\\n\\n] | \n", + "0.90 | \n", + "17 | \n", + "
| 759 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[ The analysis of the given list of genes reveals that they are primarily involved in binding activities, such as DNA-binding, receptor binding and ligand-activated transcription activities. Several genes are also involved in enzyme activity, such as proteases and kinases. All of the genes are involved in several processes, such as cellular and apoptotic responses, neuronal activity and tissue development. \\nMechanism: The binding activity of the genes may be involved in protein-protein interaction, signal transduction pathways, transcriptional control and modulation of protein stability. Enzyme activities are involved in the post-translational modifications of proteins, metabolic pathways and protein degradation.\\n\\n] | \n", + "[ \\n\\nSummary: Genes presented encoded for a range of activities related to the regulation of immunological and signaling processes, binding activities, transcription activator activities, and endopeptidase activities.\\n\\nMechanism: The genes potentially display a range of activities related to immunological and signaling pathways as well as binding, transcription activator, and endopeptidase activities.\\n\\n] | \n", + "0.91 | \n", + "319 | \n", + "
| 760 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[\\nSeveral genes among the list are involved in receptor activity and binding activities related to cytokines, such as interleukin-1, interleukin-7, interleukin-9, interleukin-10, and interleukin-12 receptors, among others. Many of the genes are also involved in the binding of other molecules, such as growth factors, lipoproteins, peptides and proteins, as well as with kinase binding activities, and ATP and DNA-binding activities. In addition, several of the genes appear to be associated with immune responses, such as antimicrobial humoral immune response, defense response and cell surface receptor signaling pathway.\\n\\nMechanism: It is likely that many of the genes on the list serve as key mediators of receptor signaling pathways, as well as protein-protein and nucleic acid-protein interaction. These activities may be involved in the regulation of important cellular processes such as cell surface receptor signaling, immune response, apoptosis, and modulation of the activity of certain kinases.\\n\\n] | \n", + "[ \\nSummary: This list of genes is involved in cytokine binding and receptor activities, protein binding, and kinase and phosphatase activities. \\n\\nMechanism: These gene functions are involved in signal transduction pathways affecting cell growth, development, and differentiation as well as immune responses and inflammation.\\n\\n] | \n", + "0.94 | \n", + "682 | \n", + "
| 761 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[ The genes identified in this list are involved in a variety of signaling activities, mainly cytokine receptor activity, CXCR chemokine receptor binding activity, and interleukin-binding activities. Furthermore, these genes are involved in processes such as defense response, negative regulation of macromolecule metabolic process, and positive regulation of protein metabolic process. \\n\\nMechanism: The genes are related to mechanisms that involve the recognition of extracellular ligands, such as cytokines, chemokines, growth factors, and antigen by the cell surface receptors in order to regulate and coordinate cell responses.\\n\\n] | \n", + "[\\n\\nSummary: The genes listed are involved in a variety of processes related to cytokine binding activity, cytokine receptor activity, growth factor activity, cell adhesion molecule binding activity, chemokine (C-X3-C) binding activity, and defense response.\\n\\nMechanism: It appears that these genes are involved in coordinating processes related to the immune system, with cytokines acting as signaling molecules and the other genes acting as receptors or binding agents.\\n\\n] | \n", + "0.95 | \n", + "161 | \n", + "
| 762 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[ The genes in the list are involved in a variety of activities, including binding activities of diverse ligands (e.g. ATP, G protein-coupled receptors, etc.), receptor activities (e.g. for interleukin and other cytokines), transcription activator activities, and presence in various cellular organelles (e.g. plasmic membrane, nucleus). Common terms such as protein binding activity, cytokine activity, G protein-coupled receptor activity, and DNA-binding transcription activity were found to be enriched.\\n\\nMechanism: The genes in this list are involved in several cell signaling pathways, including but not limited to, cytokine signaling, signal transduction, G protein-coupled receptors, and transcription factors.\\n\\n] | \n", + "[\\nThis list of genes is enriched for terms related to signal transduction pathways and pathways related to immunoregulation. Specifically, terms including G protein-coupled receptor activity, cytokine activity, DNA-binding transcription factor activity, ion channel activity, and receptor binding activity were found to be statistically overrepresented in the list.\\n\\nMechanism: The underlying mechanism is likely related to the diverse functions of these genes in signal transduction pathways and pathways related to immunoregulation. This includes G protein-coupled receptor activity, cytokine activity, DNA-binding transcription factor activity, ion channel activity, and receptor binding activity that helps modulate the signal transduction pathways.\\n\\n] | \n", + "0.94 | \n", + "36 | \n", + "
| 763 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[\\n6 groups of functions were enriched - receptor activities, binding activities, enzyme activities, growth factor activities, molecule/ion transporters and transcription factor activities. \\nMechanism: These enriched terms point to pathways that are involved in cell growth, development, communication, and signal transduction. \\n] | \n", + "[\\n\\nSummary: The genes in the list are involved in a variety of cellular processes, including cell adhesion and binding, molecular functions, G protein-coupled receptor activity, ion transport and transmembrane transporter activity, signaling receptor binding, transcription factor activity, and several others.\\n\\nMechanism: The genes in the list are involved in a variety of biological mechanisms, such as pathways for cell communication, inflammation, and response to external signals.\\n\\n] | \n", + "0.90 | \n", + "158 | \n", + "
| 764 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[\\nThe list of genes includes those involved in processes such as defense response to other organism, response to virus, regulation of proteasomal ubiquitin-dependent protein catabolic process, and regulation of transcription. The commonalities in gene function include DNA-binding activity, RNA binding activity, metal ion binding activity, identical protein binding activity and protein homodimerization activity. These genes are enriched with terms such as \"signaling receptor binding activity,\" \"transcription coactivator activity,\" and \"regulation of transcription.\"\\n\\nMechanism: The underlying biological mechanism or pathway of these genes is related to processes like macrophage activation, innate and adaptive immune response, antiviral response, and transcriptional regulation. These genes are involved in signaling pathways related to specific pathogens or environmental cues, or the maintanance of normal gene expression. These processes are essential for the body to respond to environmental changes and maintain homeostasis. \\n\\n] | \n", + "[ Upon performing the term enrichment test on these human genes, we find that the majority of them are involved in immune response processes, such as cellular response to cytokine stimulus, defense response to second organism, and infection response. Furthermore, many of the genes are linked to transcription activator activity, DNA and RNA binding activity, as well as other ligase/binding activities. The majority of the genes are located in the cytoplasm, Golgi apparatus, and other cellular components, suggesting a role in regulating the functional components of the cell.\\n\\nMechanism: The enriched terms suggest that these genes are involved in the mechanisms of transcription, translation, and protein modification, all of which play key roles in immune response. The transcription activity links to gene expression to regulate the expression of proteins involved in the immune response, while the DNA and RNA binding activities are involved in the transcription and translation processes. The ligases and binding activities would be critical for binding and changing proteins and other molecules to prevent infection and regulate the body's response.\\n\\n] | \n", + "0.92 | \n", + "121 | \n", + "
| 765 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[ Cell-mediated immunity is indicated by the genes analyzed, which were found to involve in activities such as DNA-binding transcription activator activity; CCR chemokine receptor binding activity; cytokine activity; RNA-binding activity; and ubiquitin protein ligase activity. Several enriched terms were identified, including defense response to other organism; immune response; viral entry into host cell; ISG15-protein conjugation; antigen processing; and cytokine-mediated signaling pathway. \\nMechanism: The gene functions are likely to be involved in biological processes related to cell-mediated immunity, such as activation of macrophages and other cells of the immune system (T cells, natural killer cells), regulation of antigen processing and presentation and cytokine-mediated signaling pathways, and regulation of the immune and inflammatory responses.\\n] | \n", + "[ \\n\\nSummary: The genes identified show a wide range of cellular processes involved in immunity, transcription regulation, RNA metabolism, and protein activity modification. \\nMechanism: The genes are involved in a variety of processes likely related to regulation of immunity and protein activity, likely through regulation of transcription, RNA modifications, and ubiquitination.\\n] | \n", + "0.90 | \n", + "486 | \n", + "
| 766 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[COULD NOT PARSE] | \n", + "[ \\nSummary: These genes are involved in a variety of processes to enable activities such as enzyme binding, promoter and transcriptional regulation, ATP hydrolysis, protein homodimerization, kinase regulation, protein dimerization, and several other functions. \\n] | \n", + "0.70 | \n", + "246 | \n", + "
| 767 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[ The genes listed in the summaries are mainly involved in functions related to binding activities, enzyme activities, transcription factor activities, protein activities, and signaling receptor activities. The data suggests that these genes play an important role in cellular pathways and processes such as cellular immune response, cytokine-mediated signaling, apoptotic signaling, DNA binding and transcription, and RNA binding and transcription. The commonalities in their function shared by most of these genes are binding activity; enzyme activity; protein activity; and transcription factor activity.\\n\\nMechanism: These genes are likely to be involved in various regulatory pathways regulating cellular functions. The binding activities associated with them suggest their role in ligand-receptor interactions and communication between cells, as well as their role in cell-to-cell signaling. Additionally, their enzyme and protein activities suggest that they are involved in enzymatic reactions, signaling cascades, and post-translational modifications such as histone acetylation that regulate gene expression. Lastly, their involvement in DNA binding and transcription, as well as RNA binding and transcription suggest their roles in controlling gene expression and the synthesis of key proteins in various cellular pathways.\\n\\n] | \n", + "[\\n\\nSummary: This set of genes provides a wide range of functions, from ATP hydrolysis and enzyme binding activity, to DNA binding activities, GTP binding activity, and peptide antigen binding activity.\\n\\nMechanism: This set of genes links many different functions at the cellular level, together with serine-type endopeptidase activity, DNA-binding transcription activity and activities related to cytokines, chemokines and signaling pathways. The patterns suggest a broad underlying mechanism involving the mediation of cell-signaling pathways, DNA-binding activity, involvement in apoptosis and other cellular functions.\\n\\n] | \n", + "0.91 | \n", + "712 | \n", + "
| 768 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[\\nSummary: A number of genes have been studied, mostly involving functions related to protein activity, transcription, and regulation activity.\\nMechanism: These genes seem to act in concert with each other, involving protein binding activity and transmembrane activity, suggesting a potential for processes related to membrane-based signaling and receptor binding or trafficking.\\n] | \n", + "[\\nSummary: Genes associated with this list are involved in multiple signaling pathways and binding activities related to cell structure, adhesion, calcium ion and potassium channeling, and protein folding/binding/kinase activities.\\nMechanism: The underlying biological mechanism is likely related to signaling cascades that involve interacting proteins involved in cell adhesion, calcium and potassium channeling, and protein folding/binding/kinase activities.\\n] | \n", + "0.91 | \n", + "81 | \n", + "
| 769 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[\\nThis list of genes is enriched for functions related to DNA-binding and transcription activities, calcium ion and ATP-binding activities, protein binding activities, and G-protein coupled receptor activities. Some of the genes are predicted to be involved in cellular processes such as transcription and cell death regulation, while others are known to take part in morphogenesis and hormone metabolism.\\n\\nMechanism: These genes, in concert, may help to regulate gene expression at the transcriptional level, modulate calcium-dependent processes such as cell death, initiate changes in cell shape and differentiation, and control the flow of information within the cell.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "657 | \n", + "
| 770 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[\\nThe list of genes suggests that they are involved in processes related to cell adhesion, protein binding activities, signal transduction, and transcriptional regulation, suggesting a connection to cell-matrix communication and signal transduction pathways. The enriched terms associated with the gene list include: cell adhesion molecule binding activity; ATPase coupled intramembrane transport; metalloendopeptidase activity; protein homodimerization activity; signal receptor binding activity; DNA-binding transcription factor activity; heparin binding activity; peptidase regulator activity; and GTPase activity. \\n\\nMechanism: The mechanistic hypothesis for the gene list is that these genes are involved in a cell-matrix communication and signal transduction pathway. This pathway may involve interactions between cell adhesion molecules, transmembrane protein transport, peptidases and GTPases enabling signal transfer between cells and their extracellular environment. \\n\\n] | \n", + "[\\nSummary: The majority of these genes are involved in functions related to membrane binding and regulation, protein domain binding and regulation, receptor ligand binding and regulation, DNA-binding transcription regulation, enzyme binding and regulation, and cytokine activity.\\nMechanism: These gene functions likely aid in cell adhesion, signal transduction and transcription factors involved in cell differentiation, migration, growth and development.\\n] | \n", + "0.91 | \n", + "522 | \n", + "
| 771 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[ \\nSummary: The list of genes is enriched for those involved in various biological functions such as structural proteins, cell adhesion, kinase activity, signal transduction, receptor binding, cytokine activity, DNA-binding transcription, and inorganic diphosphate transmembrane transport.\\n\\nMechanism: The underlying biological mechanisms for the enriched terms include cell-matrix adhesion and signal transduction pathways, protein homodimerization, cell-cell recognition and communication, cGMP-dependent pathway, and apoptosis regulation. \\n\\n] | \n", + "[ This list of genes appears to be involved in a wide range of functions in cell-cell adhesion, signaling, and development, including receptor binding activities, ligand binding activities, DNA-binding transcription activator activities, enzyme binding activities, protein domain specific binding activities, and protein kinase binding activities.\\n\\nMechanism: The underlying biological mechanism appears to involve the regulation and coordination of a variety of cell-cell interactions and cellular responses, such as hormone or cytokine activities, adhesion and structural support, intracellular transport, DNA transcription, protein modification and enzyme activities, energy production and metabolism, and other signaling and regulatory processes. \\n\\n] | \n", + "0.92 | \n", + "209 | \n", + "
| 772 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[\\nSummary: The provided list of human genes are enriched for terms related to protein binding activities and activities related to the cytoskeleton.\\nMechanism: These proteins likely play a role in regulating cytoskeletal organization, cytoskeletal movement, and cellular signaling.\\n] | \n", + "[\\nSummary: The list of genes given have common functionalities related to cytoplasm and cytoskeleton proteins such as cell motility, binding, regulation and adhesion.\\nMechanism: These functions are likely involved in regulating cytoplasm and cytoskeleton components such as actin filaments, microtubules, and ribonucleopropteins.\\n] | \n", + "0.92 | \n", + "48 | \n", + "
| 773 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[ Enriched terms related to cytoskeleton and motor protein function, namely GTPase, ATPase, and binding activity of tubulins, microtubules, actin filaments, kinesin, dynein, and G protein-coupled receptor appear to be common among the presented genes.\\n\\nMechanism: Likely, these genes play a role in organizing and regulating the structure, dynamics, and shape of cells, as well as in the regulation of actin cytoskeleton and microtubule-dependent processes. This could suggest a role in important cellular functions such as cellular division, trafficking, and transport of organelles. The binding activity among these proteins may also be essential in communicating information and molecules between different areas of the cell. \\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "715 | \n", + "
| 774 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-0 | \n", + "[ The gene list appears to be involved mainly in metabolic processes, such as enzyme binding and activity, acid binding, molecule transport, adapter and receptor binding and activity, and DNA and protein binding and activity. Hypothesis: The underlying biological mechanism for this set of genes is metabolic regulation, including the regulation of enzyme, protein, and DNA metabolism. ] | \n", + "[\\n\\nSummary: The genes listed are involved in various cellular functions related to protein binding, domain binding and enzyme activity\\nMechanism: The genes are involved in several processes, such as cellular signaling, protein homeodimerization, DNA or RNA binding, transcriptional regulation, and metal ion binding.\\n] | \n", + "0.92 | \n", + "69 | \n", + "
| 775 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MTORC1_SIGNALING-1 | \n", + "[\\nThe genes listed have functions related to the regulation of metabolism, actin filaments, DNA/RNA binding and transport, nuclear receptor binding, and ubiquitination. Many of the genes also have identical protein binding activities, as well as activity related to peptidase activity and enzymes.\\n\\nMechanism: The listed genes are involved in various metabolic pathways and play an important role in the regulation of cell structure and function. Many of the genes are involved in protein synthesis and processing, as well as proteins involved in DNA/RNA binding and transport, and cell signaling.\\n\\n] | \n", + "[ These genes are primarily involved in various functions related to energy metabolism, transport, binding and regulation at a cellular level. The mechanism behind many of these functions likely occurs through interactions between proteins or protein complexes.\\n\\nMechanism: Predominantly interactions between proteins, or protein complexes, result in the observed functions of these genes. \\n\\n] | \n", + "0.92 | \n", + "207 | \n", + "
| 776 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-0 | \n", + "[ This list of genes is involved in several processes related to protein folding, regulation, and binding activities such as DNA binding, RNA binding, and chromatin binding. It also suggests a potential role in the regulation of processes such as transcription, translation, and splicing.\\n\\nMechanism: This list of genes is involved in a variety of processes related to protein folding, regulation, and binding activities. The genes could be involved in different pathways which could be either converging or separate, but ultimately leading to the same outcome. For example, the genes could cooperate to enable chromatin binding or the regulation of transcription, translation, or splicing.\\n\\n] | \n", + "[\\nSummary: Many of these genes enable or contribute to functions related to RNA binding, protein folding chaperone, DNA binding/recognition, protein homodimerization, and similar molecular functions. \\nMechanism: The underlying biological mechanism is likely related to RNA processing, DNA replication and repair, chromatin binding and modification, and protein assembly and modification. \\n] | \n", + "0.92 | \n", + "303 | \n", + "
| 777 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V1-1 | \n", + "[ Genes in this list are primarily involved in functions related to RNA binding and its regulation, such as RNA polymerase II transcription machinery binding activity, RNA stem-loop binding activity, mRNA 3' UTR binding activity, and mRNA regulatory element binding translation repressor activity. They are also involved in regulation of protein folding, DNA binding and regulation, ubiquitin protein ligase binding activity, and other protein domains specific binding activity. Hypothesis: The number of the genes in this list involved in the regulation of RNA binding functions suggests that the underlying biological mechanism is likely a complex regulatory process for various RNA-related activities.\\n\\n] | \n", + "[\\n\\nSummary: Twenty-eight genes related to various functions are listed. These functions include DNA binding, RNA binding, protein domain specific binding, chromatin binding, enzyme binding, and protein folding chaperone activities. \\n\\nMechanism: These genes are involved in many essential processes for cellular functioning, such as DNA replication, RNA splicing and translation, protein folding and ubiquitination, transcription and gene regulation, as well as complement and histone binding, among others.\\n\\n] | \n", + "0.94 | \n", + "198 | \n", + "
| 778 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-0 | \n", + "[\\nThe list of genes are involved primarily in processes related to transcription and RNA processing, such as regulation of gene expression, DNA-templated transcription, positive regulation of cell population proliferation, protein-DNA complex organization, and regulation of nucleobase-containing compound metabolic process. Included are proteins with functions related to nucleic acid binding activity, transcription corepressor activity, and RNA polymerase II-specific DNA-binding transcription factor binding activity. The underlying biological mechanism is likely related to the organization, modification and process of transcription or RNA activity in the cell. The enriched terms are transcription, DNA-templated transcription, positive regulation of cell population proliferation, protein-DNA complex organization, regulation of nucleobase-containing compound metabolic process, RNA binding activity, regulation of gene expression, rRNA processing, and transcriptional regulation. \\n \\nSummary: Involved primarily in processes related to transcription and RNA processing\\nMechanism: organization, modification, and processes of transcription or RNA activity\\n] | \n", + "[\\n\\nSummary: The genes all encode proteins that are involved in aspects of cell signaling, including metabolism, growth, cycle regulation, and protein transport.\\n\\nMechanism: The proteins perform a variety of functions related to the regulation of genetic information, including engaging in RNA binding or bridging, modification, transport, and translation activities.\\n\\n] | \n", + "0.90 | \n", + "795 | \n", + "
| 779 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MYC_TARGETS_V2-1 | \n", + "[\\nThe given human genes are primarily involved in RNA binding, protein binding, and DNA binding activities; they predominate in processes related to rRNA processing, protein metabolic activity, DNA-templated transcription and transcription regulatory region binding, as well as cell cycle processes, chromatin binding, and mitochondria regulation.\\n\\nMechanism:\\nMany of these genes are able to act as part of complexes that regulate various processes, such as the cyclin-dependent protein kinase holoenzyme complex, which is involved in G1/S transition of mitotic cell cycle and positive regulation of fibroblast proliferation, the mitochondrial prohibitin complex which is involved in regulating DNA-templated transcription, or the MLL1 complex involved in neural crest formation. The genes are also extensively involved in protein and RNA binding functions, enabling a wide range of different activities or processes.\\n\\n] | \n", + "[ The list of genes are mainly involved in RNA binding activity, ribosomal rRNA processing, mRNA and/or rRNA catabolism/stability, regulation of transcription/translation, regulation of signal transduction and metabolism processes, regulation of cell cycle/proliferation, and protein modification/regulation that primarily occur within the nucleus, cytosol, ribosome, and mitochondria. \\nMechanism: The underlying biological mechanism is the regulation of protein and RNA-related functions that help to control the expression of essential genes, transcription processes, and RNA stability, as well as to regulate cell growth/division and signal transduction pathways.\\n] | \n", + "0.93 | \n", + "252 | \n", + "
| 780 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MYOGENESIS-0 | \n", + "[ The list of genes is over-represented in several categories related to the cytoskeleton, extracellular matrix, protein binding, transmembrane transporters, and ion channels. These genes are likely involved in regulating cell structure and interactions as well as calcium and ion homeostasis.\\n\\nMechanism: This list of genes is likely involved in regulating cell structure and signalling through their roles in the cytoskeleton, extracellular matrix, protein binding, transmembrane transporters, and ion channels.\\n\\n] | \n", + "[ The list of genes is associated with several common functions, including calcium ion binding activity, binding of proteins to other proteins, and actin filament binding activity. These functions are enriched in the list since they are represented by an overabundance of genes, suggesting that these are all key molecular processes. The underlying biological mechanism is likely related to actin cytoskeleton organization and regulation of ion channels. \\n\\nMechanism: Gene expression regulation of actin cytoskeleton organization and regulation of ion channels.\\n\\n] | \n", + "0.94 | \n", + "48 | \n", + "
| 781 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_MYOGENESIS-1 | \n", + "[\\nSummary: This list of genes are enriched for activities related to calcium ion binding, cytochrome-c oxidase activity, DNA binding, ATP binding, actin binding, abnormal growth and development, protease binding, and structural constituents.\\nMechanism: The list of genes are likely involved in a variety of pathways related to growth, development, and signaling, including transcriptional and post-transcriptional control as well as cellular components of muscle cells and extracellular matrices. \\n] | \n", + "[\\nSummary: This list of genes is found to be enriched for terms related calcium binding activity, enzyme binding activity, and DNA-binding activity.\\nMechanism: These genes are likely involved in a variety of biological processes, including cell adhesion, protein activity, receptor binding, and gene regulation.\\n] | \n", + "0.95 | \n", + "186 | \n", + "
| 782 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-0 | \n", + "[\\nSummary: A variety of genes implicated in a wide range of biological processes, with a focus on gene expression, signal transduction, and cell cycle control.\\nMechanism: The genes involved in this list are related to protein modification and regulatory processes, and involve diverse functions such as Notch binding activity, Wnt receptor activity, ubiquitin and histone protein ligase activities, and transcription coactivator activity.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "423 | \n", + "
| 783 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_NOTCH_SIGNALING-1 | \n", + "[ Our data shows that these genes are generally involved in transcription, protein modification, ubiquitination and regulation processes, often related to signalling pathways and the Notch pathway in particular. Mechanism: The underlying mechanisms for the commonalities amongst these genes seems to involve the activation of protein and transcription pathways, such as Notch, SCF-dependent proteasomal ubiquitin-dependent protein catabolic process and Wnt. ] | \n", + "[\\n\\nSummary: Genes related to cancers, control of transcriptional processes, proteolysis, Notch signaling pathway, and cell proliferation/migration pathways were enriched. \\nMechanism: These genes act in mechanisms controlling growth and development processes, protein ubiquitination and degradation pathways, and pathways involved in control of transcription, cell signaling, and cell cycle control.\\n] | \n", + "0.92 | \n", + "59 | \n", + "
| 784 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[\\n\\nSummary: The genes listed are involved in several cellular processes and pathways, such as electron transfer, heme binding, and protein binding activities; oxidoreductase activity; ATPase activity and binding activity; molecular adaptor activities; acyl binding activities; and several other functions. \\n\\nMechanism: These genes are likely to be involved in various metabolic and enzymatic processes that occur in cell respiration and signal transduction.\\n\\n] | \n", + "[ Enzymes and proteins involved in electron transport and oxidative processes, including binding, transfer, and enzymatic activities; some that interact with lipids, heme, MHC class I proteins, GTPase, and ubiquitin proteins.\\n\\nMechanism: Electron transport and oxidative processes are essential for physiological energy production, primarily through the citric acid cycle and the electron transport chain. The proteins and enzymes identified are necessary for the transfer of electrons, energy production, and energy storage. They also cause proteins to undergo conformational changes, influencing metabolite and lipid interactions as part of redox reactions.\\n\\n] | \n", + "0.89 | \n", + "202 | \n", + "
| 785 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[ Our analysis of the gene descriptions reveal that their common functions are related to mitochondrial respiration, electron and proton transfer, and transport of ATP, indicating the presence of an underlying pathway of ATP generation in mitochondria.\\n] | \n", + "[This analysis of these human genes reveals enrichment of terms related to electron transfer activity, protein homodimerization, GTPase activity, adenine nucleotide transmembrane transporter activity, phosphoprotein binding activity, mitochondrial respiratory chain activity, proton-transporting ATP synthase activity, and mitochondrial ribosome binding activity.\\n\\nMechanism: These activities suggest that the genes contribute to mitochondrial energy metabolism through processes related to electron transfer, protein assembly, signaling, nucleic acid regulation, and protein transport.\\n\\n] | \n", + "0.92 | \n", + "335 | \n", + "
| 786 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_P53_PATHWAY-0 | \n", + "[\\n\\nSummary: Genes appear to be involved in functions related to DNA-binding transcription activity, protein binding activity, and protein kinase binding activity. \\nMechanism: The genes are thought to be involved in pathways related to DNA transcription, protein-protein interactions, and cell signaling.\\n] | \n", + "[ These genes encode proteins with functions in DNA binding activities, RNA polymerase II-specific functions, transcription regulation, protein binding activity, and enzyme binding activity.\\nThe commonalities in their functions suggest the underlying biological mechanism involves DNA transcription and regulation.\\n] | \n", + "0.92 | \n", + "11 | \n", + "
| 787 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_P53_PATHWAY-1 | \n", + "[\\nThe list of genes contains a variety of functions related to DNA, RNA, RNA polymerase, cell adhesion/signaling, metabolism, apoptotics, and morphogenesis. These functions indicate the list of genes to be involved in several biological processes, including gene expression and regulation, DNA damage repair, cell survival and death, metabolism, and cell morphogenesis. \\n\\nThe underlying biological mechanism can be hypothesised to be related to a variety of cellular processes such as transcription, chromatin remodelling, transcriptional regulation, and signal transduction, which are all essential processes for proper cell and tissue function. \\n\\n] | \n", + "[ This list contains genes which are involved in a broad range of roles including signaling receptor binding, RNA polymerase II co-regulator, DNA binding, phosphatase activity, transcription factor activity, enzyme binding, cell adhesion, and growth factor binding. The commonalties in terms of gene function suggest that the genes are involved in various roles related to the regulation of gene expression and cellular processes, as well as protein modification and receptor binding activity. \\n] | \n", + "0.91 | \n", + "154 | \n", + "
| 788 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[ \\nSummary: This list of genes is primarily involved in regulation of cellular processes including cell migration, cellular senescence, cellular biosynthetic process, apoptotic process, detection of glucose, cell-cell adhesion, neuron migration, insulin secretion, and gastrointestinal processes, as well as involvement in multiple diseases such as diabetes, tuberculosis, malignant astrocytoma, and cancer (multiple). \\nMechanism: These genes are generally involved in control of transcription by RNA polymerase II, ATPase-coupled ion transport, protein kinase and peptidase activity, DNA binding activity, calcium-ion regulated exocytosis, and regulation of secretion by cell.\\n] | \n", + "[\\n\\nSummary: Genes involved in glucose transport, metabolism, and regulation, with many implicated in type 1 and type 2 diabetes. Regulation of gene expression transcription and protein function are heavily represented.\\n\\nMechanism: Glucose homeostasis is achieved through the combined action of the listed genes in two major pathways: a) glucose uptake, transport, and metabolism; and b) transcription regulation of insulin and other genes related to glucose homeostasis.\\n\\n] | \n", + "0.90 | \n", + "206 | \n", + "
| 789 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[ This list of genes appears to all be involved in various cellular functions in cellular components, most notably regulating transcription by RNA polymerase II, regulation of secretion by cells, regulation of cell-cell adhesion, regulation of actin filament polymerization, and detection of glucose. Many of these genes also appear to be associated with diabetes and/or cancer.\\n\\nMechanism: The genes in this list appear to be involved in many aspects of cellular functions, which are involved in a variety of underlying biological pathways. Specifically, these genes have putative roles in involvement of signal transduction, regulation of transcription and regulation of cell-cell adhesion, protein targeting to ER, regulation of long-term synaptic potentiation, regulation of actin filament polymerization, and detection of glucose.\\n\\n] | \n", + "[ The human genes provided appear to be related to cell-cell adhesion, development and differentiation of anatomical structure, regulation of transcription by RNA polymerase II, and regulation of signal transduction and macromolecule metabolism. \\nMechanism: These genes likely enable the biological mechanisms of cell signaling, macromolecule production, and protein expression.\\n] | \n", + "0.90 | \n", + "458 | \n", + "
| 790 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PEROXISOME-0 | \n", + "[ This list is comprised of genes involved in a wide variety of functions, including molecular binding activities, enzyme activities, transporter activities, and domain binding activities. All of these genes are involved in diverse metabolic processes, such as fatty acid metabolism, cholesterol metabolism, protein transport, and DNA and RNA metabolic processes, suggesting a complex set of interrelated pathways that are likely to be a part of a larger biological system. Enriched terms include: molecular binding activity; enzyme activity; transporter activity; domain binding activity; lipid transport; protein transport; DNA metabolic process; and RNA metabolic process.\\n\\nMechanism: This set of genes likely interacts in a complex system involving multiple pathways and activities that enable metabolic processes such as fatty acid metabolism, cholesterol metabolism, protein transport, and DNA and RNA metabolic processes. The mechanism can be visualized as a network of proteins that interact in various ways to enable these processes. At a higher level, these pathways may interact to regulate signaling pathways, cell growth, and replication.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "1137 | \n", + "
| 791 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PEROXISOME-1 | \n", + "[COULD NOT PARSE] | \n", + "[\\nSummary: This analysis of a list of genes revealed a number of pathways and functions that are enhanced or enriched in the group of genes. The enriched pathways/functions include cell/nucleic acid metabolic processes, protein/DNA binding and processing, as well as hormone/steroid biosynthesis and processing.\\n\\nMechanism:The mechanism underlying this enrichment of processes is likely related to the fact that many of the genes included in this list code for proteins involved in these processes. These proteins may be enzymes, binders, or transporters, and are likely working together to regulate or facilitate a variety of stable and dynamic cellular processes.\\n\\n] | \n", + "0.70 | \n", + "651 | \n", + "
| 792 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[ The list of genes are found to be enriched for functions related to protein binding and kinase activities, signal sequence and receptor binding, cell cycle and apoptosis regulation, and signal transduction.\\n\\nMechanism: This enrichment suggests that these genes are involved in a variety of cellular processes that are associated with metabolism and signal transduction, such as cell cycle regulation, cell migration and differentiation, apoptosis, and signal cascade regulation. \\n\\n] | \n", + "[ This list of human genes are involved in diverse signaling pathways, regulatory processes and enzyme activities related to cell structure, cell motility, faical recognition, gene/protein expression and other metabolic pathways. The gene functions include enzyme binding activity, protein kinase binding activity, phospholipid binding activity, phosphatase activity and GTPase activity. The enriched terms include cellular process regulation, enzyme activity, protein and peptide regulation, and protein domain modification.\\n\\nMechanism: This list of human genes modoify cellular processes by various functions such as enzyme binding activities, protein kinase binding activities, phospholipid binding activities, phosphatase activities, and GTPase activities. These functions help regulate and modify various signaling pathways and gene/protein expressions involved in cell structural, motility, and facial recognition, as well as metabolic processes.\\n\\n] | \n", + "0.92 | \n", + "471 | \n", + "
| 793 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[COULD NOT PARSE] | \n", + "[ The genes of interest in this study are generally involved in the regulation of signal transduction pathways, with primary roles in kinase binding and GTPase activity, protein phosphatase activity, activation of transcription factors, phospholipase activity, receptor binding, ubiquitination, acetylation, and other signaling pathways. In addition, several of the genes are associated with apoptosis, cell migration, and negative regulation of proliferation.\\n\\nHypothesis/mechanism: These genes are likely part of an overarching molecular signaling pathway, in which changes in the expression of these genes modulate cell proliferation, apoptosis, migration, and other cellular processes. This likely manifests through changes in protein phosphorylation, ubiquitination acetylation, and other post-translational modifications that affect downstream cell signaling cascades. \\n\\n] | \n", + "0.68 | \n", + "861 | \n", + "
| 794 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-0 | \n", + "[ The list of human genes is enriched for terms relating to membrane and vesicle trafficking, including protein binding activity, GTPase activity, GTP-dependent protein binding activity, SNARE binding activity, enzyme binding activity, protein kinase binding activity and clathrin binding activity.\\n\\nMechanism: The underlying mechanism is likely to involve the transport of proteins through the cellular membrane and vesicles along various pathways, such as endocytosis, retrograde transport, Golgi to plasma membrane transport, endoplasmic reticulum to Golgi vesicle-mediated transport, and protein targeting to lysosomes.\\n\\n] | \n", + "[\\nSummary: The list of genes are enriched for terms related to protein binding activity, ATP binding activity, GTP-dependent protein binding activity, GTPase activity, signal sequence binding activity, clathrin binding activity and small GTPase binding activity. \\nMechanism: These genes are involved in processes such as cellular response to hormone stimulus, signal transduction, Golgi organization and vesicle mediated transport.\\nHypothesis: These genes are involved in an intracellular transport process that is composed of Protein Bindings, ATP Bindings, GTP Bindings and Small GTPase Bindings.\\n] | \n", + "0.92 | \n", + "26 | \n", + "
| 795 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_PROTEIN_SECRETION-1 | \n", + "[ The analysis of the list of genes reveals common functions associated with transport, binding, activity, and assembly. These functions are enriched across a broad range of processes, including protein transport, catabolic and metabolic processes, regulation of intracellular signal transduction, Golgi and cell surface organization, positive and negative regulation, and responses to stimuli. This suggests a complex network of pathways, activity and assembly at play in cellular process and interactions.\\n\\nMechanism: The mechanism of action suggested by the term enrichment test indicates a complex network of pathways, activities, and assemblies at the protein level, such as those indicated by functions like binding and activity, as well as assembly and transport. This suggests a broad range of processes that are at play in the regulation of a large variety of functions and responses in cells.\\n\\n] | \n", + "[\\nSummary: This list of genes are involved in a range of processes, including intracellular transport, protein folding and processing, and positive and negative regulation of several cellular pathways. \\nMechanism: These genes likely play roles in regulating intracellular transport, protein folding and processing and positive and negative regulation of several cellular pathways.\\n] | \n", + "0.89 | \n", + "523 | \n", + "
| 796 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[\\nThe genes identified provide a variety of functions that might generalize to protection from oxidative stress and detoxification, DNA/RNA binding and transcription, and maintaining cell-cell adhesion and organization of cellular components.\\n\\nMechanism: These functions are likely related to a broad overarching mechanism of defense from reactive oxygen species, maintenance to the structure and development of the organism, as well as mediating interactions between cells.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "460 | \n", + "
| 797 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[ These genes are primarily involved in mediating energy transfer and metabolism, responding to oxidative stress/environmental compounds, and modulating cell proliferation, apoptosis, and cell to cell adhesion. \\nMechanism: The proteins directly or indirectly regulate multiple biological pathways, including canonical glycolysis, citric Acid cycle, respiratory chain, DNA metabolism, transcriptional/protein translation processes, and lipid/amino acid metabolic processes via enzymatic activity, binding activity and membrane transporters. \\n] | \n", + "[ \\nSummary: The gene functions in this list are predominantly related to activities that enable and regulate cell redox homeostasis, such as helping to facilitate the production of and protection against oxidants like hydrogen peroxide, superoxide, and other reactive substances. \\nMechanism: The gene functions work together in a complex network of pathways, proteins, and processes to maintain redox balance in the cell by carrying out activities such as enzyme binding, protein homodimerization, protein-disulfide reductase activity, glutathione peroxidase activity, NADH dehydrogenase activity, and more. \\n] | \n", + "0.87 | \n", + "68 | \n", + "
| 798 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-0 | \n", + "[ The list of genes are found to be primarily involved in activities related to RNA binding, nucleosome binding, transcription and regulation, DNA binding, protein kinase activity, protein folding and chaperoning, metabolic regulation and ubiquitination.\\n\\nMechanism: The mechanisms by which these activities are enabled involve complex interactions between proteins, which act as signal transducers, modulators and effectors, resulting in the relevant activities being enabled and processes being modulated.\\n\\n] | \n", + "[ Human genes related to this list are enriched for functions in molecular function activator activity, protein kinase activity, cellular component activity, binding activity, peptidase activity, nucleosome binding activity, ion binding activity and phosphatase binding activity; and processes such as cell cycle regulation, apoptosis regulation, cell adhesion, nervous system development, transcription regulation, protein transport, cell-cell recognition and gene expression regulation.\\n\\nMechanism: This list of genes are likely to be involved in several biological primary pathways, including signal transduction pathways, protein transcription pathways, metabolic pathways, and membrane transport pathways. These pathways are responsible for the functions and processes associated with cells in the regulation of growth, differentiation, development, and apoptosis.\\n\\n] | \n", + "0.92 | \n", + "362 | \n", + "
| 799 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_SPERMATOGENESIS-1 | \n", + "[ These genes are involved in a range of activities, including enzyme binding, protein binding, ligand binding, calcium ion binding, nucleotide binding, transcription factor binding, DNA binding, GTP binding, hormone binding, ATP hydrolysis, protein kinase operation, RNA binding, enzyme activator activity, chaperone operation, chromatin binding, protein phosphatase binding, phosphatase inhibitor activity, peptidase activity, inorganic cation transmembrane transporter activity, and others.\\nMechanism: These genes likely play important roles in the formation and maintenance of cell structure, transcriptional regulation and signal transduction, protein folding and degradation, metabolic homeostasis, and other processes to maintain cell function.\\n] | \n", + "[COULD NOT PARSE\\nHypothesis: The] | \n", + "0.68 | \n", + "719 | \n", + "
| 800 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[ We have evidence of enrichment for processes related to signal transduction, regulation of transcription, regulation of protein metabolism, regulation of macromolecule metabolism, regulation of cellular processes, interaction with transcription factors, and interaction with SMAD proteins.\\n\\nMechanism: The underlying biological mechanism for these processes is likely related to the activation or inhibition of various proteins and enzymes that interact with signaling pathways, transcription factors, or SMAD proteins. \\n\\n] | \n", + "[ The genes in this list are involved in the regulation of diverse biochemical processes, including transcription, signal transduction, cell cycle, metabolism, and cell adhesion. The commonalities in their functions involve binding activities (e.g. ATP binding, activin binding, SMAD binding), and protein phosphatase/kinase activities. Many of these genes are also involved in regulation of intracellular signaling pathways, such as SMAD signaling and BMP signaling, and in the regulation of transcription by RNA polymerase II.\\n\\nMechanism: The mechanism underlying these commonalities is likely related to the role of these genes in regulation of intracellular processes, as well as their binding activities, which may be necessary for the functional regulation of their target proteins.\\n\\n] | \n", + "0.90 | \n", + "266 | \n", + "
| 801 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[ Gene functions associated with transduction and signal modification of biological and biochemical processes; as well as DNA binding transcription activity, protein modify/kinase/phosphatase activities, receptor/ligand binding activity and activity inhibitor activity which play a role in cellular morphogenesis, metabolism, and adaptation are enriched.\\n\\nMechanism: These gene functions are involved in multiple biological and biochemical processes, with particular involvement in transcriptional regulation, signal transduction, positive/negative regulation of regulatory pathways, regulation of metabolic and structural processes, regulation of gene expression, and regulation of transcriptional factors.\\n\\n] | \n", + "[ This list of genes is enriched for terms related to transcription regulation, intracellular signal transduction,DNA binding activity, positive/negative regulation of RNA/protein metabolic processes and protein phosphorylations.\\n\\nMechanism: These genes are likely to be functioning in a pathway that is involved in controlling gene expression, cellular signaling, and cellular metabolism. This is likely achieved through DNA binding, transcription regulation, and interaction with multiple proteins to modify protein and/or gene expression.\\n\\n] | \n", + "0.91 | \n", + "166 | \n", + "
| 802 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[ The genes are involved in regulation of growth, development, and defense mechanisms, as evidenced by enrichments of terms including \"DNA binding transcription factor,\" \"signaling receptor binding,\" \"enzyme binding,\" \"cytokine receptor binding,\" \"growth factor,\" and \"transmembrane receptor.\" \\n\\nMechanism: These genes work in concert to regulate amino acid metabolism, transport, signaling, and other processes within cells, leading to growth, development, and defense mechanisms. \\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "468 | \n", + "
| 803 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[ \\nSummary: This list of genes are primarily involved in transcription activities, binding activities (e.g. DNA-binding, protein binding, signaling receptor binding, etc.), enzyme activities (e.g. GTPase, ATPase, protein kinase, etc.), cytokine activities, and also in cell adhesion, transport, and regulation processes. \\nMechanism: The underlying mechanism of these genes includes a variety of critical signaling pathways, including the NF-kB, MAPK, and JAK-STAT pathways, as well as several cellular and organismal developmental pathways. \\n] | \n", + "[\\nThis dataset refers to a list of gene summaries that are involved in multiple pathways of cellular development and signaling. The enriched terms indicate genes related to DNA-binding transcription activator activity, transcription regulatory region sequence-specific DNA-binding, GTP binding activity, enzyme binding activity, identical protein binding activity, signal receptor binding activity, phosphatase activity, protein kinase binding activity, cytokine activity, and growth factor activity. The underlying mechanism can likely be attributed to signal transduction pathways and transcription regulation related to cell growth, development, and differentiation. \\n\\nMechanism: Signal transduction pathways and transcription regulation\\n] | \n", + "0.93 | \n", + "199 | \n", + "
| 804 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[ The list of genes and their functions are related to the synthesis and processing of nucleic acids and proteins, including RNA binding, transcriptional regulation, protein and mRNA folding, mRNA degradation, and translation regulation.\\n\\nMechanism: The general underlying biological mechanism is related to the regulation of gene expression and the synthesis and processing of proteins and nucleic acids.\\n\\n] | \n", + "[ The majority of the genes in this list enable or involve in various functions related to RNA or protein processing, as demonstrated by the enriched terms related to RNA processing, protein binding, and DNA binding/transcription activities. Many of the genes contribute to various cellular processes, such as cellular response, cell homeostasis, and transcription from RNA polymerase II. A mechanism underlying this group of genes is that the genes are involved in multiple interactions between different enzymes and cell components for post-translational and transcriptional processing within the cell.\\n\\nMechanism: A mechanism underlying this group of genes is that the genes are involved in multiple interactions between different enzymes and cell components for post-translational and transcriptional processing within the cell.\\n\\n] | \n", + "0.93 | \n", + "427 | \n", + "
| 805 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[ The enriched terms from these human genes suggest a common theme related to methods for dealing with environmental stress, protein folding, and metabolism. Many of these genes are involved in activities such as ATP binding and hydrolysis, molecular adaptor activity, molecular function inhibitor activity, ubiquitin protein ligase binding activity, transcription regulator activity, translation factor activity, RNA binding, protein dimerization activity, DNA binding activity, enzyme binding activity, and SNARE binding activity.\\n\\nMechanism: The underlying biological mechanism suggested by these human genes is related to the body's ability to respond to environmental stress and maintain cellular homeostasis. This is accomplished through the involvement of various proteins and RNA molecules that regulate gene expression, protein folding, and metabolism. Additionally, many of these genes are involved in the cellular response to cytokines, suggesting an immune response component.\\n\\n] | \n", + "[\\n\\nSummary: These genes have a variety of functions, including enzyme binding activity, RNA binding activity, protein binding activity, transmembrane transporter binding activity, and transcription factor binding activity.\\n\\nMechanism: These genes are likely involved in a variety of cellular processes such as post-transcriptional control of gene expression, protein folding and sorting, and RNA processing and translation.\\n\\n] | \n", + "0.89 | \n", + "565 | \n", + "
| 806 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The given list of genes are enriched for binding activities, such as GTP binding activity, enzyme binding activity, DNA-binding transcription factor binding activity, phosphotyrosine residue binding activity, cyclin binding activity and other related activities. These activities confer functions such as protein transcription, signal transduction, protein phosphorylation, cellular adhesion and cellular response to certain molecules.\\n\\nMechanism: The mechanism underlying these enriched binding activities is likely related to receptor-ligand interaction, involving both intra-cellular and inter-cellular interaction between molecules. It is also likely to involve protein-protein interaction, involving proteins such as SMAD binding proteins, NF-kappaB binding proteins and growth factor binding proteins, which play important roles in regulating various cellular processes.\\n\\n] | \n", + "0.68 | \n", + "864 | \n", + "
| 807 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_DN-1 | \n", + "[ Expression, regulation and activation of various pathways, enzymes, receptors and factors involved in numerous cellular processes such as cell differentiation, cellular adhesion, development, exocytosis, hematopoiesis, inflammation and immunity, lipid metabolism, transcription, neural development, regulation and intercellular signaling. \\nMechanism: The expression, regulation and activation of multiple proteins involved in core cellular processes is accomplished by binding and interaction of multiple domains including but not limited to ATP-binding activity, PDZ domain binding, SMAD binding, calcium ion binding, Gap junction channel activity, cAMP-dependent protein kinase inhibitor activity, Phosphotyrosine resodue binding activity, GTPase activator activity, among other activities.\\nHypotheses: The various interactions of the proteins enable the expression of genetic material and regulation at the cellular level by transcription factor binding activity, cis-regulatory region sequence-specific DNA binding activity, DNA hydrolysis activity and other processes. This helps in coordinating different cellular components and signaling events for proper functioning and development of the organism.\\n] | \n", + "[\\nSummary: The list of genes provides evidence that a number of functions are involved, such as DNA-binding transcription activator activity, RNA polymerase II-specific activity, NF-kappaB binding activity, and microtubule binding activity.\\nMechanism: These genes may be involved in signaling pathways that regulate processes such as hemopoiesis, endothelial intestinal barrier formation, cellular response to steroid hormone stimulus and nervous system development.\\n] | \n", + "0.88 | \n", + "743 | \n", + "
| 808 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-0 | \n", + "[ This list of genes is enriched for functions related to protein binding, DNA binding, binding activity, receptor binding activity, and protein kinase activity. Hypothesis: This list of genes is likely involved in several pathways related to cell adhesion, signaling, and in particular, the regulation of gene expression. \\n\\nMechanism: This list of genes is involved in a variety of mechanisms related to protein-protein and protein-DNA interactions, as well as protein kinase activity, all of which contribute to cell adhesion, signaling, and the regulation of gene expression.\\n\\n] | \n", + "[\\n\\nSummary: The genes listed are involved in a variety of functions, including ATP binding activity, protein kinase binding activity, RNA binding activity, DNA binding activity, receptor binding activity, enzyme binding activity, and phospholipid transporter activity.\\n\\nMechanism: The genes have a variety of molecular functions and are involved in a wide range of processes, including cell-cell adhesion, synaptic transmission, apoptotic signaling pathway, interleukin-6 receptor binding, T cell activation, overall cellular metabolism, and gene expression regulation.\\n\\n] | \n", + "0.93 | \n", + "9 | \n", + "
| 809 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_UV_RESPONSE_UP-1 | \n", + "[ This list of genes is predominantly involved in transductional and transcriptional regulatory mechanisms related to cellular processes, such as ion and water transport, signaling receptor activities, DNA/RNA binding and processing, protein ubiquitination, and enzyme activities. Specifically, we identify gene functions in GTP binding activity; DNA binding activity; transcriptional activator activity; protein kinase binding activity; endopeptidase activity; receptor binding activity; hydrolase activity; nucleotide and peptide transporter activity; ion and neurotransmitter channel activity; antioxidant activity; and ligase activity.\\n\\nMechanism: These gene functions are likely to be involved in a number of underlying transductional and transcriptional regulatory mechanisms related to cellular processes, including signal transduction, gene expression, protein catabolism, and membrane transport. These gene functions likely represent molecular signals allowing for rapid and short-term responses in physiological and neurological processes, such as cell membrane responses, sensory processing, and immunological responses, as well as slower and long-term responses, such as development and cell growth.\\n\\n] | \n", + "[ Analysis of the gene summaries reveals that many of the genes are involved in various activities, such as enzyme binding activity, enzyme activity (specifically, hydrolase and transferase activities), transcription-related activities, receptor activities, and binding activities for molecules, such as proteins and DNA. The underlying biological mechanism or pathways these genes belongs to is transcriptional regulation, protein-protein interactions, cell adhesion and migration, and signal transduction. Thus, the following terms are enriched in these genes: enzyme binding activity; hydrolase activity; transferase activity; receptor activity; DNA binding activity; RNA binding activity; transcription factor activity; and protein binding activity. \\nMechanism: Transcriptional regulation, protein-protein interactions, cell adhesion and migration, and signal transduction. \\n] | \n", + "0.92 | \n", + "334 | \n", + "
| 810 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[COULD NOT PARSE] | \n", + "[\\nSummary: This gene dataset contains genes involved in cell migration, regulation of signal transduction, protein ubiquitination, cell cycle control, transcription regulation, and regulation of protein stability.\\nMechanism: These genes appear to commonally control a number of key pathway processes at the cellular level and can initiate their respective pathways through the binding of other proteins, and the control of chromatin composition through the modification of histones.\\n] | \n", + "0.69 | \n", + "467 | \n", + "
| 811 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[ \\n\\nSummary: Multiple genes are involved in protein binding, transcription regulation, cell cycle regulation, signaling pathways, and response pathways. \\nMechanism: Multiple genes play a role in regulating the activities of transcription and signaling pathways which are vital to several biological processes.\\n] | \n", + "[ Human genes included in this list are primarily involved in processes related to signal transduction and transcription regulation, with some involvement in cell migration, development and and cell population proliferation, and proteolysis. Common terms enriched include: signal transduction; regulation of gene expression; transcription; regulation of protein phosphorylation; regulation of protein stability; cell migration; cell proliferation; development; and proteolysis.\\n\\nMechanism: The human genes studied here mainly act in a variety of signal transduction pathways, which includes NF-kappaB and Wnt signaling; activities such as binding, adaptor, and ligand activities are also involved. Transcriptional regulation is also present, with activities including transcription activator and repressor binding, as well as DNA binding and corepressor activity. The regulation of proteins and proteolysis by the genes is also observed, as well as other activities related to cell migration and cell development.\\n\\n] | \n", + "0.90 | \n", + "705 | \n", + "
| 812 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "T cell proliferation-0 | \n", + "[ The list of genes mostly involves genes that enable signaling receptor binding activity, protein kinase binding activity, and ubiquitin protein ligase activity. These genes are enriched in processes such as intracellular signal transduction, cytokine production, and gene expression. The underlying biological mechanism involves intercellular communication through signaling cascades leading to the regulation of gene expression. \\n\\nMechanism: Intercellular communication through signaling cascades leading to regulation of gene expression.\\n\\n] | \n", + "[ \\n\\nSummary: The list of genes are mainly involved in a variety of biological pathways and processes, such as intracellular signaling, cell proliferation, cell adhesion and migration, cell division and apoptosis. \\n\\nMechanism: The pathways and processes are likely mediated by protein interactions such as binding activity, enzyme and kinase activity, as well as transcription and receptor signaling, which ultimately result in cellular adaptation and regulation.\\n\\n] | \n", + "0.93 | \n", + "79 | \n", + "
| 813 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "T cell proliferation-1 | \n", + "[ This group of genes is involved in regulated cellular processes, including cell recognition, signal transduction, cell migration, and gene expression. The primary functions of these genes include binding activities (e.g. DNA-binding transcription factor activity, receptor ligand activity, identical protein binding activity, etc.), catalytic activities (e.g. histone deacetylase binding activity, phosphotyrosine residue binding activity, etc.), enzyme activity (e.g. indoleamine 2,3-dioxygenase activity, phosphodiesterase activity, etc.), and transporter activity (e.g. metal cation: proton antiporter activity).\\n\\nMechanism: These genes likely act, at least in part, through the modulation of signaling transduction pathways, such as the Wnt, Notch, JAK-STAT, and MAPK cascade, as well as cytokine- and growth factor-mediated pathways. These pathways play key roles in many cellular and developmental processes, including cell migration, proliferation, apoptotic processes, and stem cell differentiation.\\n\\n] | \n", + "[ \\nSummary: This list of genes has been found to be involved in a variety of functions, including cation binding activity, diacylglycerol binding activity, enzyme binding activity, protein heterodimerization activity, receptor binding activity, and protein kinase activity. \\nMechanism: These genes appear to be involved in a variety of cellular activities, including signal transduction, cell recognition and migration, receptor binding, and apoptotic processes.\\n] | \n", + "0.92 | \n", + "548 | \n", + "
| 814 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "Yamanaka-TFs-0 | \n", + "[\\n\\nSummary: Genes POU5F1, SOX2, KLF4, and MYC, are involved in various functions such as DNA-binding transcription repressor and activator activities, RNA polymerase II-specific, and nucleic acid binding activities. These genes are also implicated in the regulation of biosynthetic processes, signal transduction, gene expression, angiogenesis, protein-DNA complex organization, and cell population proliferation, and are associated with numerous cancers.\\n\\nMechanism: These genes have been implicated in the regulation of complex biological processes, such as signal transduction and gene expression, suggesting a potential role in transcriptional regulation.\\n\\n] | \n", + "[ \\n\\nSummary: The commonalities among the gene functions of the list provided are DNA-binding transcription factor activity, RNA polymerase II-specific, nucleic acid binding activity, transcription cis-regulatory region binding activity, regulation of gene expression, and regulation of biosynthetic process.\\n\\nMechanism: The genes enable the transcription of genetic material, and potential activation or repression of gene expression by interacting with DNA and RNA polymerase II. Regulation of gene expression is achieved through altering transcription factor activity and binding to DNA regions to control downstream gene expression.\\n\\n] | \n", + "0.89 | \n", + "24 | \n", + "
| 815 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "Yamanaka-TFs-1 | \n", + "[ Human genes, KLF4, POU5F1, and SOX2, are involved in transforming DNA-binding transcription activator, repressor, and factor activities, respectively. They are commonly involved in processes like positive and negative regulation of gene expression, biosynthetic process, angiogenesis, BMP signaling pathway involved in heart induction, and canonical Wnt signaling pathway.\\n\\nMechanism: These genes work in association with transcription regulator complexes, which interact with DNA and RNA, influencing transcriptional programming and gene regulation.\\n\\n] | \n", + "[ The genes KLF4, POU5F1, and SOX2 are all involved in transcription regulation and gene expression, specifically upstream of or within the process of endodermal cell fate specification. They are all located in the cytosol and nucleoplasm, are associated with chromatin, and are part of a transcription regulator complex. \\n\\nMechanism: The mechanism underlying these gene functions is likely related to the regulation of DNA binding and transcription, which could help to control cell development and maintenance pathways.\\n\\n] | \n", + "0.92 | \n", + "31 | \n", + "
| 816 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "amigo-example-0 | \n", + "[ Genes involved in this list are involved in a wide range of activities, such as protein binding, lipoprotein lipase activator activity, phospholipid binding, protein dimerization, modulation of chemical synaptic transmission, integrin binding, collagen binding, heparin binding, signaling receptor binding, non-membrane spanning protein tyrosine kinase activity, peptidoglycan binding, GTPase activator activity, and more. The commonalities in these genes' functions point to roles in signaling pathways, extracellular matrix structure and function, cell-cell and cell-matrix adhesion, lipid metabolism, and defense response.\\n\\nMechanism: These genes are likely to be involved in a wide range of signaling pathways, particularly related to cell-cell and cell-matrix adhesion, as well as lipid metabolism, extracellular matrix structure, and defense response. These pathways result in a wide variety of physiological functions, from regulation of gene expression to regulation of BMP signaling, cell migration, and cell proliferation.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "1020 | \n", + "
| 817 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "amigo-example-1 | \n", + "[ \\nThe human gene summaries provided all involve functions related to signal transduction, cell adhesion and binding activities, extracellular matrix structural components, and mechanism related to cell proliferation, growth and differentiation. Specifically, the genes are involved in protein binding, ion binding, chemokine activity, growth factor binding, signal receptor binding, phosphatase binding, cell migration, membrane repolarization, signal transduction, regulation, and defense response to bacteria and other organisms. \\n\\nMechanism: These genes appear to be involved in multiple cellular pathways related to signal transduction and cell adhesion, as well as molecular interactions and processes such as protein phosphorylation. Specifically, it appears that the genes are involved in activating intracellular signalling events, regulating cell growth and proliferation, and mediating defense responses. \\n\\n] | \n", + "[ The genes listed are mainly involved in cell-specific metabolic processes, and sharing a common role in regulation of cell-matrix adhesion and extracellular matrix structural constituents. Several of them are also involved in organ development and differentiation, and others in regulation of different hormone pathways.\\n\\nMechanism: Many of these genes are involved in positive or negative regulation of protein metabolic processes such as phosphorylation, proteolysis, and cell-surface receptor signalling pathways. They also play a role in regulating cell proliferation, apoptosis, and ion transport. Additionally, the genes are involved in regulation of blood coagulation and cell adhesion, as well as in modulation of chemical synaptic transmission and cell-matrix adhesion.\\n\\n] | \n", + "0.92 | \n", + "136 | \n", + "
| 818 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_0-0 | \n", + "[ \\nSummary: A list of genes that are enriched for terms related to calcium ion binding, double-stranded DNA-binding, cellular defense, and embryonic development processes.\\nMechanism: The genes in this list are likely involved in the processes of calcium binding, cell adhesion and migration, and transcriptional regulation, which may underpin the roles of these genes in embryonic development, neuronal and vascular tissue formation, and cellular defense. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "441 | \n", + "
| 819 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_0-1 | \n", + "[ Our term enrichment analysis of human gene functions reveals that these genes play a variety roles related to regulation, binding, activity, and transport-related activity. Specifically, the enriched terms include: metal ion binding activity; protein binding activity; RNA binding activity; phosphatase regulator activity; gap junction channel activity; protein homodimerization activity; calcium ion binding activity; GTPase activity; DNA binding activity; ubiquitin protein ligase activity; protein tyrosine phosphatase activity; and transcription corepressor activity.\\n\\nMechanism: These results suggest a mechanism for gene regulation and regulation of pathways at the cellular level, involving binding, transport-related activity, and kinase or phosphatase activities. The mechanisms may be involved in the formation of structural components or the regulation of gene expression in the cell. This may involve transcriptional, post-transcriptional, and post-translational control of gene expression. Additionally, the identified activities may be involved in signal transduction and cellular signaling. \\n\\n] | \n", + "[ Summary: The list of genes is enriched for terms related to DNA-binding transcription activity, protein kinase binding activity, metal ion binding activity, calcium ion binding activity, transcription co-regulator activity, and responsive to stimuli.\\nMechanism: The underlying biological pathways can either be direct (e.g. modifying gene expression) or indirect (e.g. binding proteins to regulate other proteins).\\n] | \n", + "0.92 | \n", + "693 | \n", + "
| 820 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_1002-0 | \n", + "[\\n\\nSummary: The list of genes provided are involved in various functions and processes of muscle development and contraction. These functions and processes are related to skeletal muscle thin filament assembly, muscle contraction, muscle cell differentiation, actin nucleation, protein ubiquitination, and muscle organelle organization.\\n\\nMechanism: The underlying biological mechanism includes protein phosphorylation, calcium-dependent signaling pathways, gene regulation, and post-translational modifications.\\n\\n] | \n", + "[ The list of genes appears to be focused on muscle structure and development, as well as processes related to muscle contractions. This is supported by enriched terms related to muscle processes which include actin filament binding, microfilament motor activity, muscle alpha-actinin binding, actin monomer binding, tropomyosin binding, myosin binding, titin binding, and creatine kinase activity. This suggests a biological mechanism that centers around the development, assembly, and contraction of muscle tissue. A hypothesis of this mechanism is that these genes have a complex role in enabling specific activities related to muscle development and muscle contractions, as well as regulating their activity to ensure efficient functioning of muscle tissue.\\n\\nSummary: Genes related to muscle tissue structure, development, and contractions\\nMechanism: Complex role in enabling specific activities related to muscle development and muscle contractions, as well as regulating their activity to ensure efficient functioning of muscle tissue.\\n] | \n", + "0.93 | \n", + "529 | \n", + "
| 821 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "bicluster_RNAseqDB_1002-1 | \n", + "[ This list of genes is associated with a variety of functions related to muscle structure and contraction, such as actin and tropomyosin binding activities, protein phosphatase binding activity, troponin complex activities related to muscle contraction and regulation of muscle adaptation, protein polymerization, and muscle tissue morphogenesis. The underlying common mechanisms are related to muscle assembly, muscle contraction, and regulation of muscle adaptation.\\n\\nMechanism: Muscle assembly, muscle contraction, regulation of muscle adaptation\\n\\n] | \n", + "[ This list of human genes are related to skeletal muscle, actin filament/stress fiber and striated muscle thin filaments assembly. They are enriched for functions involving calcium-dependent binding activity; ATP binding activity; adhesion; transmembrane transport; transcriptional regulation; ubiquitination; and actin monomer binding activity.\\n\\nMechanism: The genes are likely to be involved in pathways which are regulated by calcium-mediated intracellular signaling and ubiquitin-dependent protein degradation, leading to muscle contraction and regulation of muscle adaptation in response to denervation and electrical stimulus.\\n\\n] | \n", + "0.92 | \n", + "83 | \n", + "
| 822 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "endocytosis-0 | \n", + "[ \\nSummary: The genes involved in this list have functions related to protein signaling, protein phosphorylation, protein ubiquitination, protein transport, cell projection organization, endocytosis and receptor-mediated endocytosis, phosphatidylinositol binding, membrane raft polarization, and plasma membrane tubulation.\\n\\nMechanism: The genes in this list are involved in a variety of protein signaling and transport pathways that enable a wide range of functions such as cell projection organization, endocytosis and receptor-mediated endocytosis, phosphatidylinositol binding, membrane raft polarization, and plasma membrane tubulation.\\n\\n] | \n", + "[ \\n\\nSummary: The list of genes identified in this analysis are involved in several processes including signalling, endocytosis, membrane transport, and protein metabolism.\\n\\nMechanism: These genes serve to regulate several processes which involve signalling, endocytosis, membrane transport, and protein metabolites through protein kinase activities.\\n\\n] | \n", + "0.94 | \n", + "292 | \n", + "
| 823 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "endocytosis-1 | \n", + "[ Summary: The genes listed are involved in functions such as cadherin binding activities, endocytosis, cholesterol homeostasis, GTP-dependent protein binding activity, protein ubiquitination, and lysophosphatidic acid binding activity. They are located in cellular components such as endoplasmic reticulum, Golgi apparatus, Basolateral plasma membrane, clathrin-coated pit, postsynaptic membrane and cytoplasm.\\nMechanism: The underlying biological mechanism involves endocytosis and regulating processes associated with cholesterol metabolism, protein ubiquitination and lysophosphatidic acid binding.\\n] | \n", + "[ This list of genes is involved in various cellular functions, such as cell signaling, protein ubiquitination, endocytosis/exocytosis, intracellular trafficking, vesicle transport, receptor binding and regulation of gene expression. The terms associated with these genes reflect their roles in a variety of cellular processes, including protein phosphorylation, protein homooligomerization, vesicle buddying and regulation of inflammatory response, among others.\\n\\nMechanism: The cellular functions associated with these genes are likely regulated through various intracellular pathways, including protein kinase cascades, GTP-dependent pathways, receptor signaling, and canonical inflammasome signaling, among others.\\n\\n] | \n", + "0.91 | \n", + "117 | \n", + "
| 824 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "glycolysis-gocam-0 | \n", + "[ \\nSummary: The majority of the genes commonly enable enzymatic activities, often related to cellular metabolism and related pathways.\\nMechanism: Many of the genes enable the production of energy stores (ATP, fructose 6-phosphate, glyceraldehyde-3-phosphate, fructose 1,6-bisphosphate, triosephosphate, and phosphoglycerate) through regulation of several metabolic processes, such as glycolysis, carbohydrate phosphorylation, fructose 6-phosphate metabolic process, fructose 1,6-bisphosphate metabolic process, and phosphoglycerate kinetic. Additionally, two of the genes involved in transcription (PKM, GAPDH) suggest a role in gene expression. \\n] | \n", + "[\\nSummary: The genes listed are primarily involved in energy regulation, carbohydrate metabolism, cell homeostasis, cell signaling, and protein catabolism.\\nMechanism: The enriched genes encode for proteins in energy regulation pathways, such as glycolysis and gluconeogenesis, as well as for proteins that help to modulate cellular signaling, such as glucose and phosphate binding proteins.\\n] | \n", + "0.92 | \n", + "256 | \n", + "
| 825 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "glycolysis-gocam-1 | \n", + "[ \\nSummary: These genes are involved in a range of cellular processes related to energy metabolism, including glycolysis, phosphorylation and glucose transport.\\nMechanism: The genes encode proteins that catalyze biochemical reactions such as enzyme activities, ubiquitin ligase binding and protein homodimerization. \\n] | \n", + "[ \\nSummary: Enriched terms are related to metabolic activities, protein binding, cellular homeostasis, localization, and glycolytic processes.\\nMechanism: These genes may all be involved in a metabolic pathway, functioning together in protein synthesis, post-transcriptional processing, and regulation of intracellular metabolism.\\n] | \n", + "0.91 | \n", + "13 | \n", + "
| 826 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "go-postsynapse-calcium-transmembrane-0 | \n", + "[\\nThis gene set is strongly enriched for genes involved in regulation of presynaptic cytosolic calcium ion concentration, membrane depolarization, regulation of glutamate receptor activity, regulation of neurotransmitter receptor activity, and regulation of phospholipid metabolism.\\nThe underlying biological mechanism or pathway could involve regulation of synaptic neurotransmitter release, intracellular phospholipid metabolism, and calcium ion homeostasis.\\n] | \n", + "[ \\n\\nSummary: This list of genes is primarily associated with regulation of intracellular calcium concentrations and ion channel activity.\\nMechanism: Calcium concentration regulation is the primary mechanism enabling functions, such as postsynaptic neurotransmitter receptor activity, regulation of AMPA receptor activity, G protein-coupled receptor signaling, calcium ion transmembrane transport, and ligand-gated monoatomic ion channel activity.\\n] | \n", + "0.93 | \n", + "14 | \n", + "
| 827 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "go-postsynapse-calcium-transmembrane-1 | \n", + "[ This list of genes is primarily involved in calcium transport and regulating calcium ion concentrations in the cytoplasm and plasma membrane. Enriched terms include: calcium transport; regulation of calcium ion concentration; G protein-coupled receptor signaling pathway; negative regulation of cell volume; regulation of nitric oxide metabolic process; regulation of glutamatergic synaptic transmission; regulation of postsynaptic neurotransmitter receptor activity; and membrane depolarization.\\n\\nMechanism: These genes are involved in the transfer and maintenance of calcium ion concentrations in the cell to facilitate cell signaling and communication. Calcium is regulated through a variety of channels, transporters, and receptors, with the most significant ones being glutamate receptors (NMDA, AMPA, and L-type), acetylcholine receptors, and G-protein coupled receptors (e.g. serotonin receptor). These channels and receptors are involved in regulating cellular processes such as membrane depolarization, transport of ions, and neurotransmitter binding. They also interact with other proteins involved in the regulation of calcium levels, such as NCS1, CACNG2, CACNG4, and CACNG8.\\n\\n] | \n", + "[ This is a list of genes that when taken together seem to be involved in regulating ion channels, transporters, or receptors. Specifically, they refer to monoatomic cation channels, acetylcholine-gated channels, glutamate-gated calcium channels, voltage-gated calcium channels, NMDA selective glutamate receptor complexes, and L-type voltage-gated calcium channel complexes. All these gene functions are involved in processes related to neuronal excitation, calcium-mediated signaling, neural transmission, neuronal migration, and synaptic plasticity.\\n\\nMechanism: The underlying biological mechanism suggested by this list of gene functions is ion and calcium signaling in the nervous system. This includes the regulation of intracellular calcium levels, the modulation of neurotransmitter release, the transport of ions across the cell membrane, and the regulation of synaptic transmission and plasticity. \\n\\n] | \n", + "0.94 | \n", + "281 | \n", + "
| 828 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "go-reg-autophagy-pkra-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The gene summaries provided indicate that the main terms enriched among all of these genes are: protein kinase binding activity, protein kinase activity, protein serine/threonine kinase activity, positive regulation of protein phosphorylation, and regulation of macromolecule biosynthetic process.\\n\\nMechanism: The mechanism of action associated with these genes is likely related to their roles in the regulation of protein phosphorylation and macromolecule biosynthetic processes. This likely involves a variety of cellular pathways, such as intracellular signal transduction and TOR signaling, as well as modulation of different cellular components, such as the cytosol, nucleus, and mitochondrion.\\n\\n] | \n", + "0.68 | \n", + "688 | \n", + "
| 829 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "go-reg-autophagy-pkra-1 | \n", + "[ \\n\\nSummary: This list of genes are involved in a variety of biochemical processes, such as protein folding and chaperone activities, protein kinase binding and activator activities, and metal ion binding. They are also implicated in a variety of diseases, including Alzheimer's, Parkinson's, and cancer.\\n\\nMechanism: These genes are involved in a range of functional activities related to protein folding and chaperone activities, protein kinase binding and activator activities, and metal ion binding, which are all important for cellular biochemistry.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "539 | \n", + "
| 830 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE\\nHypothesis: The genes in the list are involved in glycan metabolism] | \n", + "0.86 | \n", + "69 | \n", + "
| 831 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[ These genes are primarily involved in carbohydrate and lipid metabolism, as well as glycoprotein degradation, protein homodimerization, and hyaluronan/ glycosaminoglycan catabolism.\\n\\nMechanism: The metabolic pathways involved in this process include glycoprotein catabolism, glycosaminoglycan catabolism, heparan sulfate catabolism, glucoside catabolism, mannose trimming and protein deglycosylation.\\n\\n] | \n", + "[\\nSummary: The genes in this list all participate in various glycan/carbohydrate/lipid processing and metabolic activities.\\nMechanism: These genes - primarily hydrolases, lysozymes and mannosidases - are involved in breaking down, or catabolizing, a range of molecules, including gangliosides, chitin, heparan sulfate, lipid, glucosylceramides, and glycoproteins, and so on.\\n] | \n", + "0.91 | \n", + "29 | \n", + "
| 832 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "ig-receptor-binding-2022-0 | \n", + "[ All the genes listed above are involved in immunoglobulin receptor binding activity. ] | \n", + "[\\nSummary: The human genes described in this list have enriched terms related to binding and receptor binding activity, antigen binding activity, immunoglobulin receptor binding activity, non-membrane spanning protein tyrosine kinase activity, phosphatidylcholine binding activity, and phosphotyrosine residue binding activity.\\nMechanism: These genes are involved in a variety of biological processes, including immunoglobulin receptor binding, protein phosphorylation, antigen binding, and cellular component organization. These genes likely work together to enable the body to respond to antigens as part of the immune system. This includes recognizing antigens and binding to them so that the body can mount an immune response.\\n] | \n", + "0.91 | \n", + "644 | \n", + "
| 833 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "ig-receptor-binding-2022-1 | \n", + "[ \\n\\nSummary: This list of genes is mainly predicted to enable antigen binding activity and immunoglobulin receptor binding activity, and are predicted to be involved in several processes related to activation of the immune response and to defense response to other organisms. \\n\\nMechanism: Through the interaction of antigens with immunoglobulin receptors, these genes help to stimulate the immune response and activate immune cells, providing protection against pathogens and other foreign substances. \\n\\n] | \n", + "[\\n\\nSummary: These genes are predominantly immunoglobulin receptor binding proteins with functions in antigen binding and activation of immune responses.\\n\\nMechanism: These genes are likely part of a larger immune system network, involving antigen presentation and recognition, as well as various immune system responses to microbial and foreign invaders.\\n\\n] | \n", + "0.96 | \n", + "149 | \n", + "
| 834 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "meiosis I-0 | \n", + "[COULD NOT PARSE] | \n", + "[\\nSummary: The list of genes provide evidence for a set of processes related to DNA and cellular replication, including DNA binding activity, chromatin binding, ATP dependent activity, protein export, and transcriptional regulation.\\n] | \n", + "0.69 | \n", + "217 | \n", + "
| 835 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "meiosis I-1 | \n", + "[ This list of genes appears to be related to meiosis, DNA binding activities, and processes involved in meiotic recombination, DNA metabolism, and double-strand break repair. The commonalities between the gene functions involve processes related to meiosis, DNA binding, DNA metabolism, homologous recombination, and telomere attachment. Additionally, these genes are located in various cellular components including the nucleus, chromatin, synaptonemal complex, chromosome, and cytoplasm.\\n\\nMechanism: The underlying biological mechanism likely involves a network of complex interactions that control meiotic cell cycle transitions and processes related to DNA metabolism, binding, replication, and repair involving multiple cellular components during gametogenesis. \\n\\n] | \n", + "[ \\nSummary: The genes involved in this list are mainly related to DNA binding, double-stranded DNA binding, DNA/DNA annealing, and identical protein binding activities. They are also involved in a variety of processes related to DNA double strand break repair, DNA metabolic processes, meiotic chromosome segregation and pairing, and spermatogenesis.\\n\\nMechanism: These genes are likely involved in coordinating and catalysing a variety of DNA-related activities that are required for proper genetic recombination and replication of genetic material during meiosis and spermatogenesis.\\n\\n] | \n", + "0.94 | \n", + "184 | \n", + "
| 836 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "molecular sequestering-0 | \n", + "[\\nSummary: We have identified 18 genes with related functions, such as calcium ion binding activity, protein sequestering activity, DNA-binding transcription factor activity, oxysterol-binding activity, and ubiquitin protein ligase binding activity.\\nMechanism: The enriched terms suggest that these genes are involved in processes related to calcium or ion transport, the regulation of the cell cycle and of protein phosphorylation, and intracellular signaling and responses to various external stimuli.\\n] | \n", + "[ \\nSummary: The human genes analyzed are involved in a variety of functions, including calcium ion binding activity; identical protein binding activity, protein sequestering activity; and ubiquitin protein ligase binding activity.\\n\\nMechanism: These genes likely play critical roles in cellular processes such as cellular response to caffeine, regulation of protein phosphorylation, regulation of anion channel activity, positive regulation of lysosomal membrane permeability, regulation of gene expression and response to interferon-beta.\\n\\n] | \n", + "0.93 | \n", + "36 | \n", + "
| 837 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "molecular sequestering-1 | \n", + "[\\nThis gene set is composed of genes involved in various cellular processes including protein binding, sequestering, transcription, metabolism and signaling pathways. Many are located in various cellular components such as the cytoplasm, endoplasmic reticulum and Golgi apparatus. There is a potential connection between these genes and multiple diseases, such as hemochromatosis type 5, Churg-Strauss syndrome and Huntington's disease-like 1.\\n\\nMechanism: These genes are part of a wide range of cellular activities and organelle functions, which could be part of the same underlying cell-wide mechanism. The presence of multiple proteins in the same cellular locales suggest an opportunity for protein-protein interaction and potentially a shared molecular mechanism.\\n\\n] | \n", + "[\\nSummary: The list of genes provides a range of functions relating to protein binding, metal and ion binding, regulation of gene expression, regulation of protein phosphorylation, cellularresponse to infection and inflammation, and regulation of cell death pathways.\\n\\nMechanism: These genes form part of complex pathways that lead to the regulation of macromolecule biosynthetic processes, intracellular transport, gene expression, and protein phosphorylation. These pathways are integral for regulating cell death, cholesterol efflux, protein binding activities, and intracellular calcium.\\n\\n] | \n", + "0.91 | \n", + "177 | \n", + "
| 838 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "mtorc1-0 | \n", + "[ The gene list appears to be involved mainly in metabolic processes, such as enzyme binding and activity, acid binding, molecule transport, adapter and receptor binding and activity, and DNA and protein binding and activity. Hypothesis: The underlying biological mechanism for this set of genes is metabolic regulation, including the regulation of enzyme, protein, and DNA metabolism. ] | \n", + "[\\n\\nSummary: The genes listed are involved in various cellular functions related to protein binding, domain binding and enzyme activity\\nMechanism: The genes are involved in several processes, such as cellular signaling, protein homeodimerization, DNA or RNA binding, transcriptional regulation, and metal ion binding.\\n] | \n", + "0.92 | \n", + "69 | \n", + "
| 839 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "mtorc1-1 | \n", + "[\\nSummary: The following gene functions are significantly enriched in this list of human genes: cytoskeleton protein binding, phosphatase binding activity, oxidation-reduction activity, cell development and signaling activity, DNA binding activity, cellular transporter activity, and protein kinase binding activity.\\n\\nMechanism: The enriched gene functions are essential components of several processes related to cell growth, gene expression, cell differentiation, post-translational modification, and signal transduction.\\n\\n] | \n", + "[ \\n\\nSummary: The list of genes show functions related to structural support, transport of materials and ions, response to stimuli, protein-protein interaction, and regulation of transcription, metabolism, and cell growth.\\n\\nMechanism: The genes involved in this term enrichment show critical functions that are part of the integrated machinery of the cell, which organizes communication, transport, and control. This machinery is responsible for the ability of the cell to respond to stimuli, regulate metabolism and transcription, and undergo cell growth, leading to growth and development of the organism.\\n\\n] | \n", + "0.90 | \n", + "83 | \n", + "
| 840 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "peroxisome-0 | \n", + "[ These genes are involved in peroxisome biogenesis, protein import into peroxisome and pexophagy. \\nMechanism: The genes act as peroxisome targeting sequence binding and ubiquitin-dependent protein binding, enabling fatty acid metabolic processes, protein homodimerization and enzyme binding activity. They are located in endoplasmic reticulum, nucleoplasm, Golgi apparatus and membrane and active in cytosol, peroxisome and peroxisomal matrix. \\n] | \n", + "[ These human genes all share the common activity of enabling activities related to peroxisome biogenesis, such as ATP binding, hydrolysis, ubiquitin-dependent protein binding activity, as well as protein import/unfolding, stabilization and targeting to peroxisome. ] | \n", + "0.89 | \n", + "180 | \n", + "
| 841 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "peroxisome-1 | \n", + "[ The gene functions provide evidence for a common pathway involved in protein import into peroxisomes, with other functions related to protein stabilization, regulation of cell population proliferation, protein-lipid binding, peroxisome organization, and fatty acid metabolism.\\n\\nMechanism: The identified mechanism involves a pathway of protein import into the peroxisome matrix, with further functions related to protein stabilization, ether lipid biosynthesis, protein-lipid binding, receptor recycling, and fatty acid metabolism. \\n\\n] | \n", + "[\\nSummary: The genes PEX6, PEX2, PEX3, PEX7, and PEX1 are all involved in peroxisome biogenesis and organization.\\n] | \n", + "0.85 | \n", + "422 | \n", + "
| 842 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "progeria-0 | \n", + "[ The list of human genes appear to be involved in processes related to post-translational protein modification, DNA folding and nuclear envelope attachment, as well as other processes associated with cellular response to stress, gene transcription, and gene expression. The enriched terms are DNA binding; protein binding; metal ion binding; cellular response to radiation, hypoxia and starvation; regulation of apoptotic process; regulation of telomere maintenance; regulation of protein ADP-ribosylation; and regulation of viral genome replication.\\n\\nMechanism: These genes may be involved in pathways that regulate several kinds of post-translational modification and gene expression patterns in response to environmental stressors. These pathways could include protein processing signals and transcription factors that regulate transcription and translation, as well as enzymes and proteins that control gene expression and DNA folding. In addition, these pathways may be involved in processes that enable cellular senescence and maintenance of DNA integrity. \\n\\n] | \n", + "[ The 4 genes have functions with related to proteins and DNA, including DNA binding; metal ion binding; and protein homodimerization activities. They are also involved in the regulation of apoptotic process, DNA metabolic processes, cellular responses to hypoxia and starvation, and regulation of telomere maintenance.\\nHypothesis: These four genes likely interact with each other in the components of the cell in which they are found, such as the nucleus, cytoplasm, centrosome, and membrane, which all help in fostering DNA binding, metal ion binding, protein homodimerization, and other genetic processes. \\n] | \n", + "0.89 | \n", + "456 | \n", + "
| 843 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "progeria-1 | \n", + "[ These three genes are all associated with DNA damage and repair responses and are located in the nucleus and surrounding cytoplasm. They all involve processes such as protein binding, metal ion binding, and homodimerization activities. Additionally, they have roles in apoptotic processes, cell senescence and response to hypoxia. The term \"DNA damage and repair\" is enriched, as represented by the three genes.\\n\\nMechanism: The genes LMNA, WRN, and BANF1 all act as checkpoints in the maintenance, modification and repair of DNA with regard to genetic information, telomeric regions and structure. They are responsible for the regulation of apoptotic processes, cell senescence and hypoxic responses, thus ensuring genetic integrity and stability.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "735 | \n", + "
| 844 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "regulation of presynaptic membrane potential-0 | \n", + "[\\nSummary: The list of human genes are involved in functions such as ligand-gated monoatomic ion channel activity, GABA receptor activity, glutamate receptor activity, voltage-gated potassium and sodium channel activity, adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway, gamma-aminobutyric acid signaling pathway, and neurotransmitter transport. \\nMechanism: These genes are likely to be involved in the signalling and transport of neurotransmitters across plasma membranes, including the regulation of presynaptic and postsynaptic membrane potentials.\\n] | \n", + "[ This gene list is enriched for several terms related to ion channels, transporters, and receptors. The enriched terms include both ligand-gated and voltage-gated ion channel and transporter activities, as well as several types of receptor activities such as G protein-coupled receptors, AMPA glutamate receptors, and kainate-selective glutamate receptors. These genes also appear to be involved in several processes such as membrane potential, chloride transmembrane transport, gamma-aminobutyric acid signaling pathway, and neurotransmitter transport.\\n\\nMechanism: The underlying biological mechanism likely involves the regulation of electrical and chemical signals in neurons, thereby enabling communication between different types of cells in the central and peripheral nervous systems. \\n\\n] | \n", + "0.93 | \n", + "218 | \n", + "
| 845 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "regulation of presynaptic membrane potential-1 | \n", + "[ Genes in this list are primarily involved in ion channel activity, membrane potential regulation, and ligand-gated monoatomic ion channel activity, as well as pathways enabled by those activities such as G protein-coupled receptor signaling, chloride transmembrane transport, gamma-aminobutyric acid signaling pathway, and potassium ion transmembrane transport.\\n\\nMechanism: Genes in this list are part of the electrical signaling pathways that regulate chemical synaptic transmission in neurons and other cells, controlling neuronal action potentials, membrane potentials, the transport of ions across cellular membranes, and the assembly of neurotransmitters and synapses.\\n\\n] | \n", + "[\\nSummary: The genes listed here are involved in neurotransmitter signaling, ion channel activity, membrane transport, calcium ion homeostasis, and ionotropic glutamate receptor signaling. \\nMechanism: These genes provide the molecular machinery for neurotransmitter signaling by establishing ion channels, helping to carry ions in and out of cells, and regulating calcium ion homeostasis.\\n] | \n", + "0.94 | \n", + "288 | \n", + "
| 846 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "sensory ataxia-0 | \n", + "[ The genes in the list are all involved in many functions including DNA-binding, RNA polymerase II-specific activity, metal ion binding, ubiquitin protein ligase binding, and positive regulation of transcription by RNA polymerase II. These genes are also likely to be involved in several processes including positive regulation of immunoglobulin production, regulation of ERBB signaling pathway, regulation of intracellular protein transport, monoatomic cation transport, nucleic acid metabolic process, protein hexamerization, glycosaminoglycan catabolic process, nervous system development, heme transport, and mitochondrial transport.\\n\\nMechanism: These genes likely coordinate a combination of transcription activities to maintain cell function, health, and development. They are also likely to be involved in transporting and processing essential molecules needed for maintaining normal neural and sensory functionality as well as involved in transporting and processing essential molecules for cell metabolism.\\n\\n] | \n", + "[ Analysis of the given list of genes suggests a common thread of involvement in the development and function of peripheral nerves, particularly with regard to varying forms of Charcot-Marie-Tooth disease, in addition to their role in nucleic acid and glycan metabolic pathways. \\n] | \n", + "0.85 | \n", + "738 | \n", + "
| 847 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "sensory ataxia-1 | \n", + "[\\nSummary: A set of genes involved in positive/negative regulation of transcription by RNA polymerase II, nucleic acid and glycosaminoglycan metabolism, 5'-3' DNA helicase activity, protein hexamerization, alpha-N-acetylglucosaminidase activity, cytoskeletal motor activity, mechanosensitive monoatomic cation channel activity, myelination in peripheral nervous system, regulation of RNA splicing, transmission of nerve impulse, glucose-6-phosphate isomerase activity, alanine-tRNA ligase activity, heme transmembrane transporter activity, 3'-5' exonuclease activity, DNA-directed DNA polymerase activity, induction of egg chambers in Drosophila, nuclear import signal receptor activity, misfolded protein binding activity, protein ubiquitination, metal ion binding activity, cell-cell adhesion via plasma-membrane adhesion molecules and myelination.\\nMechanism: The genes may be shared among a number of biological pathways involving nucleic acid metabolism, cytoskeletal motor activity, myelination, and protein folding.\\n] | \n", + "[\\nSummary: Eighteen human genes related to various neurological processes and diseases are analyzed.\\n] | \n", + "0.83 | \n", + "921 | \n", + "
| 848 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "term-GO:0007212-0 | \n", + "[ The genes provided are likely to be involved in G protein-coupled receptor signal transduction, regulation of cytosolic calcium ion concentration, regulation of DNA templated transcription, regulation of neurodegeneration, signal transduction, neural development, enzyme and protein kinase binding, endosomal transport, signal receptor binding and cell organization. Mechanism: These genes are likely to play a role in signal transduction pathways that regulate multiple biological processes, including G protein-coupled receptor signaling pathways, phospholipase-c activating dopamine receptor signaling pathways, and adenylate cyclase-modulating G protein-coupled receptor signaling pathways. ] | \n", + "[\\nThe genes in the given list are predominantly involved in G protein-coupled receptor signaling pathways, regulation of cytosolic calcium ion concentration, regulation of transcription by RNA polymerase II, regulation of neuronal death and apoptotic processes, cAMP biosynthetic processes and protein phosphorylation pathways. The underlying biological mechanism for these processes is likely related to cellular and tissue homeostasis, i.e. the maintenance of physiological equilibrium. \\n\\nMechanism: Maintenance of cellular and tissue homeostasis.\\n\\n] | \n", + "0.93 | \n", + "146 | \n", + "
| 849 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "term-GO:0007212-1 | \n", + "[\\n\\nSummary: A wide variety of gene functions have been identified, including those involved in cAMP and calcium signaling pathways, G-protein coupled receptor signaling, apoptosis, gene regulation and transcription, membrane transport, and ion channels. \\n\\nMechanism: A wide variety of genes play a role in providing signals to the cells, controlling the transport of molecules across membranes, regulating genes and allowing for cells to respond to various stimuli.\\n\\n] | \n", + "[ This list of genes is related to G protein-coupled receptor signaling pathways, associated with diseases such as Alzheimer's disease, Parkinson's disease, hypertension and kidney failure. ] | \n", + "0.87 | \n", + "277 | \n", + "
| 850 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "tf-downreg-colorectal-0 | \n", + "[ The genes identified in the list are involved in various activities, such as DNA and RNA binding, transcription factor binding, protein kinase and chromatin binding, transcription coactivator and repressor activities, protein dimerization, and other enzymatic activities. The common function they share is to regulate gene expression.\\n\\nMechanism: These genes are likely involved in transcriptional regulation by binding to genes and enhancers to either activate or repress transcription, and by modifying chromatin structure to regulate gene expression.\\n\\n] | \n", + "[ The genes are predominantly involved in transcriptional activation and/or repression of gene expression, often as part of complexes involved in the regulation of signal transduction, DNA-templated transcription, cell cycle, and transcription by RNA polymerase II; they also enable chromatin binding activities and zinc ion binding.\\n\\nMechanism: The human genes work together to regulate various biological processes via the modulation of signal transduction, DNA-templated transcription, cell cycle, and transcription by RNA polymerase II pathways. This involves the binding of DNA to transcription factors, the deacetylation of histones, and the binding of specific protein ligases/cofactors resulting in the transcriptional activation or repression of specific genes. The regulation of gene expression and signal transduction, in turn, allows for the control of multiple downstream processes such as cell differentiation, apoptosis, cell migration, angiogenesis and metabolism.\\n\\n] | \n", + "0.92 | \n", + "425 | \n", + "
| 851 | \n", + "text-davinci-003 | \n", + "ontological_synopsis | \n", + "tf-downreg-colorectal-1 | \n", + "[ This list of genes are all primarily involved in the regulation of transcription by RNA polyerase II and in cellular processes of transcription, such as positive and negative regulation of gene expression, DNA repair and cell differentiation. The statistically over-represented terms include: transcription; DNA-binding; RNA polymerase II-specific; transcription activator/transcription repressor; cis-regulatory region sequence-specific; transcription coregulator binding; regulation of DNA-templated transcription; nucleosome disassembly; and regulation of signal transduction. \\nMechanism: The underlying biological mechanism is associated with regulation of gene expression, which is dependent on the DNA-binding capability of the transcription factors, as well as their ability to recognize the proper sequence and initiate transcription of the downstream genes.\\n] | \n", + "[\\nSummary: The list mainly consists of genes which play a role in regulation that involves DNA-binding transcription activator and repressor activity, regulation of gene expression, regulation of DNA-templated transcription and positive/negative regulation of transcription by RNA polymerase II.\\nMechanism: The genes in the list are involved in a variety of mechanisms that function to give cells control over their activities and to regulate transcription.\\n] | \n", + "0.94 | \n", + "411 | \n", + "
| prompt_variant | \n", + "model | \n", + "method | \n", + "geneset | \n", + "v1 | \n", + "v2 | \n", + "sim | \n", + "length_diff | \n", + "
|---|---|---|---|---|---|---|---|
| 568 | \n", + "\n", + " | RANDOM | \n", + "EDS-0 | \n", + "[ The nine genes are associated with extracellular matrix (ECM) components and their regulators. Mechanism: The proteins coded by these genes could be involved in the regulation of the expression of ECM components, which can contribute to the formation of the physical integrity of the ECM and its interaction with the cellular environment. ] | \n", + "[\\n\\nSummary: The genes in the list are associated with a broad range of functions involved in skeletal development, collagen production and other extracellular matrix processes.\\n\\nMechanism: The mechanism appears to involve different genes acting on multiple pathways related to the synthesis, remodeling, and maintenance of extracellular matrix components.\\n\\n] | \n", + "0.81 | \n", + "16 | \n", + "
| 569 | \n", + "\n", + " | RANDOM | \n", + "EDS-1 | \n", + "[ This list of genes is enriched in proteins involved in the Extracellular Matrix (ECM) protein network, which is a component of the larger Cell Adhesion and Morphogenesis (CAM) pathway. Specifically, the genetic list is enriched for components involved in the processes of collagen fibril formation, collagen fibril organization, extracellular matrix (ECM) protein network assembly, ECM protein network stabilization, epidermal cell fate commitment, epithelial tube growth and branching morphogenesis, collagen modification and deposition, and zinc-finger protein motif binding.\\n\\nMechanism: The ECM protein network mediates cell-cell and cell-matrix interactions in order to regulate the adhesive, motile, and proliferative states of cells. It consists of a variety of molecules, including ECM proteins, which serve as substrates to guide cell migration, growth and differentiation. ECM proteins are those that contain one or more structural domains capable of interacting with the ECM components, such as extracellular domains, as well as those containing adhesive domains. \\n\\n] | \n", + "[ The genes listed above are associated with various development processes and tissue formation, such as collagen production, connective tissue development, matrix remodeling, and zinc finger protein regulation.\\nMechanism: The underlying known mechanism is the combination of transcriptional regulation and post-translational modification of the proteins encoded by these genes.\\n] | \n", + "0.90 | \n", + "699 | \n", + "
| 570 | \n", + "\n", + " | RANDOM | \n", + "FA-0 | \n", + "[COULD NOT PARSE\\nHypothesis: The genes in this list are likely involved in the regulated repair of DNA double strand breaks due to replication-mediated damage, with the coordinated action of the Fanconi Anemia protein complex and the shared components of the ubiquitin ligase complex.] | \n", + "[ The list of genes is significantly and specifically associated with homologous recombination and DNA repair, as evidenced by an enrichment in terms related to these processes, such as \"dna repair\", \"homologous recombination\", \"excision repair\", and \"nuclease activity\".\\n\\nMechanism: The genes in this list are involved in a variety of DNA repair activities, such as excision repair and homologous recombination. These processes are important for maintaining the correct sequence of DNA and avoiding mutations that can lead to disease. \\n\\n] | \n", + "0.89 | \n", + "253 | \n", + "
| 571 | \n", + "\n", + " | RANDOM | \n", + "FA-1 | \n", + "[ Several genes involved in DNA repair and homologous recombination processes, such as FANCL, RAD51C, FANCE, MAD2L2, ERCC4, FANCA, BRCA2, FANCF, XRCC2, BRIP1, FANCD2, SLX4, FANCB, FANCG, UBE2T, RAD51, PALB2, and FANCC, were observed to be statistically enriched for terms related to DNA damage recognition and repair, DNA damage response, and homologous recombination processes.\\n\\nMechanism: These genes enable the cellular response to double-stranded breaks (DSBs) by providing components of the DNA damage recognition and repair variety. They also function in the homologous recombination pathway for DNA repair, which is used for error-free repair of damaged DNA strands. \\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.88 | \n", + "660 | \n", + "
| 572 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_ADIPOGENESIS-0 | \n", + "[ Enrichment analysis of this list has revealed that many of the genes are involved in energy metabolism and fatty acid metabolism, such as ATP1B3, ACOX1, ACADM, SLC19A1, SLC25A10, PGM1, UCP2, GPX3 and GPX4. They are also related to adipogenesis, with genes such as ADIPOR2, APLP2, LEP, ADIG and ADIPOQ. Lastly, several of the genes are involved in cholesterol and bile acid synthesis, such as DHCR7, DHRS7, CYP4B1 and HMGCR.\\n\\nMechanism: The genes identified as being involved in energy metabolism and fatty acid metabolism appear to share a common mechanism in which these molecules are generated from multiple sources to form energy. The genes involved in adipogenesis appear to be related to the regulation and development of fat cells and adipose tissue. Similarly, the genes involved in cholesterol and bile acid synthesis appear to be related to the synthesis of these molecules from multiple sources.\\n\\n] | \n", + "[ \\nSummary: A term enrichment test on the above list of genes based on biological classification hierarchies has identified terms related to metabolic and cellular functions that are statistically over-represented.\\nMechanism: These commonalities likely indicate a shared pathway, mechanism or process as related to metabolic and cell regulation functions.\\n] | \n", + "0.86 | \n", + "553 | \n", + "
| 573 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_ADIPOGENESIS-1 | \n", + "[ This term enrichment test revealed a group of genes associated with energy metabolism, regulation of cell death, cell proliferation and signaling, DNA replication/remodeling, RNA processing, and lipid metabolism.\\nMechanism: This group of genes may be involved in binding, regulating, or expressing other proteins in order to influence the cell's metabolic and signaling status. \\n] | \n", + "[\\nSummary: This list of genes are mainly involved in energy metabolism and signal transduction. \\nMechanism: The genes in this list form a biochemical pathway responsible for the production of energy and for the detection and execution of cellular signals.\\n] | \n", + "0.81 | \n", + "125 | \n", + "
| 574 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_ALLOGRAFT_REJECTION-0 | \n", + "[ This enrichment test examines a list of 73 human genes and reveals enrichments for the functions related to cell surface molecules, cytokines, immunology, receptor signalling, transcriptional regulation and apoptosis.\\n\\nMechanism: These genes are involved in a variety of pathways that include cytokine signaling, cell surface molecules, transcriptional regulation, apoptosis, and receptor signaling.\\n\\n] | \n", + "[ Genes related to the list are largely enriched for immune signalling/activation, regulation of cell cycle and differentiation, and transcriptional regulation.\\nMechanism: This likely indicates involvement of these genes in the processes of immune signalling, development or tissue remodelling, and metabolic regulation.\\n] | \n", + "0.87 | \n", + "82 | \n", + "
| 575 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_ALLOGRAFT_REJECTION-1 | \n", + "[ This analysis results in the enrichment of genes functions related to immune system regulation, including antigen presentation, signaling, B and T cell metabolism, cytokine production and chemotaxis. Mechanism: The genes identified in this list are involved in controlling a range of processes that are necessary for proper immune system functioning, such as antigen presentation, signaling pathways, metabolizing T and B cells, production and secretion of cytokines, and chemotaxis of immune cells. These functions are necessary for the body to defend itself against pathogens. ] | \n", + "[COULD NOT PARSE\\nHypothesis: It is likely] | \n", + "0.82 | \n", + "539 | \n", + "
| 576 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_ANDROGEN_RESPONSE-0 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE] | \n", + "0.87 | \n", + "0 | \n", + "
| 577 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_ANDROGEN_RESPONSE-1 | \n", + "[ \\nSummary: The genes are enriched in terms related to regulation, signaling, and metabolism.\\nMechanism: The genes are likely to be involved in molecular mechanisms governing cellular activities and pathways, with signaling pathways such as Wnt, MAPK, and PKA pathways playing an important role. \\n] | \n", + "[ \\nThe genes provided are significantly enriched in terms related to gene transcription and regulation, protein translation and metabolism, cytoskeletal organization, and lipid metabolism.\\nMechanism: These genes are likely to be involved in the regulation of genetic expression, transcriptional regulation, protein translation and metabolism, improvement of cell structure, and lipid metabolism. \\n] | \n", + "0.83 | \n", + "100 | \n", + "
| 578 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_ANGIOGENESIS-0 | \n", + "[ \\n\\nSummary: A set of 34 genes related to extracellular matrix formation and maintenance, fibrous tissue development, vascular development, and extracellular secreted signaling. \\n\\nMechanism: Together, these genes encode proteins involved in multiple signaling pathways to regulate the development, maintenance and repair of the extracellular matrix (ECM), including fibrous, collagen, and laminin-fibrillin proteins, along with proteins involved in vascular regulation, cell-cell communication and migration, and extracellular secreted signaling molecules. \\n\\n] | \n", + "[ The list of gene terms are involved primarily in cell communication processes like extracellular matrix organization, adhesion, and cell surface interactions. Specifically, they encode proteins involved in the aggregation of endothelial cells and vascularization processes. Mechanism: The proteins encoded by the genes in the list are likely involved in regulating the growth, development, extracellular environment, and adhesiveness of cells. ] | \n", + "0.84 | \n", + "113 | \n", + "
| 579 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_ANGIOGENESIS-1 | \n", + "[ Genes in this list are primarily associated with development, vascular remodeling and cell-cell communication.\\nMechanism: These genes likely play a role in various aspects of development, including morphogenesis, tissue development, extracellular matrix organization, inflammation, vascular remodeling and cell-cell communication.\\n] | \n", + "[ \\n\\nSummary: This list of genes appears to be involved in growth and morphogenesis of cells, including development of muscle, bone, and neuronal networks. \\nMechanism: Growth appears to be mediated by signals from cytokines and hormones, most notably VEGFA and PDGF, and mediated by transmembrane and extracellular matrix proteins, including LUM, VTN, and S100A4.\\n] | \n", + "0.81 | \n", + "30 | \n", + "
| 580 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_APICAL_JUNCTION-0 | \n", + "[COULD NOT PARSE] | \n", + "[\\nThis list of genes is related to development, tissue morphogenesis, contractile organs, extracellular matrix and cytoskeletal proteins. Enriched terms include bone, joint, muscle and connective tissue development; cell adhesion; adhesion receptor complex formation; signal transduction; and receptor-mediated signaling cascades.\\n\\nMechanism:\\nThese genes likely act together to facilitate the intricate networks of molecular and cellular pathways involved in development, homeostasis, and tissue repair. These include extracellular matrix formation and remodeling; cell adhesion; and signaling pathways associated with cell migration, proliferation, differentiation, and growth. The genes may work in tandem to promote changes in gene expression, stability, and intercellular communication involved in development and tissue repair processes.\\n\\n] | \n", + "0.85 | \n", + "829 | \n", + "
| 581 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_APICAL_JUNCTION-1 | \n", + "[\\nSummary: The genes in this list are involved in a wide variety of processes, including development, growth, morphology, and molecular signaling.\\nMechanism: These genes appear to be involved in the regulation of cellular processes by mediating signals that modulate development, growth and morphology.\\n] | \n", + "[ Our term enrichment analysis of the list of genes provided revealed statistically over-represented terms in gene function associated with cell adhesion, cell migration, migration and interaction, cytoskeletal organization, actin cytoskeletal regulation, signaling pathways, and regulation of the actin cytoskeletal organization. \\nMechanism: These results suggest that the underlying biological mechanism likely involves cytoplasmic signaling and regulation of the cytoskeletal organization, which would provide mechanical integrity to the cells, their adhesion to neighboring cells, and their migratory ability. This is supported by the evidence that many of the enriched terms relate to cell adhesion, migration and interaction, and cytoskeletal organization.\\n] | \n", + "0.88 | \n", + "460 | \n", + "
| 582 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_APICAL_SURFACE-0 | \n", + "[\\nSummary: The list of genes provided is enriched for terms relating to cell migration, membrane receptor signaling, and glycoprotein metabolism.\\nMechanism: These gene functions serve to coordinate cell migration and receptor-mediated signaling, as well as metabolism. \\n] | \n", + "[ The list of genes is enriched for terms related to cell regulation, signal transduction, cell adhesion, protein folding, extracellular matrix organization.\\nMechanism: The list of genes are likely involved in a variety of cell regulation mechanisms such as activating responses to extracellular signals, influencing protein folding and assembly, regulating cell adhesion, and mediating phosphorylation cascades. \\n] | \n", + "0.81 | \n", + "144 | \n", + "
| 583 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_APICAL_SURFACE-1 | \n", + "[\\nSummary: The genes provided are involved in diverse biological pathways related to cell signaling, development, transcription, and metabolism.\\nMechanism: The genes likely represent an underlying biological mechanism that is involved in cellular proliferation and the regulation of gene expression.\\n] | \n", + "[ This list of genes appears to be involved in the development and maintenance of various organs, tissues and cellular processes. Specifically, enriched terms for this gene list include cell adhesion and migration; cell signaling; cell differentiation; protein kinase and phosphatase activities; transcription and DNA metabolism; immunomodulation; glycosylation and carbohydrate metabolism; and cell growth and proliferation. \\n\\nMechanism: The genes in this list play a role in a variety of molecular mechanisms that are important for normal development and tissue homeostasis. On the molecular level, these genes are involved in cell-cell adhesion, translation and translation regulation, signal transduction, and other processes. Moreover, the genes in this list regulate the expression of various cellular receptor, kinase, and phosphatase pathways, which may lead to downstream changes in cell growth, proliferation, and differentiation. \\n\\n] | \n", + "0.70 | \n", + "643 | \n", + "
| 584 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_APOPTOSIS-0 | \n", + "[ The list of human genes given is statistically significantly enriched for the gene functions of transcriptional regulation/control, cell-cycle/apoptosis, and immune responses.\\nMechanism: The genes listed encode proteins involved in transcriptional regulation through control pathways such as the activation of caspases, the inhibition of cyclin-dependent kinase activity, and the upregulation of apoptosis-related proteins. They also encode molecules involved in immune-related processes such as the binding and activation of proinflammatory cytokines, the formation of interferon gamma receptor complexes, and the regulation of major histocompatibility complex class I molecules. \\n] | \n", + "[\\n\\nSummary: The human genes provided in this list are mainly related to apoptosis, transcription, cell cycle progression, and inflammation.\\nMechanism: These genes likely act together to execute pathways related to the regulation of cell growth and maintenance, DNA replication and repair, oxidative stress response, and immune system activation.\\n] | \n", + "0.89 | \n", + "338 | \n", + "
| 585 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_APOPTOSIS-1 | \n", + "[COULD NOT PARSE] | \n", + "[ This list of genes is enriched for terms related to cell death regulation, inflammation, immune reaction, and growth and morphogenesis, which is a mechanism indicative of homeostasis in several biological functions.\\t\\n\\nMechanism: Expression of these genes contributes to cell survival by regulating the balance between cell death and survival, restraint of pro-inflammatory responses and activation of pro-inflammatory responses, promoting expression of genes involved in innate and adaptive immune responses and playing a part in promoting tissue growth, remodeling and morphogenesis. \\n\\n] | \n", + "0.85 | \n", + "573 | \n", + "
| 586 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_BILE_ACID_METABOLISM-0 | \n", + "[\\nSummary: The genes listed are enriched in terms related to metabolic pathways, lipid transport, and development of connective tissues.\\nMechanism: The functions of the genes appear to involve a number of metabolic pathways, such as fatty acid and bile acid synthesis, xenobiotic metabolism, and steroidogenesis, as well as pathways related to cellular transport and signaling, including those related to lipid transport and receptor-mediated signal transduction.\\nIn addition, several of the genes are involved in connective tissue formation, as well as development of digits and limbs.\\n] | \n", + "[ This list of genes is enriched for functions related to lipid metabolism and transport, development of vital organs, and cell signaling pathways.\\nMechanism: The enrichment of these genes suggests roles in cellular metabolic processes such as breakdown, transport, and synthesis of lipids, as well as cell-signaling pathways involved in development of vital organs such as liver, heart, and brain. \\n] | \n", + "0.90 | \n", + "187 | \n", + "
| 587 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_BILE_ACID_METABOLISM-1 | \n", + "[COULD NOT PARSE] | \n", + "[ A large proportion of the genes provided are involved in lipid and fatty acid metabolism, including the movement and processing of lipids, such as through cytochrome P450 superfamily enzymes, hydroxyacyl-CoA dehydrogenases, SLCO1A2, FADS2 and SLC27A2. As well as lipid metabolism, genes are also enriched for other metabolic processes, such as glutamate metabolism (IDH1, 2, HSD17B6) and serine metabolism (SERPINA6 and PIPOX). In addition, there are genes associated with the regulation of transcription factors, including RXRA, LCK, and optineurin, as well as those involved in oxidative stress (SOD1, CTH, PNPLA8).\\n\\nMechanism: The enriched terms implicate a cross-regulatory and potentially inter-linked metabolic network involving lipid, fatty acid and disulphide bridge metabolism, with potential connections to oxidative stress response and gene expression regulatory mechanisms. \\n\\n] | \n", + "0.87 | \n", + "874 | \n", + "
| 588 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-0 | \n", + "[COULD NOT PARSE] | \n", + "[\\nSummary: A number of genes involved in lipid and cholesterol metabolism, cell signaling and regulation, development, cell adhesion, apoptosis and transcription have been identified.\\nMechanism: Genes associated with lipid and cholesterol metabolism are involved in regulating the synthesis, degradation and transport of lipids, while genes associated with cell signaling and regulation are involved in regulating cell growth, differentiation and apoptosis. Additionally, genes related to development, apoptosis, and transcription act in the regulation of cell adhesion, differentiation and development.\\n] | \n", + "0.71 | \n", + "588 | \n", + "
| 589 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_CHOLESTEROL_HOMEOSTASIS-1 | \n", + "[\\nSummary: The genes populated are predominantly involved in lipid metabolism (eg. HMGCR, PMVK, FDPS), transcription regulation (eg. ACTG1, NRAF), cellular adhesion (eg. CD9, ANXA13, COUNTY), and other development related processes (eg. S100A11, MVD, IDI1).\\nMechanism: The genes are associated with a number of different functions but are likely involved in maintaining cellular homeostasis, regulating transcription, and participating in development processes.\\n] | \n", + "[ Proteins involved in lipid and lipid metabolism pathways, related to cholesterol control.\\nMechanism: Proteins involved in cholesterol regulation, such as HMGCR, PMVK, FADS2, SREBF2, S100A11, and MVK are likely to be involved in the upregulation and modulation of cholesterol levels. These proteins regulate the breakdown of fatty acids and also mediate the synthesis of bile acids, both of which are important in cholesterol metabolism. ] | \n", + "0.90 | \n", + "23 | \n", + "
| 590 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_COAGULATION-0 | \n", + "[\\nSummary: Several of the human genes on this list play a role in extracellular matrix formation, inflammatory response, and proteolytic activities.\\nMechanism: The common functional mechanisms included in this term enrichment test are the regulation of the inflammatory response, regulation of extracellular matrix formation, and proteolytic activities.\\n] | \n", + "[ Genes in this list represent functions related to extracellular matrix remodeling, angiogenesis and vascular development, immune response and platelet activation, collagen and fibronectin metabolism and regulation, and endocytosis and signal transduction.\\n] | \n", + "0.71 | \n", + "96 | \n", + "
| 591 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_COAGULATION-1 | \n", + "[\\nSummary: The genes identified are predominantly involved in matrix molecular regulation, pathways related to proteolysis and coagulation, signal transduction, and extracellular matrix organization.\\nMechanism: The genes act as regulators of specific molecular functions and as mediators of signal transduction pathways. The identified genes are likely involved in the processing and remodeling of the extracellular matrix because of their relation to proteolysis and other matrix-related functions.\\n] | \n", + "[ The term enrichment test suggests that proteins involved in cell adhesion, proteolysis regulation, and interactions between extracellular proteins and cells are significantly enriched in this gene list. \\n\\nMechanism: These proteins likely act together in a coordinated manner to modulate cell adhesion, proteinase activity, and communication between cells. \\n\\n] | \n", + "0.79 | \n", + "141 | \n", + "
| 592 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_COMPLEMENT-0 | \n", + "[\\nSummary: These genes are enriched in functions related to extracellular matrix organization, immune system/inflammation/interferon response, and transcription factor activity.\\nMechanism: These genes could be involved in a pathway that is responsible for coordinating and controlling aspects of extracellular matrix organization, immune system/inflammation/interferon response and the activity of transcription factors.\\n] | \n", + "[ Our term enrichment test suggests that the commonalities in function of these genes are related to the regulation of cell growth and development, signal transduction pathways, and immunity. Specifically enriched terms include development of tissue and organs; signal transduction; cell surface receptor binding; response to stimulus; immune system; immune response; and cytokine activities.\\n\\nMechanism: These functions likely occur through a combined mechanism of modulating transcription factors, receptor-ligand binding, cytokine release and signaling, and a balance of intracellular concentrations of proteins and lipids.\\n\\n] | \n", + "0.80 | \n", + "207 | \n", + "
| 593 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_COMPLEMENT-1 | \n", + "[ This enrichment test revealed several terms related to immune system functioning, cell adhesion and regulation, and extracellular matrix organization, which are likely the underlying mechanisms behind the commonalities among the listed genes. Enriched terms include: immunoglobulin like domains; B cell activation; T cell receptor signaling pathway; integrin mediated cell adhesion; apoptosis; regulation of transcription; signal transduction; receptor mediated endocytosis and exocytosis; extracellular matrix organization; and calcium mediated signaling. \\n\\nMechanism: These findings suggest that the genes involved in this test collectively contribute to a range of processes related to immune system functioning, cell adhesion, extracellular matrix organization, and intracellular communication. \\n\\n] | \n", + "[\\nThe list of genes provided is heavily enriched for functions related to cellular signalling, inflammatory responses, and cellular stress response.\\nMechanism: These genes are typically involved in regulating and mediating signalling pathways, activating and responding to the inflammatory response, activating and functioning in the cell stress response, and facilitating cell-cell interactions.\\n] | \n", + "0.83 | \n", + "406 | \n", + "
| 594 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_DNA_REPAIR-0 | \n", + "[ Gene functions related to DNA and RNA metabolism, protein synthesis, DNA damage repair, transcription, and chromatin organization are significantly over-represented.\\nMechanism: It is likely that many of these genes are involved in the same pathway related to the fundamental processes of DNA replication, transcription, and protein synthesis.\\n] | \n", + "[ The common functions for the human genes are involved in various developmental processes and DNA replication, with enrichment of terms such as \"developmental process\" and \"DNA replication\". \\n\\nMechanism: The genes act together to facilitate a variety of molecular processes in the cellular pathways to support embryonic and post-natal development, as well as DNA replication, transcription, and translation.\\n\\n] | \n", + "0.92 | \n", + "65 | \n", + "
| 595 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_DNA_REPAIR-1 | \n", + "[ \\nSummary: These genes are enriched for roles in DNA replication, transcription, translation and post-translational modifications.\\nMechanism: These genes are involved in various biological processes, including DNA replication, transcriptional regulation, translation, and post-translational modifications involved in gene expression. \\n] | \n", + "[\\nSummary: Our genes are primarily involved in nucleic acid metabolism, transcription, and post-transcriptional modifications.\\nMechanism: The proteins encoded by the genes in our list likely play roles in the various biochemical steps involved in transcription, such as chromatin remodelling, pre-mRNA splicing, DNA repair, RNA polymerization, mRNA processing, mRNA transport, and translation initiation.\\n] | \n", + "0.90 | \n", + "69 | \n", + "
| 596 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_E2F_TARGETS-0 | \n", + "[ Genes on the list are primarily involved in DNA cell cycle and replication, gene regulation, transcription and translation, chromatin modification, and DNA repair. \\n\\nMechanism: The genes are involved in the regulation of DNA replication and transcription, chromatin modification, and DNA repair processes during cell cycle progression. \\n\\n] | \n", + "[ The provided gene list is over-represented for transcriptional regulation, chromatin modification and mitotic division/cell cycle components.\\nMechanism: The underlying mechanism of this gene set is that the enrichments are involved in the regulation of transcription for gene expression, maintenance of chromatin and DNA structure and function, and regulation of mitotic division and cell cycle checkpoints.\\n] | \n", + "0.83 | \n", + "70 | \n", + "
| 597 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_E2F_TARGETS-1 | \n", + "[\\nSummary: The genes in the list are involved in diverse functions related to DNA replication, transcription, chromosome condensation and transcriptional regulation.\\nMechanism: These functions are likely related to canonical pathways and processes involved in coordinating and regulating DNA replication, the transcription of genetic information into proteins, and maintaining appropriate chromosome condensation states.\\n] | \n", + "[ This list of genes is enriched for functions related to DNA replication and repair, chromatin modification, transcriptional and translational regulation, network formation, spindle formation and kinesin and dynein motor proteins. Mechanism: These genes are likely to function as part of an interconnected cellular pathway and/or network that allows for the generation of daughter cells and the coordination of transcriptional activity and post-translational modifications. ] | \n", + "0.84 | \n", + "54 | \n", + "
| 598 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The list of genes provided show enrichment for terms relevant to extracellular matrix composition, cell adhesion and motility, cell-matrix interactions, growth factor and cytokine signaling, and matrix remodeling. \\n\\nMechanism: The mechanisms underlying the enrichment of these terms likely involve cell-matrix interactions, growth factor and cytokine signaling, and matrix remodeling.\\n\\n] | \n", + "0.75 | \n", + "372 | \n", + "
| 599 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1 | \n", + "[ Our enrichment test uncovered several terms related to extracellular matrix function, morphogenesis, and reproduction/growth. These terms include extracellular matrix organization; morphogenesis; collagen production; matrix metalloproteinase activity; glycoprotein metabolism; cytoskeletal component organization; regulation of growth and reproduction; and regulation of skin morphogenesis. Mechanism: The underlying biological mechanisms related to these genes likely involve the extracellular matrix (ECM), which provides structural and biochemical support to the cells and tissues. ECM components, such as collagen, can regulate activities such as cell signaling, structure formation and growth, and gene expression. Morphogenesis is likely modulated by ECM components, as well as by signaling pathways. ] | \n", + "[ The identified genes are enriched for terms related to skeletal morphogenesis, cell-cell adhesion and motility, extracellular matrix production and remodeling, development and differentiation of connective tissue, collagen production and turnover, and cytokine and chemokine signaling. \\n\\nMechanism: It is likely that these genes are involved in mechanisms that coordinate protein interactions during skeletal development and morphogenesis, cell adhesion and migration, and the maintenance of a healthy extracellular matrix. In addition, these genes likely contribute to the production and turnover of extracellular matrix components such as collagens and chemokines and cytokines involved in development and differentiation of connective tissue. \\n\\n] | \n", + "0.89 | \n", + "60 | \n", + "
| 600 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-0 | \n", + "[\\nSummary: The list of genes identified are associated with cell morphology, homeostasis and regulation, innervation, and cellular metabolism.\\n] | \n", + "[\\nThis list of human genes was analysed in a term enrichment test. The test revealed that many of these genes were involved in a common pathway which supports normal cellular processes including DNA replication, transcription and gene expression, cell growth and differentiation, protein processing and trafficking. Furthermore, many of these genes were involved in bone morphogenesis and cancer-related pathways.\\n\\nMechanism:\\nThe underlying biological mechanism likely involves a number of distinct pathways, each with its own mechanism of action. Common processes shared by many of these genes include DNA replication, translation, and post-translational modification. Additionally, several of these genes are involved in cell-cell adhesion and the control of cellular migration and matrix remodeling, indicating roles in tissue morphogenesis. Furthermore, many of these genes are involved in intracellular signaling and signaling pathways that are essential for the processing and coordination of external and internal signals, which can ultimately result in cell growth, differentiation, and apoptosis.\\n\\n] | \n", + "0.78 | \n", + "964 | \n", + "
| 601 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_ESTROGEN_RESPONSE_EARLY-1 | \n", + "[ Our analysis of the 34 human genes suggests an enrichment of gene functions related to cell signaling, regulation and morphology, including: immunological response; cell adhesion; transcription regulation; cell migration; development of epidermis, bones and muscle; transport of proteins between cellular compartments; and apoptosis. \\n\\nMechanism: These gene functions are likely related to the regulation of diverse mechanisms within the cell, such as protein-protein interactions, transcription signaling, and intracellular trafficking. \\n\\n] | \n", + "[ \\nSummary: The gene list includes genes involved in transcriptional regulation, signal transduction, membrane transport and lipid biosynthesis.\\nMechanism: The genes exhibit common patterns of transcriptional regulation and signal transduction, with a focus on protein-protein interactions and membrane transport.\\n] | \n", + "0.87 | \n", + "228 | \n", + "
| 602 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-0 | \n", + "[\\nThe genes in the list are enriched for functions in the genomics and cytoskeletal processes, as well as immune response and extracellular modification.\\n\\nMechanism:\\nThe gene functions are implicated in various biological processes that are orchestrated by genetic control and/or regulation pathways. These pathways typically involve protein interactions and cellular processes. Additionally, these pathways often correlate to extracellular modification, immune response, and/or modulation of receptor signaling.\\n\\n] | \n", + "[ Genes related to extracellular matrix organization, cellular adhesion and migration, cell mobility and growth factor-mediated signaling pathways;\\nMechanism: This gene list suggests that extracellular matrix organization, adhesion and migration, cell motility, and growth factor signaling pathways are involved in gene expression in these genes. \\n] | \n", + "0.83 | \n", + "166 | \n", + "
| 603 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_ESTROGEN_RESPONSE_LATE-1 | \n", + "[COULD NOT PARSE] | \n", + "[ The genes are enriched for terms related to the structural organization of cells, transcriptional regulation, signal transduction, and immune responses.\\n\\nMechanism: These genes likely comprise a network that influences the physical and biochemical properties of the cell, including its membrane integrity, signal transduction pathways, gene expression, and immunomodulatory functions. \\n\\n] | \n", + "0.87 | \n", + "373 | \n", + "
| 604 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_FATTY_ACID_METABOLISM-0 | \n", + "[ This list of genes is highly enriched for metabolic processes such as fatty acid metabolism and oxidation, cholesterol biosynthesis, glycogen metabolism, nucleotide metabolism and transport, and electron transport activity. This suggests that the list reflects a highly coordinated and interconnected network of metabolic processes to maintain the homeostasis of the cell. Enriched terms include: fatty acid metabolism; oxidation of lipids; cholesterol biosynthesis; glycogen metabolism; nucleotide metabolism; nucleotide transport; nucleotide biosynthesis; electron transport activity; enzyme regulation and regulation of metabolic pathways; and apoptosis. \\nMechanism: This set of genes likely acts through a number of interconnected pathways to maintain cellular homeostasis. Lipid metabolism is known to be important in cellular signaling, while other metabolic pathways interact with each other through enzyme regulation and regulation of metabolic pathways. Additionally, many of the genes are associated with cell death pathways, suggesting that these can also act in a coordinated way to respond to stress and maintain cellular homeostasis. \\n] | \n", + "[\\nSummary: The genes shown here are involved in a wide range of metabolic pathways and cellular functions, such as energy metabolism, lipid metabolism, amino acid metabolism, DNA damage repair, and cell signaling.\\n] | \n", + "0.81 | \n", + "937 | \n", + "
| 605 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_FATTY_ACID_METABOLISM-1 | \n", + "[\\n\\nSummary: There is a strong enrichment of genes involved in metabolic processes, energy production and storage, lipid metabolism and transport, as well as acetyl-CoA biosynthesis and catalysis.\\n\\nMechanism: The identified genes likely influence the metabolic processes, energy production and storage, lipid metabolism and transport, as well as acetyl-CoA biosynthesis and catalysis by modulating cellular processes, protein and enzyme production, and functional metabolic pathways, such as oxidation and fatty acid metabolism.\\n\\n] | \n", + "[ Genes are enriched in roles associated with lipid metabolism and the cell cytoskeleton. Both pathways involve important signaling and metabolic roles. Mechanism: Lipid metabolism pathways involve synthesizing and degrading lipids, transporting lipids, and their oxidation. The cell cytoskeleton is involved in a variety of functions, including building of cell membranes, cell motility and traffic. ] | \n", + "0.82 | \n", + "128 | \n", + "
| 606 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_G2M_CHECKPOINT-0 | \n", + "[\\nGene functions involved in cell cycle regulation, DNA replication, and chromatin remodeling are enriched among the provided list of genes. This could reflect a core pathway of regulation that has been conserved across multiple species.\\n\\nMechanism:\\nThe enriched terms suggest that this gene list could be involved in the G1/S transition of the cell cycle, DNA replication, and chromatin remodeling or modification. Specifically, cell cycle progression and DNA replication is likely driven by cyclin B-CDK1 activation, which is facilitated by Cks1b and Cdc25A mediated activation and either Wee1 or Cdc20-anaphase promoting complex-cyclosome (APC/C)-mediated inhibition. Chromatin modification is likely driven by histone H2A and H2B acetylation and lysine methylation, which involve various proteins, such as Hmga1, Hmgn2, H2az1, H2bc12, and Myc.\\n\\n] | \n", + "[ \\nSummary: This list of human genes are enriched for functions related to cell cycle and/or development, such as DNA replication and transcription, and may be involved in a variety of pathways and processes.\\nMechanism: These genes may be involved in pathways related to DNA replication, transcription and expression, and cell cycle regulation.\\n] | \n", + "0.81 | \n", + "504 | \n", + "
| 607 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_G2M_CHECKPOINT-1 | \n", + "[ \\nSummary: This list of human genes are primarily involved in nuclear processes such as DNA replication, gene transcription, chromatin remodelling and cell cycle control.\\nMechanism: The genes may be involved in the regulation of a number of biological processes such as DNA repair, cell cycle regulation, gene expression, and gene regulation.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.84 | \n", + "328 | \n", + "
| 608 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_GLYCOLYSIS-0 | \n", + "[\\nSummary: Our term enrichment test shows that many of the genes on this list are involved in various aspects of developmental and morphogenic processes, including digit development, cell differentiation, angiogenesis, and metabolism.\\nMechanism: These genes are likely to be involved in biological pathways involving the development and maintenance of cellular structure, binding and transporting of molecules, energy metabolism and other metabolic processes, and cell signaling.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.89 | \n", + "464 | \n", + "
| 609 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_GLYCOLYSIS-1 | \n", + "[ The list of genes are primarily involved in essential metabolic functions in the cell. Specifically, they are involved in carbohydrate and energy metabolism, microtubule assembly, DNA binding and replication, actin cytoskeleton dynamics, ion channel regulation, transcriptional regulation, and cell adhesion. The mechanism is likely related to the coordination of these processes in order to maintain homeostasis and proper cell functioning.\\n\\nSummary: Genes mainly involved in metabolic processes. \\n\\nMechanism: Coordination of these processes to maintain cellular homeostasis.\\n\\n] | \n", + "[ \\nThis gene list is enriched for proteins involved in structural development and energy metabolism, such as structural proteins and enzymes of glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle. These terms are supported by evidence from gene ontologies (GO) assigned to the genes in the list.\\n\\nMechanism: \\nThe list of genes is involved in pathways which facilitate the efficient production and utilization of energy, such as glycolysis, the pentose phosphate pathway, and the tricarboxylic acid (TCA) cycle. They are also involved in the dynamic assembly of integral structures, such as the cytoskeleton, cell adhesion serve, proteoglycan synthesis, and extracellular matrix formation.\\n\\n] | \n", + "0.85 | \n", + "140 | \n", + "
| 610 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_HEDGEHOG_SIGNALING-0 | \n", + "[\\nSummary: Many of the genes listed are involved in the development and morphogenesis of neurons and other cells. \\nMechanism: These genes are likely to work together to regulate cell and tissue shaping and differentiation, providing for the formation of specialized neuron structures and neural pathways. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.85 | \n", + "290 | \n", + "
| 611 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_HEDGEHOG_SIGNALING-1 | \n", + "[\\n\\nSummary: This group of genes is commonly associated with morphogenesis, cell adhesion, development, and neuronal signaling\\nMechanism: The underlying biological mechanism is likely related to the regulation of cell proliferation, migration, differentiation, and neural plasticity during development. \\n] | \n", + "[ The genes appear to be involved in the development of various cell types, organs, and other growth processes, including neuron formation, cell adhesion and migration, signal transduction, tissue morphogenesis, and development of the nervous system. \\nMechanism: These genes likely act in a number of ways to promote and coordinate these processes, including recognizing and binding signaling molecules, relaying signals to other molecules, and affecting transcription of target genes. \\n] | \n", + "0.90 | \n", + "184 | \n", + "
| 612 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_HEME_METABOLISM-0 | \n", + "[\\nSummary: The genes in this list are highly enriched for functions related to membrane transport, energy metabolism, ribosomal proteins, and nucleic acid binding.\\nMechanism: The underlying biological mechanism or pathway may involve regulation and control of cellular functions and transcription activity, with multiple proteins interacting to ensure proper functioning of a variety of cellular pathways.\\n] | \n", + "[ The list of genes has a statistically significant enrichment of terms related to cellular metabolism, energy production and transport, cytoskeleton modification and remodelling, and cell adhesion. \\nMechanism: The molecular mechanisms involve the transfer of energy, metabolic pathways, and the coordination of cellular transport and reorganization.\\n\\n] | \n", + "0.87 | \n", + "54 | \n", + "
| 613 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_HEME_METABOLISM-1 | \n", + "[\\n\\nSummary: The human genes identified in this list are predominantly involved in cell development, gene expression, organogenesis and nucleic acid metabolism.\\n\\nMechanism: The human genes identified in this list are likely to be involved in processes that regulate cell development, including transcriptional regulation and organogenesis, as well as nucleic acid metabolism. \\n\\n] | \n", + "[ The enriched terms for this list of human genes suggest a common functional theme in organ development, morphogenesis and growth, immune system function, and transport processes. Enriched terms include: embryonic development; skeletal system development; organogenesis; morphogenesis; growth; immune system process; cell motility; steroid hormone receptor activity; receptor signaling pathway; transport; endocytosis; and cellular homeostasis.\\n\\nMechanism: The underlying biological mechanism suggested by the enriched gene functions is that these genes are involved in various organ and skeletal system development processes, in particular morphogenesis and growth, as well as immune system and transport processes. Specifically, these genes are involved in organogenesis, morphogenesis, growth, and cell motility through receptor signaling pathways, endocytosis, transport processes, and cellular homeostasis. Additionally, the genes are involved in steroid hormone receptor activity, further contributing to organ and skeletal system development.\\n\\n] | \n", + "0.80 | \n", + "675 | \n", + "
| 614 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_HYPOXIA-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The list of genes is involved in a variety of pathways and functions related to cell differentiation, metabolism, protein processing, and the regulation of gene expression. Specifically, this list was enriched for terms related to cell cycle, remodeling proteins, stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, transcription factors, chromatin-associated proteins, and kinases.\\n\\nMechanism: The overall mechanism of action of the genes appears to be related to the regulation of cellular processes via the modulation of expression of target genes, primarily through the regulation of epigenetic and transcriptional factors, in order to enable proper differentiation, metabolism, and protein processing. This is further supported by the enrichment of terms related to stress response proteins, calcium signaling proteins, hypoxia-inducible factor proteins, transcription factors, chromatin-associated proteins, and kinases.\\n\\n] | \n", + "0.93 | \n", + "951 | \n", + "
| 615 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_HYPOXIA-1 | \n", + "[ \\nSummary: Genes related to cell development, cell metabolism, transcription, and regulation are enriched in this set.\\nMechanism: These genes regulate a variety of cellular processes such as cell cycle regulation, transcriptional regulation, and energy metabolism.\\n] | \n", + "[ Genes identified in this set are associated with several DNA/RNA binding and regulatory processes, including transcription and epigenetic modification. Statistically over-represented functions in these genes include development, cell structure and movement, cell cycle and division, signal transduction, transport, and energy production; proteins involved in these processes include transcription factors, kinases, histones, and other enzymes. Mechanism: This enrichment likely reflects the underlying biological pathways governing various aspects of gene expression and regulation. ] | \n", + "0.82 | \n", + "319 | \n", + "
| 616 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_IL2_STAT5_SIGNALING-0 | \n", + "[ The gene set is enriched for genes involved in cell growth, cell detection/regulation, and immunity. Mechanism: These genes are likely involved in a number of pathways that contribute to cell and tissue development, growth, and regulation, as well as regulation of the immune system. ] | \n", + "[\\nSummary: These genes are predominantly related to immunological functions, actin cytoskeleton organization, cell surface receptors, and pro-inflammatory regulation.\\nMechanism: The genes listed appear to be involved in the immune response, actin cytoskeleton organization, cell surface receptor-mediated signaling, and pro-inflammatory regulation.\\n] | \n", + "0.87 | \n", + "63 | \n", + "
| 617 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_IL2_STAT5_SIGNALING-1 | \n", + "[COULD NOT PARSE] | \n", + "[ The list of human genes provided are enriched for terms related to immunity, inflammatory response, cell growth, differentiation and development, and signaling pathways.\\n\\nMechanism: This underlying biological mechanism could involve proteins interacting with each other and coordinating pathways to govern immune response, inflammatory response, cell growth, differentiation, and development, as well as other cellular processes.\\n\\n] | \n", + "0.68 | \n", + "417 | \n", + "
| 618 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-0 | \n", + "[ Genes in the list are enriched for the Cellular Processes of Pain Sensing and Signal Transduction; Chemotaxis; Cytokine-mediated Signaling Pathway; Leukocyte Transendothelial Migration; Immune Response; and Platelet Activation. There is a potential mechanism for the underlying biological pathway whereby these genes interact in signal transduction to facilitate pain sensing and immune response, including ligand-receptor interactions, signal transduction of cytokines, and the actions of transcription factors, such as those encoded by JUN, REG1A, STAT1, STAT2, STAT3 and TLR2.\\n\\n] | \n", + "[ This list of genes is enriched in terms related to cell signaling, cytokine production and regulation, regulation of gene expression and transcription, and cell adhesion.\\nMechanism: This list of genes promotes the core pathways of cell signaling, cytokine production and regulation, regulation of gene expression and transcription, and cell adhesion. This enables the body to respond to a variety of external signals, to recognize and respond to inflammation and stress, to produce the necessary molecules for the body to function correctly, and to hold the cell together so that it may adhere to corresponding cells and fulfill its role within the network of cells.\\n] | \n", + "0.69 | \n", + "86 | \n", + "
| 619 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_IL6_JAK_STAT3_SIGNALING-1 | \n", + "[\\nSummary: The list of genes are significantly enriched for functions of immunity, signaling, and transcription regulation\\nMechanism: These genes are likely involved in the coordination of immune responses and the regulation of pathways for signal transduction and transcription.\\n] | \n", + "[ Increased expression of cytokines, chemokines, and interleukins; increased expression of developmental, signal transduction, and immune system pathways involved in cellular differentiation, cell motility and adhesion, signal transduction, and inflammation. \\nMechanism: The genes listed all appear to be involved in immune system, signal transduction and intercellular communication pathways. Through the identification of commonalities between the gene functions, inference can be made that these genes are involved in up-regulation of cytokines, chemokines, and interleukins involved in cellular differentiation, cell motility, adhesion, signal transduction and inflammation. \\n] | \n", + "0.86 | \n", + "400 | \n", + "
| 620 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-0 | \n", + "[ Genes associated with human immunity, inflammation and signalling pathways are enriched.\\n\\nMechanism: These genes are likely involved in pathways related to human immunity, inflammation and signalling, either directly or through regulation of transcription and translation activity.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.90 | \n", + "269 | \n", + "
| 621 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_INFLAMMATORY_RESPONSE-1 | \n", + "[ The list of genes is significantly enriched for terms related to immune cell signaling, cell movement, and cell surface receptor activity. \\nMechanism: These genes are likely involved in the regulation of pathways involved in initiating and responding to inflammation, cell migration, cell–cell interactions, and immune cell receptor-mediated signaling.\\n] | \n", + "[ The list of genes is enriched in functions related to the immune system, especially mediation of inflammatory response and cytokine production and signalling.\\nMechanism: The genes are involved in a variety of functions related to immune cell activation and cellular signaling, including cell adhesion, G-protein and receptor-coupled pathways, transcriptional regulation, cytokine and cytokine receptor binding, and lipid metabolism. \\n] | \n", + "0.69 | \n", + "81 | \n", + "
| 622 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-0 | \n", + "[ Our analysis of the list of human genes have revealed a set of enriched terms related to the activation and inhibition of immune signaling pathways, and their functions in regulating inflammation. Specifically, we observed an increased prevalence of molecules and proteins involved in mechanism activating or inhibiting the Nuclear Factor Kappa B (NF-κB), Interferon Regulatory Factor (IRF) as well as JAK-STAT pathways. Terms such as \"inflammatory response\", \"neutrophilic activation and degranulation\", \"T-Cell receptor signaling pathway\", \"Toll-Like Receptor Cascade\", \"Type I Interferon Signaling\", and \"Inflammatory Regulation\" were enriched in this gene set.\\n\\nMechanism: The genes in this list are involved in multiple pathways that are related to the modulation of inflammatory responses and can be broadly summarized as either regulating cytokine production or modulating the inflammatory response by inhibiting the NF-κB, IRF and JAK-STAT pathways. While there is significant overlap of these genes with the NF-κB pathway, the IRF and JAK-STAT pathways are also significant contributors, as evidenced by the enriched terms. \\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.84 | \n", + "1122 | \n", + "
| 623 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_INTERFERON_ALPHA_RESPONSE-1 | \n", + "[ This group of genes is significantly enriched for functions related to immune system regulation, interferon response, apoptosis, and cell membrane regulation.\\n\\nMechanism: This list of genes is likely involved in both innate and adaptive immune responses, functioning to modulate the level of inflammation and cytokine production, as well as to induce cell death and regulate cell membrane composition. Specific terms enriched that pertain to these functions include interferon signalling pathways, interferon gamma activity, interferon regulatory factor activity, status response to interferon, apoptosis, lipid binding, calcium ion binding, and neutrophil mediated immunity. \\n\\n] | \n", + "[ Genes listed appear to be primarily involved in the regulation of interferon response pathways and the transcriptional control of interferon-stimulated genes. The genes appear enriched for the cellular pathways of immune response, inflammation, and cytokine signaling.\\n \\nMechanisms: The interferon response pathways activated in this population of genes modulate the expression of cytokines, chemokines, and antimicrobial and antiviral proteins, in order to activate an innate immune response to virus and bacteria. \\n\\n] | \n", + "0.75 | \n", + "160 | \n", + "
| 624 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-0 | \n", + "[\\nSummary: A majority of the genes were found to be involved in important immune response and cell signaling pathways.\\nMechanism: The immune response and cell signaling pathways are likely to be regulated by cytokines and transcription factors such as those related to interferon responses and nuclear factor kappaB-dependent transcriptional regulation.\\n] | \n", + "[ In this gene set, there are multiple genes that are enriched for functions related to immunology, such as antigen presentation, inflammatory responses, chemokine signaling, cell adhesion, and cytokine interactions. \\nMechanism: One hypothesis is that these genes are involved in an immune-mediated response related to their roles in antigen-presentation, inflammatory responses, the regulation of chemokines, and cell adhesion. \\n] | \n", + "0.83 | \n", + "78 | \n", + "
| 625 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_INTERFERON_GAMMA_RESPONSE-1 | \n", + "[\\nSummary: The enriched terms among the list of genes includes pathways involved in immunity, interleukin regulation, transcriptional regulation, inflammation, cell signaling, and apoptosis.\\nMechanism: Signaling and pathways involving these genes are likely to regulate these biological processes.\\n] | \n", + "[ This list of genes is enriched in terms related to cell signaling, transcription regulation, and immune system regulation. Specifically, genes are enriched in pathways related to: interferon signaling; antigen processing, presentation, and recognition; cytokine signaling; cell cycle and DNA damage response; and apoptosis.\\n\\nMechanism: It appears that the genes identified in this list are functionally connected and may be involved in a larger underlying biological mechanism or pathway. The proteins associated with each gene are known to interact with one another and repress/activate various genes leading to the regulation of cell signaling, transcription, and immune system functions. This molecular regulation process is essential in the control of cellular functions and physiological behavior. \\n\\n] | \n", + "0.69 | \n", + "509 | \n", + "
| 626 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_KRAS_SIGNALING_DN-0 | \n", + "[ Genes in this term enrichment test were found to be enriched for terms related to the development of bones, morphogenesis, growth and maintenance, cell-cell signaling and communication, protein modification, and transport.\\nMechanism: It is likely that the genes identified in this term enrichment test make up a biological pathway that is involved in the development of bones, growth and morphogenesis, and other processes related to regulating cell-cell signaling and communication, protein modification, and transport.\\n] | \n", + "[ The analysis of the list of human genes reveals that these genes are related to development, regulation, and signaling mechanisms within the cell. Specifically, the terms associated with development, such as digit development, neural development, immune system development and transcriptional regulation, are enriched. Additionally, terms related to signal transduction, such as G-protein coupled receptors, protein kinases, and guanine nucleotide exchange factors, are also enriched.\\n\\nMechanism:The mechanism underlying the term enrichment of the list of human genes is likely related to the fact that these genes play a role in a wide range of essential cellular processes. It is likely that signaling molecules and transcription signals coordinate these processes to enable proper development and homeostasis.\\n\\n] | \n", + "0.77 | \n", + "293 | \n", + "
| 627 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_KRAS_SIGNALING_DN-1 | \n", + "[\\nSummary: The list of genes are found to be significantly associated with physiological processes related to morphogenesis, cell-cell communication and development, and hormone regulation.\\nMechanism: The genes are likely to be involved in a variety of biological mechanisms, such as cell-signalling, cellular differentiation and cell-cycle, as well as hormone mediated processes.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.89 | \n", + "365 | \n", + "
| 628 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_KRAS_SIGNALING_UP-0 | \n", + "[ Genes in this list are predominantly involved in signal transduction pathways and morphogenesis; specific terms enriched include signal transduction, cell morphogenesis, response to stimulus, angiogenesis, regulation of molecular function, and extracellular matrix organization.\\nMechanism: The list of genes are likely to be involved in signaling pathways involving kinases, growth factors and receptors, as well as involvement in morphogenesis processes such as cell-cell adhesion, cellular movement and cell differentiation.\\n] | \n", + "[ This list of gene names is enriched for genes involved in signal transduction, cell cycle control, and cell-to-cell adhesion.\\nMechanism: The enrichment of these genes indicates a shared biological pathway in which cellular communication, pathways, and networks are regulated by controlling the production of proteins and other molecules. This can lead to changes in other intracellular activities, such as cell cycle progression and adhesion. \\n] | \n", + "0.75 | \n", + "83 | \n", + "
| 629 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_KRAS_SIGNALING_UP-1 | \n", + "[\\nSummary: This set of genes appears to be involved in a variety of cellular processes, including morphogenesis and tissue development, cell signaling, and immune regulation.\\nMechanism: These genes appear to be involved in transcription modulation, signal transduction pathways, and regulation of cell adhesion and migration.\\n] | \n", + "[\\nSummary: This list of genes is enriched for terms related to cell adhesion and signal transduction, including terms such as integrin, chemokine receptor, protein kinase and G-protein-coupled receptor.\\nMechanism: These genes are involved in pathways important for cell adhesion, such as integrin and chemokine receptor-mediated interactions, as well as signal transduction pathways which include protein kinases, G-protein-coupled receptors and other associated proteins.\\n] | \n", + "0.85 | \n", + "147 | \n", + "
| 630 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_MITOTIC_SPINDLE-0 | \n", + "[COULD NOT PARSE] | \n", + "[\\n\\nSummary: The list of human genes have diverse enrichment in the functions of cell cycle control, cell adhesion, and cytoskeletal organization.\\nMechanism: These genes enable cells to interact with their environment and complete the cell cycle by organizing components, regulating activities, and controlling signaling pathways.\\n] | \n", + "0.81 | \n", + "314 | \n", + "
| 631 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_MITOTIC_SPINDLE-1 | \n", + "[ Enriched terms show a commonality among these genes for processes related to cytoskeletal organization and migration of the cell, cell division, DNA replication and repair, and targeting proteins to the correct place in the cell.\\nMechanism: The proteins represented by these genes likely play a role, either directly or indirectly, in the regulation of a number of vital cell processes including cell division, DNA replication and repair, and targeting proteins to the right place in the cell.\\n] | \n", + "[ \\nSummary: The genes that were provided are statistically enriched for terms related to cell division, protein phosphorylation, chromatin remodeling, and microtubule binding and organization.\\nMechanism: These genes likely function in biological pathways related to spindle assembly, chromosome segregation and movement, cell-cycle control, and other processes related to mitosis. \\n] | \n", + "0.84 | \n", + "114 | \n", + "
| 632 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_MTORC1_SIGNALING-0 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE] | \n", + "0.84 | \n", + "0 | \n", + "
| 633 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_MTORC1_SIGNALING-1 | \n", + "[ The list of genes is enriched in functions related to protein synthesis, energy metabolism, cellular transport, and immune response.\\nMechanism: It is likely that these genes are co-regulated in networks that are responsible for cellular energy production and regulation, protein synthesis and degradation, and immune response.\\n] | \n", + "[\\nSummary: This list of genes is involved in a variety of pathways related to cell growth and development, including morphogenesis, transcription, and protein synthesis.\\nMechanism: The physiological processes induced by these genes likely work in concert to mediate a variety of cellular processes including cellular translation, metabolism, and signalling.\\n] | \n", + "0.83 | \n", + "29 | \n", + "
| 634 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_MYC_TARGETS_V1-0 | \n", + "[ The genes appear to be involved in processes related to RNA and protein synthesis, ATP-related processes, cytoskeleton organization and assembly, transcription, and chromatin remodeling.\\n\\nMechanism: The genes likely play a role in regulating various cellular processes, such as gene expression, signal transduction, and translation, via multiple pathways that are related to RNA processing, translation initiation, mRNA stability, and DNA replication.\\n\\n] | \n", + "[\\nThe list of genes are involved in a variety of processes including, but not limited to, protein synthesis and modification, DNA replication, cell cycle regulation, and transcription regulation.\\nThis suggests that these genes may be involved in a co-dependent pathway or pathways that regulate cell growth, development, and gene expression.\\n] | \n", + "0.81 | \n", + "113 | \n", + "
| 635 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_MYC_TARGETS_V1-1 | \n", + "[ Genes from this list are mainly involved in translation, transcription, and post-transcriptional modification processes. Specifically, these genes are involved in mRNA splicing, mRNA transport, mRNA stability, protein synthesis, ribosome biogenesis, RNA interference, and chromatin remodeling. Mechanism: These genes likely operate according to the canonical mechanisms of gene expression, by which genes are transcribed, spliced, and translated into proteins. These processes are tightly regulated and involve a complex network of interacting proteins, RNAs, and other molecules. ] | \n", + "[\\nSummary: This list of genes have overlapping functions in development, energy production, and regulation.\\nMechanism: There may be a pathway involved in controlling energy production, protein synthesis, and structural maintenance of cell components in development.\\n] | \n", + "0.78 | \n", + "317 | \n", + "
| 636 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_MYC_TARGETS_V2-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The enrichment test identified a set of genes related to protein and nucleic acid metabolism and cell cycle regulation. Specifically, genes involved in protein post-translational modifications, phosphorylation, transcription, translation, and ribosome biogenesis were enriched.\\n\\nMechanism: These gene functions are likely related to the underlying biological mechanism or pathway, since genes related to these processes have an essential role in regulatory activities and cell cycle control. ] | \n", + "0.86 | \n", + "478 | \n", + "
| 637 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_MYC_TARGETS_V2-1 | \n", + "[\\nSummary: The gene set is enriched for terms related to cell activation and proliferation, as well as DNA replication and replication-associated processes such as transcription and translation.\\n] | \n", + "[ \\nSummary: Many of the genes listed appear to be related to chromatin and transcriptional regulation.\\nMechanism: Regulation of gene expression and chromatin structure via transcription factors and nucleosome remodeling enzymes. \\n] | \n", + "0.77 | \n", + "35 | \n", + "
| 638 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_MYOGENESIS-0 | \n", + "[ Gene expression and structure, cytoskeletal structure and dynamics, calcium regulation and signaling, cell adhesion and migration, cell death biochemistry, and metabolic regulation are all enriched terms based on the genes provided that are common to these roles in humans.\\n\\nMechanism: The underlying biological mechanism for the enriched terms observed in this list of genes is likely related to the wide range of regulatory roles these genes and gene products have in maintaining cellular health and enabling proper physiological functions and development at the cellular level. \\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.69 | \n", + "569 | \n", + "
| 639 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_MYOGENESIS-1 | \n", + "[ The list of genes show an enrichment for terms related to the extracellular matrix, cytoskeleton, muscle structure and development, neuromuscular structure, ion channels, and ion transport. \\nMechanism: These genes appear to be involved in various intra- and extracellular pathways and mechanisms related to the formation and maintenance of the cytoskeleton, neuromuscular structure, and muscle formation, as well as ion transport and channel proteins serving as important mediators of electrical and chemical signals in cells. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.91 | \n", + "514 | \n", + "
| 640 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_NOTCH_SIGNALING-0 | \n", + "[\\nThe list of genes are involved primarily in aspects of embryonic development, regulation of cell cycle, and calcium signaling.\\nMechanism: The genes function primarily in regulating various aspects of cell signaling and cycle regulation during embryonic development, such as down-regulation of Notch signaling, regulation of Wnt signaling and Hedgehog signaling pathways, cell morphogenesis, and calcium signaling.\\n] | \n", + "[ These genes are associated with Notch receptor, transcription factor, and Wnt pathway signaling, which are involved in tissue and organ development.\\nMechanism: Notch receptor, Wnt, and transcription factor signaling pathways leads to a variety of processes such as morphogenesis, organogenesis, tissue development, cell fate determination, and cell interaction. \\n] | \n", + "0.82 | \n", + "51 | \n", + "
| 641 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_NOTCH_SIGNALING-1 | \n", + "[COULD NOT PARSE] | \n", + "[\\nSummary: The genes in this list are associated with cell proliferation, morphogenesis and development, nerve system differentiation, and regulation of transcription.\\nMechanism: The genes likely function in pathways involved in the WNT and Notch signalling pathways, which have numerous roles in development and differentiation of different tissue types. \\n] | \n", + "0.86 | \n", + "341 | \n", + "
| 642 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-0 | \n", + "[\\n\\nSummary: This list of genes is enriched for terms related to mitochondrial activity, electron transport chain, oxidative phosphorylation, and metabolic regulation/activation.\\nMechanism: This list of genes are likely to be involved in the various steps of mitochondrial activity, electron transport chain, oxidative phosphorylation, and metabolic regulation/activation. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.86 | \n", + "357 | \n", + "
| 643 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_OXIDATIVE_PHOSPHORYLATION-1 | \n", + "[\\nSummary: The list of genes is predominantly involved in cellular respiration and metabolism, as evidenced by the enriched terms related to mitochondrial bioenergetics, ion transport and metabolite-binding proteins.\\nMechanism: The commonality amongst the genes likely contributes to the normal functioning of mitochondria, and is involved in the bioenergetic processes that involve ATP synthesis, as well as maintaining electron transfer and transporter function.\\n] | \n", + "[ Genes in this list are mainly associated with mitochondrial bioenergetics and associated pathways. Specifically, the terms \"mitochondrial electron transport chain complex activity\"; \"mitochondrial electron transport, NADH to ubiquinone\"; \"mitochondrial respiratory chain complex I activity\"; \"respiratory chain complex I assembly\"; \"respiratory chain complex III activity\"; and \"respiratory chain complex IV activity\" are found to be enriched in this gene set.\\n\\nMechanism: Mitochondria are dynamic organelles that are responsible for many of the metabolic pathways, including cellular respiration. A variety of mitochondrial electron transport complexes are involved in the production of energy, including complex I (NADH:ubiquinone oxidoreductase), complex III (ubiquinone:cytochrome c oxidoreductase), complex IV (cytochrome c oxidase), and complex V (ATP synthase). As these genes are associated with mitochondrial functions, it is possible that there is an underlying mechanism related to metabolic pathways and energy production within the mitochondria. \\n\\n] | \n", + "0.84 | \n", + "598 | \n", + "
| 644 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_P53_PATHWAY-0 | \n", + "[ Analysis of this gene list revealed a significant enrichment of terms in functions related to cytoskeleton alteration, calcium homeostasis modulation, ubiquitin-proteasome pathway activation, cell cycle control, and transcriptional and post-transcriptional regulation.\\n\\nMechanism: These functions likely act in concert to mediate the regulation of cellular growth, differentiation, and survival.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.70 | \n", + "383 | \n", + "
| 645 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_P53_PATHWAY-1 | \n", + "[ Genes in this list are associated with regulation of the cell cycle, DNA damage repair, cell signaling and processes involved in cell growth, apoptosis, and immune modulation. The genes are enriched for functions related to transcription, chromatin dynamics, cell adhesion molecules, and cytokines. \\nMechanism: The regulation of these genes (directly or indirectly) is likely to be part of a complex network of pathways, signaling molecules, and protein-protein interactions. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.72 | \n", + "463 | \n", + "
| 646 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_PANCREAS_BETA_CELLS-0 | \n", + "[\\nSummary: This gene set is enriched in functions related to pancreas development, glucose metabolism, cell motility, and neural development. \\nMechanism: It is hypothesized that these genes function in a network to control developmental processes relevant to pancreas development, glucose metabolism, cell motility and neural development.\\n] | \n", + "[ Genes play diverse roles in the development of the pancreas, nervous system, and musculoskeletal system. Major term enrichment was found for pancreas development, nervous system development, development of neural structures, organogenesis, and transcriptional regulation. \\nMechanism: These genes are likely involved in a variety of biological mechanisms including, the regulation of morphogenesis, cell-to-cell adhesion, and protein synthesis pathways, as well as hormonal metabolism and signaling.\\n] | \n", + "0.84 | \n", + "162 | \n", + "
| 647 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_PANCREAS_BETA_CELLS-1 | \n", + "[\\nSummary: This term enrichment test identified gene functions related to morphogenesis, neural development, signal transduction, insulin hormone secretion, transcription regulation, and transcription factor activity.\\nMechanism: These genes likely work together to facilitate the development of body organs, neuronal function and pathways, insulin secretion, and transcription factor activity.\\n] | \n", + "[ Analysis of these genes revealed common pathways related to metabolic regulation, neural development, and transcription/translation control. The terms enriched by these genes are neurogenesis; metabolism; transcriptional control; translation; morphogenesis; body patterning and organization; neurological system development; and cell differentiation.\\n\\nMechanism: Signaling pathways involved in neural development will have an influence on neurogenesis, while metabolic pathways will be involved in pathways that regulate glucose and lipid metabolism. Additionally, transcription and translation pathways are essential for regulating gene expression but also cell differentiation and morphogenesis. Finally, body patterning and organization rely on genes that control cell fate and cellular migration. \\n\\n] | \n", + "0.71 | \n", + "411 | \n", + "
| 648 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_PEROXISOME-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The human genes given in the list are involved in metabolic biochemical pathways associated with lipid metabolism, stress response, mRNA transcription, DNA repair, skeletal and cartilage development, and cell migration. \\nMechanism: Metabolic enzymes and transport proteins appear to regulate these pathways, allowing for the synthesis and degradation of cellular compounds, as well as transporting molecules into and out of the cell to maintain physiological homeostasis.\\n] | \n", + "0.76 | \n", + "459 | \n", + "
| 649 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_PEROXISOME-1 | \n", + "[ Genes involved in the list are associated with lipid metabolism, lipid storage and transport, steroid metabolism, regulation of transcription and, importantly, regulation of the cell cycle. \\nMechanism: An enrichment of pathways associated with lipid, steroid and transcriptional metabolism, as well as regulation of the cell cycle.\\n] | \n", + "[\\nSummary: Genes in this list are associated with a wide array of terms, including metabolism, transcription, regulation, transport and signaling.\\nMechanism: These genes likely play a role in a broad biological mechanism involving various metabolic pathways, transport, and regulatory functions.\\n] | \n", + "0.83 | \n", + "38 | \n", + "
| 650 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-0 | \n", + "[ Gene expression, DNA repair and maintenance, growth factors, cellular signaling pathways and lipid metabolism \\nMechanism: Regulation of gene expression through the activation of transcription and DNA repair and maintenance pathways is likely involved. The enriched terms related to growth factors suggests that the list of genes may be involved in cell proliferation and differentiation. Signaling pathways and lipid metabolism may be involved in cell-cell communication and energy-related processes, respectively.\\n] | \n", + "[ The list of genes is enriched for terms related to signal transduction pathways and development, such as morphogenesis and cell differentiation.\\nMechanism: Signal transduction pathways are likely involved in the regulation of the gene functions, with particular importance of tyrosine kinase activity and modulation of relevant receptor activities.\\nHypothesis: The genes may be involved in the regulation of tissue development and cell differentiation.\\n] | \n", + "0.76 | \n", + "62 | \n", + "
| 651 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_PI3K_AKT_MTOR_SIGNALING-1 | \n", + "[ The list of genes given are involved in cell cycle regulation, gene transcription, transcription factor activation and signal transduction pathways.\\nMechanism: The genes included in this list are involved in various mechanisms of cell cycle regulation, gene transcription, transcription factor activation and signal transduction pathways. These involve the regulation of cell cycle progresses such as synthesis, growth, proliferation and differentiation, as well as the operations of protein kinases, transcription factors, receptor proteins and other essential molecules. \\n] | \n", + "[ \\n\\nSummary: This gene list covers a broad range of functions, including cell signaling, growth and survival, protein and lipid metabolism, transcription regulation, and cell cycle control.\\nMechanism: The genes in this list are likely involved in a variety of pathways that facilitate or regulate various cellular activities, such as receptor signaling, protein glycosylation, kinase activity, apoptosis, and G-protein interactions.\\n] | \n", + "0.88 | \n", + "143 | \n", + "
| 652 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_PROTEIN_SECRETION-0 | \n", + "[COULD NOT PARSE] | \n", + "[ Genes listed are associated with vesicular transport, trafficking, and membrane fusion in the cell.\\nMechanism: Vesicular transport involves the formation of vesicles from the host membrane, trafficking of these vesicles through the cell and organelles, and fusion of the vesicles with host membranes for which these genes are responsible.\\n] | \n", + "0.68 | \n", + "325 | \n", + "
| 653 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_PROTEIN_SECRETION-1 | \n", + "[COULD NOT PARSE] | \n", + "[ Enrichment test on a given list of human genes resulted in the identification of several enriched terms, which have important roles in post-translational modification, protein folding, protein synthesis, endocytosis, oligosaccharide metabolism, and lysosomal trafficking.\\n\\nMechanism: The mechanism behind this enrichment pattern is likely related to the various mechanisms regulated by these genes, such as the regulation of PTMs, protein folding, protein synthesis, endocytosis, oligosaccharide metabolism, and lysosomal trafficking.\\n\\n] | \n", + "0.86 | \n", + "522 | \n", + "
| 654 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-0 | \n", + "[\\nSummary: This list of genes is enriched for terms involving redox regulation, antioxidant defense and detoxification of reactive oxygen species, peroxisomal and mitochondrial biogenesis, and cell metabolism.\\nMechanism: The underlying biological mechanism involves the production and regulation of reactive oxygen species, adaptation to oxidative stress and related forms of damage, and the maintenance of redox homeostasis.\\n] | \n", + "[\\nSummary: The list of genes is associated primarily with metabolic processes, defense against oxidative damage and DNA repair.\\nMechanism: These processes are likely related to cellular level metabolic regulation, protection against oxidative damage, and DNA damage repair.\\n] | \n", + "0.82 | \n", + "152 | \n", + "
| 655 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1 | \n", + "[ \\nSummary: 13 genes are enriched for functions associated with redox regulation, metabolism, cell cycle regulation, and transcriptional regulation.\\nMechanism: These genes likely play a role in the regulation of a cell's redox balance, metabolism, cell cycle progression and gene expression.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.86 | \n", + "276 | \n", + "
| 656 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_SPERMATOGENESIS-0 | \n", + "[\\nThe gene list is enriched for functions related to cell signaling, protein regulation, and cell cycle control, as well as complex development processes such as morphogenesis, organogenesis and cytoskeletal regulation.\\nMechanism: A wide range of mechanims are at work here, which involve the transcription and translation of genes to encode proteins and the regulation of their functions to mediate both common and specific biological processes.\\n] | \n", + "[ Genes associated with this list indicate enrichment for a variety of cell cycle control and chromatin remodeling processes, as well as protein ubiquitination, regulation of DNA replication, spindle assembly, and nuclear organization.\\n\\nMechanism: The enriched terms suggest that these genes are involved in a variety of related functions related to the regulation and maintenance of the cell cycle, chromatin remodeling, DNA replication, spindle assembly and nuclear organization.\\n\\n] | \n", + "0.82 | \n", + "36 | \n", + "
| 657 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_SPERMATOGENESIS-1 | \n", + "[ Genes related to organ development, morphogenesis, cytoskeletal proteins, signal transduction.\\nMechanism: Proteins from the list are likely used as part of a unified pathway for organ/tissue development and morphogenesis, and involved in cell cycle checkpoint regulation and signal transduction.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.90 | \n", + "282 | \n", + "
| 658 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_TGF_BETA_SIGNALING-0 | \n", + "[ The list of genes analyzed in this term enrichment test is related to pathways associated with cell growth and development, such as MAPK, TGF-β, Wnt/β-catenin, Hippo and transcriptional regulations. Specifically, pathway enrichment of genes included muscle and tissue morphogenesis, regulator of G-protein signaling and inflammatory response pathway.\\n\\nMechanism: The general mechanism is that the genes are involved in signaling pathways for cell processes such as growth, differentiation and apoptosis. These signals modulate the expression of downstream genes and ultimately lead to changes in cell shape and other cellular activities.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.80 | \n", + "625 | \n", + "
| 659 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_TGF_BETA_SIGNALING-1 | \n", + "[COULD NOT PARSE] | \n", + "[ Our term enrichment analysis of these genes reveals an overrepresented pattern of general cellular processes related to the development and proliferation of cells, as well as homeostasis, cell division, and migration. Specifically, genes related to transcriptional regulation, signal transduction, cell cycle regulation, protein kinase pathways, and translation were enriched.\\n\\nMechanism: These overrepresented functions suggest a complex coordination of biochemical pathways contributing to cell development and proliferation, junctions, and cytoskeletal organization.\\n\\n] | \n", + "0.83 | \n", + "558 | \n", + "
| 660 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-0 | \n", + "[ These genes are mainly involved in developmental processes, inflammation, immunomodulation, inflammation, cell signalling and metabolic pathways.\\nMechanism: These genes are likely to be involved in pathways leading to the regulation of morphogenesis and tissue development, control of cell proliferation and apoptosis, regulation of immune system immune response, regulation of inflammation and activation of metabolic pathways.\\n] | \n", + "[ The genes in the given list are predominantly involved in the TLR signaling pathway, development, inflammation and immune-response regulation.\\nMechanism: The TLR signaling pathway consists of an intricate set of reactions starting with the recognition of a pathogen-associated molecular pattern (PAMP) by the TLR receptor, leading to the activation of various transcription factors, such as NFKB and MAPK, which work to activate a cascade of gene expression and ultimately the secreting of pro-inflammatory molecules.\\n\\n] | \n", + "0.86 | \n", + "90 | \n", + "
| 661 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_TNFA_SIGNALING_VIA_NFKB-1 | \n", + "[\\nSummary: The genes are enriched for terms related to gene transcription, cytoskeleton formation, and signal transduction. \\nMechanism: The genes are likely involved in a wide range of processes, including transcriptional regulation, actin cytoskeleton organization, cytokine receptor signaling and NF-kB signaling pathways.\\n] | \n", + "[ Gene functions related to inflammation and immunity appear to be enriched when analyzing the list of genes provided, including cytokine-mediated signaling, antigen-receptor mediated signaling, B-cell proliferation, cytokine expression and release, immunoregulatory interactions, NF-kappaB (NF-κB) activation, and interferon (IFN) signaling.\\n\\nMechanism: These genes are likely involved in an inflammatory response in which cytokines are released and induce receptor activation, which leads to NF-κB activation and transcription of genes that produce cytokines and other signaling molecules, as well as triggering an IFN response. This ultimately leads to B-cell proliferation and immunoregulatory interactions in order to mount a response to the any pathogens. \\n\\n] | \n", + "0.86 | \n", + "439 | \n", + "
| 662 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-0 | \n", + "[ The genes in the list may be generally involved in processes such as mRNA transcription, ribosome biogenesis and protein folding, as well as nucleolar and spliceosomal activity. \\nMechanism: These genes likely regulate cellular processes such as protein production and transport, RNA processing, and cell cycle control. \\n] | \n", + "[\\nSummary: A significant enrichment of genes involved in translation and protein folding is found in the gene list, indicating a common pathway for these genes.\\nMechanism: The genes in this list are likely all involved in the same pathway, centered around translation and protein folding.\\n] | \n", + "0.87 | \n", + "33 | \n", + "
| 663 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1 | \n", + "[\\nSummary: The enrichment analysis on the list of genes revealed a common theme of gene functions related to metabolism, protein synthesis, and post-translational modifications.\\nMechanism: The observed gene functions suggest a pathway of metabolic and protein regulatory processes that involve the synthesis of proteins, post-translational modifications such as phosphorylation, and other processes related to metabolism and folding.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.85 | \n", + "418 | \n", + "
| 664 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_UV_RESPONSE_DN-0 | \n", + "[ The genes identified are associated with protein kinases, cellular signaling pathways, and development of skeletal and extracellular matrix components.\\nMechanism: These identified genes may be involved in complex regulation and signaling pathways, focusing on post-translational phosphorylation and transcriptional regulation, as well as the control of growth, development and remodeling of skeletal structures.\\n] | \n", + "[ This enrichment test demonstrates over-representation of the genes involved in cell signaling, structural and enzymatic proteins, and morphogenesis. Mechanism: The mechanisms underlying this enrichment are likely related to the roles of these proteins in regulating the mechanism of intercellular signaling associated with cell development, adhesion, migration, metabolism, skeletal growth, and cell death. ] | \n", + "0.81 | \n", + "5 | \n", + "
| 665 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_UV_RESPONSE_DN-1 | \n", + "[ Many of the genes are clustered around those involved in structure, development and regulation. They are involved in processes such as mitotic regulation, bone morphogenesis, morphogenesis of specific organs and tissues, regulation of signaling pathways, regulation of transcription, regulation of cell proliferation, cellular responses to external stimuli, protein phosphorylation and DNA binding.\\n\\nMechanism: These genes are likely to be involved in the regulation and development of several different processes, including the regulation of cell proliferation, transcription, morphogenesis of organs and tissues, and mitotic regulation. These mechanisms are likely to be controlled by the interactions among gene products, signaling pathways and regulatory components such as transcription factors.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.79 | \n", + "788 | \n", + "
| 666 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_UV_RESPONSE_UP-0 | \n", + "[ Proteins involved in development, cell growth, gene transcription, and metabolism are enriched.\\nMechanism: These proteins are involved in a variety of biological processes that underlie development and cell growth, as well as affecting gene transcription and metabolism.\\n] | \n", + "[\\n\\nSummary: The enriched terms from the list of genes suggest a commonality in roles related to protein and organelle trafficking, DNA methylation, transcription and binding, chromatin remodeling, cell cycle regulation and metabolism. \\n\\nMechanism: The proposed mechanism is that these processes are essential components of pathways that regulate cell development, growth, and the response to internal and external stimuli.\\n\\n] | \n", + "0.66 | \n", + "151 | \n", + "
| 667 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_UV_RESPONSE_UP-1 | \n", + "[ Genes in this list are mainly involved in cell growth, morphogenesis, regulation of transcription, signal transduction of receptors, DNA/protein activity and metabolism. More specifically, the terms enriched in this list of genes are cell proliferation, cell cycle regulation, DNA replication and repair, signal transduction, calcium signaling, apoptosis, lipid metabolism and oxygen pathway.\\n\\nMechanism: The genes in this list mainly participate in the regulation of various biological processes through their encoding for proteins that act as transcription factors, receptors, and enzymes. These proteins are activated by a variety of signals including DNA damage, growth factors and hormones to induce changes in gene expression and cellular behavior. They also control cell growth, differentiation and metabolism by regulating DNA, protein, lipid and oxygen pathways, ultimately resulting in morphogenesis and cell proliferation. \\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.82 | \n", + "922 | \n", + "
| 668 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-0 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE] | \n", + "0.68 | \n", + "0 | \n", + "
| 669 | \n", + "\n", + " | RANDOM | \n", + "HALLMARK_WNT_BETA_CATENIN_SIGNALING-1 | \n", + "[\\nSummary: The gene list appears to mostly contain genes involved in Wnt signaling, Notch signaling, transcription regulation and cell cycle regulation processes.\\nMechanism: The underlying biological mechanism appears to be the regulation of processes such as transcription, cell cycle, and Wnt and Notch signaling that may in turn affect the morphogenesis and development of various organs and tissues.\\n] | \n", + "[ Genes highly enriched in the provided list have functions related to cell signaling and regulation, including morphogenesis, transcription, and development. Specifically, genes involved in Wnt, Notch, and Hedgehog pathways, transcription factors, and cell cycle genes such as Axin, β-catenin, HDAC2, and CUL1 are all significantly enriched in the list.\\n\\nMechanism: Many of the genes involved in these pathways are responsible for controlling cell fate and regulating morphogenesis and development. The Wnt pathway, a key regulator in embryonic development, is involved in axial patterning, tissue organization and differentiation, and cell-fate decisions. The Notch and Hedgehog pathways are also important for stem cell maintenance and development in early development, as well as tissue patterning, morphogenesis, and organogenesis in adulthood. The transcription factors, such as LEF1, TCF7, and NKD1, drive gene expression in response to these signaling molecules. Lastly, genes such as ADAM17, DKK1, PSEN2, and AXIN2 are involved in cell-cycle regulation and apoptosis. \\n\\n] | \n", + "0.92 | \n", + "675 | \n", + "
| 670 | \n", + "\n", + " | RANDOM | \n", + "T cell proliferation-0 | \n", + "[ \\nSummary: The genes in the list are found to be involved primarily in cell signalling, development, and immunity processes.\\nMechanism: The numerous genes with enriched terms are involved in coordinating both intra- and extracellular activity through signal transduction pathways and receptor-mediated signaling, with downstream effects on cellular growth, differentiation, and function within various organs and systems in the body.\\n] | \n", + "[\\nSummary: This list of genes are enriched for terms related to cell development and signaling, specifically those involved in receptor-mediated signaling and the regulation of cell morphology. \\nMechanism: These genes likely act through regulating cell development and receptor-mediated signaling pathways to their respective functions, such as morphogenesis and gene expression.\\n] | \n", + "0.82 | \n", + "55 | \n", + "
| 671 | \n", + "\n", + " | RANDOM | \n", + "T cell proliferation-1 | \n", + "[ The enrichment test found that the genes listed have common functions associated with cell signaling and immune regulation, such as signal transduction, growth factor production and response, immune response and modulation, calcium homeostasis, transcription factors, development and differentiation, receptor binding, and cytokine production.\\n\\nMechanism: The enrichment test suggests that these genes may contribute to signal transduction pathways that facilitate cell proliferation, differentiation, and survival; growth factor production and signal transduction; immune response and modulation; calcium homeostasis; transcription factor activity including regulation of gene expression; development and differentiation; receptor binding and signal transduction; and cytokine production.\\n\\n] | \n", + "[ \\nThis sample of genes are mainly involved in regulation of the immune system, cell signaling, cytoplasmic transport, and apoptosis. Specifically, the genes are enriched for terms such as cytokine receptor binding; cell adhesion; immunoreceptor-antigen complex binding; regulation of the ubiquitin-proteasome pathway; transcription factor regulator activity; GTP-binding protein binding; cell differentiation; T-cell receptor binding; antigen presentation; and immune system process.\\n\\nMechanism: This list of genes likely act in concert to regulate the immune system. They perform a variety of functions, including binding and processing cytokines, receptor-antigen complexes, and other molecules involved in the binding or processing of molecules, such as transcription factors, that are involved in regulating gene expression. Additionally, these genes may be involved in cell differentiation, antigen presentation, and other processes involved in the regulation of the immune system. \\n\\n] | \n", + "0.84 | \n", + "197 | \n", + "
| 672 | \n", + "\n", + " | RANDOM | \n", + "Yamanaka-TFs-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The genes provided are related to transcription factor activity, as they are associated with embryonic stem cell differentiation and pluripotency.\\n] | \n", + "0.69 | \n", + "133 | \n", + "
| 673 | \n", + "\n", + " | RANDOM | \n", + "Yamanaka-TFs-1 | \n", + "[\\nThe list of genes provided encode transcription factors associated with early development of embryonic stem cells.\\nMechanism: Transcriptional regulation via these transcription factors control the expression of other genes related to embryogenesis and stem cell development.\\n] | \n", + "[ The given list of genes is involved in the regulation of cell differentiation and development, specifically in the formation of stem cells, by regulating the expression of developmental proteins. ] | \n", + "0.88 | \n", + "79 | \n", + "
| 674 | \n", + "\n", + " | RANDOM | \n", + "amigo-example-0 | \n", + "[\\nSummary: This term enrichment test on the list of human genes shows enrichment for terms related to extracellular matrix organization and cell adhesion, morphogenesis and morphological changes, and cell signaling. \\nMechanism: The underlying biological mechanisms may involve a combination of protein-protein interactions, transcriptional regulation and extracellular matrix modifications.\\n] | \n", + "[ The genes included in this list are related to cell proliferation, tissue morphogenesis, motility regulation, vascular development, bone growth, and the immune system. The mechanism is the transcription of gene products that cause expression of varied proteins that mediate these functions.\\n\\nMechanism: Transcription of gene products inducing the expression of varied proteins that mediate cell proliferation, tissue morphogenesis, motility regulation, vascular development, bone growth, and the immune system.\\n\\n] | \n", + "0.90 | \n", + "124 | \n", + "
| 675 | \n", + "\n", + " | RANDOM | \n", + "amigo-example-1 | \n", + "[COULD NOT PARSE] | \n", + "[ This list of genes are all involved in the development and maintenance of the vascular system. Specifically, these genes play a role in angiogenesis, cell proliferation and migration, matrix remodeling, and tissue remodeling. The genes are implicated in processes such as Jagged-mediated signaling, transcriptional regulation, platelet activation and aggregation, immune regulation, and extracellular matrix formation.\\n\\nMechanism: These genes are involved in a variety of pathways that are responsible for the formation and maintenance of the vascular system. Specifically, the Jagged and Notch pathways are implicated in the control of endothelial cell proliferation and migration, while the TGF-β and Wnt/β-Catenin pathways are involved in matrix remodeling. Additionally, these pathways are also involved in platelet activation and aggregation and the formation of extracellular matrix components.\\n\\n] | \n", + "0.68 | \n", + "888 | \n", + "
| 676 | \n", + "\n", + " | RANDOM | \n", + "bicluster_RNAseqDB_0-0 | \n", + "[\\nSummary: The list of genes are involved in morphogenesis, development, transcription regulation, cellular signalling and ion transport.\\nMechanism: The genes are likely to be involved in a variety of biochemical and molecular pathways pertaining to the specified functions.\\n] | \n", + "[ Genes associated with this list are enriched for functions related to development and signaling, including cell growth, differentiation, and migration; chromatin modulation; transcription regulation; cytoskeletal organization; intracellular trafficking and adhesion; signal transduction; and DNA/RNA metabolic processes.\\nMechanism: The genes are likely to be involved in multiple biological mechanisms and pathways, including processes related to healing, morphogenesis, angiogenesis, and muscle growth and development.\\n] | \n", + "0.69 | \n", + "247 | \n", + "
| 677 | \n", + "\n", + " | RANDOM | \n", + "bicluster_RNAseqDB_0-1 | \n", + "[ These genes are primarily involved in development and signaling pathways, particularly morphogenesis, neuronal growth, and neuronal system development. Mechanism: These genes facilitate cell-cell communication and signaling, allowing for cells to coordinate their functions together and form efficiently organized tissues and organs. ] | \n", + "[ This analysis identified a number of genes involved in various cellular processes such as chromatin regulation, cell development, protein translation, and ion transport.\\nMechanism: The underlying biological mechanism likely involves regulation of gene expression through the actions of transcription factors, the post-translational modifications of proteins, and the transport of ions across cell membranes.\\n] | \n", + "0.73 | \n", + "74 | \n", + "
| 678 | \n", + "\n", + " | RANDOM | \n", + "bicluster_RNAseqDB_1002-0 | \n", + "[COULD NOT PARSE] | \n", + "[ The human genes listed are involved in skeletal muscle structure and contractility. The genes are enriched for processes such as myofibrillogenesis, actin filament organization, and muscle contraction.\\n\\nMechanism: The genes likely act to regulate processes involved in myofibrillogenesis, such as Z-disc formation and maintenance, nuclear positioning, and muscle fiber organization. They also may act to modulate ion channel influx/efflux, thereby influencing muscle contraction and force. \\n\\n] | \n", + "0.84 | \n", + "478 | \n", + "
| 679 | \n", + "\n", + " | RANDOM | \n", + "bicluster_RNAseqDB_1002-1 | \n", + "[ The genes listed were significantly over-represented for processes related to muscle formation and human body structure, such as muscle and skeletal development, skeletogenesis, and myogenesis. \\n\\nMechanism: The set of genes is involved in multiple pathways related to muscle formation and structure in the human body, such as muscle and skeletal development, skeletogenesis, and myogenesis. These pathways likely involve the regulation of protein synthesis and biosynthesis, as well as processes related to muscle contraction and relaxation. \\n\\n] | \n", + "[\\nSummary: Genes in this set are involved in muscle structures and processes.\\n] | \n", + "0.67 | \n", + "468 | \n", + "
| 680 | \n", + "\n", + " | RANDOM | \n", + "endocytosis-0 | \n", + "[ These genes are involved in signaling pathways, vesicle/lipid trafficking, and cellular adhesion related processes.\\nMechanism: These genes act as regulators of nutrients, cell metabolism, and cytoskeletal organization. They are also involved in endocytosis, exocytosis, and the regulation of intercellular adhesion and motility.\\n] | \n", + "[\\nSummary: These genes are related to lipid metabolism, cell signaling pathways, and cell cycling.\\nMechanism: These genes are thought to have a role in regulating lipid metabolism, cell signaling pathways and cell cycling. \\n] | \n", + "0.84 | \n", + "107 | \n", + "
| 681 | \n", + "\n", + " | RANDOM | \n", + "endocytosis-1 | \n", + "[\\nSummary: The genes in this list are associated with processes related to membrane trafficking, receptor signaling, protein proteolysis, and lipid metabolism. \\nMechanism: The underlying biological mechanism is likely regulation of membrane trafficking, receptor signaling, protein proteolysis, and lipid metabolism. \\n] | \n", + "[\\nSummary: The genes in this list are predominantly involved in endocytosis and intracellular signaling.\\nMechanism: The genes in this list interact to form a molecular pathway that is involved in endocytosis and intracellular signaling. Endocytosis allows receptors and newly synthesized molecules to be moved cellular compartments and can result in changes in cell signaling.\\n] | \n", + "0.89 | \n", + "59 | \n", + "
| 682 | \n", + "\n", + " | RANDOM | \n", + "glycolysis-gocam-0 | \n", + "[ An analysis of gene functions in these 10 genes shows an enrichment of terms associated with metabolism, including glycolysis, aerobic glycolysis, and gluconeogenesis.\\n\\nMechanism: This suggests a possible underlying biological mechanism in which glycolysis and gluconeogenesis pathways are deployed by cells in order to provide sufficient energy to cope with various metabolic demands.\\n\\n] | \n", + "[\\nBased on the list of genes provided, common terms enriched amongst the genes include ATP synthesis, glycolysis, energy metabolism, and metabolic pathways.\\n\\nMechanism: \\nThe underlying biological mechanisms involve ATP synthesis by way of glycolysis and energy metabolism pathways, which produce necessary energy required for a variety of cellular activities.\\n\\n] | \n", + "0.85 | \n", + "28 | \n", + "
| 683 | \n", + "\n", + " | RANDOM | \n", + "glycolysis-gocam-1 | \n", + "[ The human genes provided in this list are enriched for metabolic functions involved in glycolysis and pentose phosphate pathways.\\nMechanism: The mechanism likely involves the direct or indirect control of enzymatic activities through the coordinated activity of multiple genes.\\n] | \n", + "[ The genes identified are related to glycolysis, the metabolic pathway that produces ATP from glucose and other carbohydrates. \\nMechanism: Glycolysis involves the series pathways in which a compound molecule of glucose is broken down into two molecules of pyruvic acid, which are further converted into ATP. \\n] | \n", + "0.89 | \n", + "30 | \n", + "
| 684 | \n", + "\n", + " | RANDOM | \n", + "go-postsynapse-calcium-transmembrane-0 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE] | \n", + "0.89 | \n", + "0 | \n", + "
| 685 | \n", + "\n", + " | RANDOM | \n", + "go-postsynapse-calcium-transmembrane-1 | \n", + "[COULD NOT PARSE] | \n", + "[\\nSummary: This gene set is primarily involved in neuronal functional regulation, including ion transport, membrane potential regulation and neurotransmission.\\nMechanism: These genes are involved in the regulation of neuronal activity, likely through the regulation of a number of ion channels, neurotransmitter receptors, and calcium/potassium regulators.\\n] | \n", + "0.83 | \n", + "341 | \n", + "
| 686 | \n", + "\n", + " | RANDOM | \n", + "go-reg-autophagy-pkra-0 | \n", + "[\\n \\nSummary: The genes in this list are involved in various aspects of biological processes, ranging from cell growth and development to immune response and proteolysis.\\n \\nMechanism: The genes interact in multiple overlapping pathways to influence cellular processes such as immune response and protein degradation. \\n \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.82 | \n", + "303 | \n", + "
| 687 | \n", + "\n", + " | RANDOM | \n", + "go-reg-autophagy-pkra-1 | \n", + "[ Several pathways related to cellular signaling and signalling transduction are enriched among this set of human genes. Specifically, phosphatidylinositol signalling, vascular endothelial growth factor receptor signalling, progesterone-mediated oocyte maturation, NF-kB signaling and neuroprotection are all enriched with five or more genes represented in the set, suggesting that the underlying biological mechanism could be related to these pathways.\\n\\nMechanism: Several pathways related to cellular signaling and signalling transduction.\\n\\n] | \n", + "[\\nThe genes provided are all involved in cell regulation and signaling pathways. Specifically, they all have roles in the activation of transcription factors, and in the activation, regulation and inhibition of signaling proteins such as Ras, Akt and calcium associated kinases.\\nMechanism: \\nThe genes all act together in order to affect the expression of various genes and proteins. They function by either upregulating or downregulating the expression of transcription factors and signaling proteins, as well as by modulating the phosphorylation state of these proteins, thus controlling their activity.\\n] | \n", + "0.85 | \n", + "62 | \n", + "
| 688 | \n", + "\n", + " | RANDOM | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-0 | \n", + "[ These human genes are involved in cellular functions related to glycosaminoglycan metabolism, lysosomal and catabolic pathways, as well as digit and skeletal development. The genes are enriched for functions in carbohydrate digestion and absorption; glycosaminoglycan and glycan metabolism; lysosomal, peroxisomal, and catabolic processes; and digit, skeletal, and limb morphogenesis. \\nMechanism: The genes likely act by providing enzymes, carriers, and structural proteins that together play essential roles in the transport and metabolism of carbohydrates, as well as help form and shape the skeleton and digits during embryonic development. \\n] | \n", + "[ These genes are apparently associated with lysozymes, mucins, glycosyltransferases, and hyaluronidases, enzymes and proteins with roles in the breakdown and regulation of glycosylation.\\nMechanism: The mechanism behind this gene cluster's biological role seems to be in the regulation of cell processes related to glycosylation, such as enzyme production and its breakdown.\\n] | \n", + "0.88 | \n", + "272 | \n", + "
| 689 | \n", + "\n", + " | RANDOM | \n", + "hydrolase activity, hydrolyzing O-glycosyl compounds-1 | \n", + "[ The human genes in this list are mostly related to glycoside hydrolase (GH) activity, but also include proteins involved in chitin and mucin biosynthesis, as well as cysteine protease and lysosomal activities. Most of the genes have either a glycoside hydrolase activator or a lysosomal enzyme function. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.83 | \n", + "291 | \n", + "
| 690 | \n", + "\n", + " | RANDOM | \n", + "ig-receptor-binding-2022-0 | \n", + "[COULD NOT PARSE] | \n", + "[\\nSummary: The genetic pathways enriched in these genes involves immunoglobulin heavy/light chain combination, antigen specific receptors, J-chain, and T-lymphocyte receptors. \\nMechanism: These genes mainly play a role in immune response, specifically the regulation of the combination of immunoglobulin heavy and light chains to form antigen-specific receptors, the formation of J-chain, the production of T-lymphocyte receptors, and the regulation of immune function.\\n] | \n", + "0.80 | \n", + "454 | \n", + "
| 691 | \n", + "\n", + " | RANDOM | \n", + "ig-receptor-binding-2022-1 | \n", + "[\\nSummary: These genes are mainly involved in Immunoglobulin Function and Blood Coagulation. \\nMechanism: The terms enriched for these genes are related to the immune system and blood clotting pathways, specifically those related to Immunoglobulins, B Cell Receptors, and Fibrinogen-related proteins. \\n] | \n", + "[COULD NOT PARSE] | \n", + "0.88 | \n", + "285 | \n", + "
| 692 | \n", + "\n", + " | RANDOM | \n", + "meiosis I-0 | \n", + "[ \\nSummary: Genes involved in DNA damage repair and meiotic recombination processes\\nMechanism: Genes in the list are involved in DNA damage recognition, DNA double-strand break repair, meiotic recombination, and chromosome segregation.\\n] | \n", + "[ This list of genes is enriched for functions related to DNA replication, repair, and replication fidelity. Mechanism: The list of genes is likely to be involved in simulating DNA synthesis, prioritizing DNA strands for replication, ensuring proper repair of damaged DNA strands, and ensuring that high-fidelity replication is taking place during the cell cycle. ] | \n", + "0.83 | \n", + "128 | \n", + "
| 693 | \n", + "\n", + " | RANDOM | \n", + "meiosis I-1 | \n", + "[ Enrichment test revealed that genes are related to DNA repair, replication, and splicing.\\n\\nMechanism: The commonalities in the function of the genes revealed in the enrichment test suggest that there may be a biological pathway that is responsible for creating and maintaining a stable genetic system. This may involve DNA repair to combat mutation and damage, replication to create new copies, and splicing for the proper expression of genes.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.84 | \n", + "431 | \n", + "
| 694 | \n", + "\n", + " | RANDOM | \n", + "molecular sequestering-0 | \n", + "[ This enrichment test indicates that the listed genes are involved in multiple pathways that are involved in cell proliferation, apoptosis, and molecular transport in diverse cell types. Specifically, some of the enriched terms associated with these genes include mechanisms involved in cell cycle checkpoints, cell adhesion/motility complexes, transcriptional complexes, protein modifications, and RNA processing complexes. \\nMechanism: These pathways likely affect cell proliferation, apoptosis, and molecular transport by responding to a variety of environmental stimuli, including calcium-based signaling, growth factor-mediated signaling, and oxidative stress. \\n] | \n", + "[ 17 of the genes in the list are related to functions involving calcium homeostasis, including calcium signaling, regulation of calcification, and regulation of calcium ion transport. Mechanism: The genes identified are involved in the regulation of calcium homeostasis and signaling, along with functions related to calcification, calcium buffering and transport, protection against calcium overload, and calcium-v influx/efflux. ] | \n", + "0.79 | \n", + "235 | \n", + "
| 695 | \n", + "\n", + " | RANDOM | \n", + "molecular sequestering-1 | \n", + "[ The analysed genes are mostly involved in calcium binding, apoptotic regulation, and immune modulation, all of which are important mechanisms for a variety of biologic processes.\\n\\nMechanism: The mechanism is likely related to the genes' ability to modulate calcium and apoptotic pathways as well as reduce oxidative stress and influence immune effectors.\\n\\n] | \n", + "[\\nSummary: Our list of human genes suggests pathways involved in cell structure regulation and metabolism.\\nMechanism: These genes are likely involved in the regulation of cell morphology, metabolic processes and apoptosis.\\n] | \n", + "0.84 | \n", + "135 | \n", + "
| 696 | \n", + "\n", + " | RANDOM | \n", + "mtorc1-0 | \n", + "[COULD NOT PARSE] | \n", + "[COULD NOT PARSE] | \n", + "0.85 | \n", + "0 | \n", + "
| 697 | \n", + "\n", + " | RANDOM | \n", + "mtorc1-1 | \n", + "[ Analysis of the genes provided shows that the genes are enriched for functions relating to energy production and metabolism, protein biosynthesis and folds, cell regulation, growth and development, and protein turnover. \\n\\nMechanism: The likely underlying biological mechanism behind these functions is likely related to the regulation, management and production of energy and metabolites to carry out processes such as cell growth and to synthesize proteins which are essential for the functioning of the cell, cell signaling and related pathway activities.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.78 | \n", + "545 | \n", + "
| 698 | \n", + "\n", + " | RANDOM | \n", + "peroxisome-0 | \n", + "[ PEX proteins are involved in peroxisome biogenesis and formation. \\nMechanism: PEX proteins play a role in driving the biogenesis of peroxisomes, a type of organelle that plays a role in various metabolic functions. \\n] | \n", + "[\\nThis list of genes is enriched for terms related to protein homeostasis and peroxisome biogenesis. The genes are likely to have roles in maintaining and regulating the levels of specific proteins, as well as helping to form and breakdown peroxisomes in the cell.\\n\\nMechanism: The mechanism underlying these functions appears to involve forming, maintaining and regulating the levels of specific proteins, as well as assisting in the formation and breakdown of peroxisomes in the cell. \\n\\n] | \n", + "0.87 | \n", + "270 | \n", + "
| 699 | \n", + "\n", + " | RANDOM | \n", + "peroxisome-1 | \n", + "[ The provided genes are all peroxisomal biogenesis factor genes and are associated with peroxisomal biogenesis, protein transport, and oxidative damage resistance.\\n\\nMechanism: These factors regulate the assembly of the peroxisome, a subcellular organelle involved in fatty acid metabolism, carbohydrate metabolism, and oxidative damage resistance.\\n\\n] | \n", + "[ The genes provided are all related to Peroxisomal Biogenesis, an important cellular process. \\nMechanism: Peroxisomal biogenesis requires the coordinated expression of multiple genes in order for the peroxisome to be expressed and maintained in cells. \\n] | \n", + "0.83 | \n", + "96 | \n", + "
| 700 | \n", + "\n", + " | RANDOM | \n", + "progeria-0 | \n", + "[ The genes in this list are all associated with a cellular carboxyl-methyl transferases, a type of protein involved in RNA and DNA metabolism. The proteins are associated with development and growth, particularly that of cell structural elements such as gene transcription and transcriptional regulation. \\nMechanism: The mechanism involves carboxyl-methyl transferase proteins that modulate gene expression and the communication between transcription factors and the DNA strand.\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.87 | \n", + "464 | \n", + "
| 701 | \n", + "\n", + " | RANDOM | \n", + "progeria-1 | \n", + "[ These genes are involved in a number of processes related to DNA replication and repair, including DNA replication and repair, nucleosome assembly, telomere maintenance, and transcriptional regulation.\\n \\nMechanism: Genes LMNA, WRN, and BANF1 are all involved in several mechanism related to the general processes of DNA replication, repair, and transcriptional regulation through the assembly and maintenance of the different levels of chromatin structure. LMNA is involved in the assembly and disassembly of the nuclear lamina, a type of intermediate filament that helps to anchor chromosomal proteins to the nuclear envelope. WRN is involved in telomere maintenance, which is critical for accurate chromosomal replication and stability. Finally, BANF1 is involved in a number of DNA repair processes, including translesion DNA synthesis, homologous recombination, and non-homologous end joining. These processes are essential for the accurate repair and replication of DNA molecules, and all require an understanding of, and proper interactions between, transcription and chromatin structure. \\n\\n] | \n", + "[ Shortly, these genes are involved in a range of functions including transcriptional regulation, DNA repair, cell cycle regulation, and cell differentiation. \\nMechanism: These genes all have common functions related to the transcription, repair, and/or regulation of DNA, which suggests that they all play a role in the response to cellular damage or stress, which in turn can influence the downstream processes of cell cycle, differentiation, and growth.\\n] | \n", + "0.78 | \n", + "642 | \n", + "
| 702 | \n", + "\n", + " | RANDOM | \n", + "regulation of presynaptic membrane potential-0 | \n", + "[\\n\\nSummary: This term enrichment test identified genes involved in signal transduction, ion transport, and regulation of neurotransmitter release.\\nMechanism: This is likely related to the regulation of excitatory and inhibitory signal transmission, potentially mediated by ion channels and signal transduction pathways associated with the G-protein coupled receptors, voltage-gated K+ and Na+ channels, and ligand-gated ion channels.\\n] | \n", + "[ Through a term enrichment test on this list of genes, we see that they are over-represented in terms related to ion conductivity and neural excitability, including ion channels, membrane proteins, and synapse formation.\\n\\nMechanism: These genes likely play a role in neural excitability, leading to the formation of specific ion channels that can conduct ions and help form synapses between neurons.\\n\\n] | \n", + "0.86 | \n", + "32 | \n", + "
| 703 | \n", + "\n", + " | RANDOM | \n", + "regulation of presynaptic membrane potential-1 | \n", + "[COULD NOT PARSE] | \n", + "[ This group of genes is enriched for terms related to ion-channel function, neuron excitability, and synaptic transmission.\\nMechanism: This group of genes suggested the underlying molecular pathway involves communication between neurons via ion-channel mediated synaptic transmission.\\n] | \n", + "0.88 | \n", + "270 | \n", + "
| 704 | \n", + "\n", + " | RANDOM | \n", + "sensory ataxia-0 | \n", + "[ This list of genes is related to muscle, central and peripheral nervous system development, as well as protein and lipid transport and metabolism. \\nMechanism: The genes appear to be involved in regulatory pathways for growth and development of the skeletal and nervous systems via coordination of morphology, protein and lipid synthesis, and transport.\\n] | \n", + "[ These genes are mainly involved in protein synthesis, metabolism, ion channel transport, and muscle contraction or development.\\n\\nMechanism: These genes function as transcriptional regulators, enzymes in metabolic pathways, ion channels, or as key mediators of neuromuscular development and contraction.\\n\\n] | \n", + "0.87 | \n", + "49 | \n", + "
| 705 | \n", + "\n", + " | RANDOM | \n", + "sensory ataxia-1 | \n", + "[\\n\\nSummary: Analysis of the genes yielded significant enrichment of terms related to protein transport, development of the central nervous system, skeletal structure and muscle formation.\\n\\nMechanism: The function of these genes likely reflects the underlying biological pathways for the development and maintenance of different organ systems, including the central nervous system, muscular system, and skeletal structure. \\n\\n] | \n", + "[ This list of genes encodes many proteins which are involved in nucleic acid metabolism, binding, and transport. Terms enriched in these genes include: Nucleic Acid Metabolism; Nucleic Acid Binding; Nucleic Acid Transport; Protein Metabolism; Protein Binding; and Protein Transport.\\n\\nMechanism: The proteins encoded by these genes are likely to be involved in nucleic acid metabolism and other related downstream processes. These proteins are likely involved in mRNA transcription, mRNA processing and/or mRNA translation. The proteins could also be involved in processes like RNA editing, DNA replication, DNA repair, and DNA recombination. These proteins are likely to be involved in the regulation of gene expression and other pathways related to this process.\\n\\n] | \n", + "0.84 | \n", + "342 | \n", + "
| 706 | \n", + "\n", + " | RANDOM | \n", + "term-GO:0007212-0 | \n", + "[ This list of genes is enriched for terms related to signal transmission and transduction, specifically the G Protein-Coupled Receptor (GPCR) family, which is associated with cell-signaling pathways and regulation of receptor activities. The specific terms enriched include G alpha subunit signaling, related GPCR activation and signaling, G Protein-Coupled Receptor (GPCR) function, and dimerization. \\n\\nMechanism: This set of genes is involved in pathways that involve the G protein-coupled receptor (GPCR) family. GPCRs can bind to extracellular molecules, such as hormones and neurotransmitters, and then activate signaling pathways inside the cell, leading to the activation of intracellular proteins, including G proteins. The G proteins then facilitate the exchange of proteins such as cAMP, DAG, and calcium ions into the cell, in order to create a signal cascade and ultimately effect changes to the cell’s behavior.\\n\\n] | \n", + "[ This gene list is enriched for terms related to G-Protein Coupled Receptors (GPCRs), G-protein subunits, adenylate cyclase, calcium channels, and kinases.\\n\\nMechanism: The GPCRs and G protein-coupled subunits are involved in signal transduction pathways that regulate a variety of cellular activities. They activate adenylate cyclases, which catalyze the synthesis of the secondary messenger cAMP. This acts downstream to activate pathways and processes such as G-protein mediated second messenger systems and cation channels. Kinases are involved in the regulation of the G-protein by phosphorylating the Gα subunits and other associated components, leading to changes in their activity, and ultimately, signaling cascades.\\n\\n] | \n", + "0.87 | \n", + "200 | \n", + "
| 707 | \n", + "\n", + " | RANDOM | \n", + "term-GO:0007212-1 | \n", + "[\\nSummary: The list of genes is involved in the regulation cellular signaling and development of the nervous system.\\nMechanism: The list of genes is likely transmitting signals through G proteins, phosphorylation cascade, and calcium signaling pathways to regulate the development of the nervous system, including alterations in the nervous system structure, indoleamine metabolism, and neurotransmission.\\n] | \n", + "[\\n\\nSummary: The enriched terms from these genes suggest a correlation with signaling pathways, cellular growth and differentiation, organization of the cytoskeleton, regulation of endocrine systems, and transcriptional regulation. \\n\\n] | \n", + "0.85 | \n", + "173 | \n", + "
| 708 | \n", + "\n", + " | RANDOM | \n", + "tf-downreg-colorectal-0 | \n", + "[ The gene list includes members of the nuclear receptor superfamily, molecules involved in transcription regulation, epigenetic regulation, cell cycle regulation, DNA binding and chromatin remodeling, developmental processes and cell signaling pathways, and components of the nuclear lamina and nuclear matrix.\\n\\nMechanism: The enriched terms suggest a molecular pathway underlying gene regulation, where transcription factors and chromatin reorganization molecules interact with nuclear receptors and other molecular mechanisms in order to regulate gene expression. Moreover, the gene list may represent a mechanism involved in the regulation of cell growth, differentiation and development.\\n\\n] | \n", + "[COULD NOT PARSE] | \n", + "0.82 | \n", + "678 | \n", + "
| 709 | \n", + "\n", + " | RANDOM | \n", + "tf-downreg-colorectal-1 | \n", + "[ The genes provided are involved in developmental pathways and functions, such as transcriptional regulation, chromatin modification, morphogenesis, cardiovascular development and differentiation.\\nMechanism: These genes are associated with a wide range of cellular processes, primarily related to embryonic development, including fetal growth and development, stem cell differentiation, and postnatal growth. \\n] | \n", + "[ The enriched terms for this list of genes are cellular growth, transcriptional regulation, and chromatin remodeling. These genes are generally involved in the regulation of transcription, chromatin modifications, and cell cycle regulation. These terms are statistically over-represented compared to the gene list provided.\\n\\nMechanism: The likely underlying biological mechanism for these genes is that they are involved in multiple pathways like transcription, chromatin modifications, and cell cycle regulation. These pathways control essential processes such as cell growth and differentiation in the body. Through these mechanisms, the genes may help to regulate embryonic development and maintain tissue homeostasis in adults. \\n\\n] | \n", + "0.92 | \n", + "324 | \n", + "
| \n", + " | \n", + " | count | \n", + "mean | \n", + "std | \n", + "min | \n", + "max | \n", + "
|---|---|---|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " | \n", + " | \n", + " | \n", + " |
| \n", + " | RANDOM | \n", + "142.000 | \n", + "0.824 | \n", + "0.064 | \n", + "0.665 | \n", + "0.925 | \n", + "
| gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "142.000 | \n", + "0.909 | \n", + "0.039 | \n", + "0.677 | \n", + "0.977 | \n", + "
| no_synopsis | \n", + "142.000 | \n", + "0.911 | \n", + "0.033 | \n", + "0.807 | \n", + "0.966 | \n", + "|
| ontological_synopsis | \n", + "142.000 | \n", + "0.917 | \n", + "0.032 | \n", + "0.803 | \n", + "0.976 | \n", + "|
| text-davinci-003 | \n", + "narrative_synopsis | \n", + "142.000 | \n", + "0.877 | \n", + "0.087 | \n", + "0.670 | \n", + "1.000 | \n", + "
| no_synopsis | \n", + "142.000 | \n", + "0.830 | \n", + "0.108 | \n", + "0.663 | \n", + "1.000 | \n", + "|
| ontological_synopsis | \n", + "142.000 | \n", + "0.868 | \n", + "0.093 | \n", + "0.676 | \n", + "0.957 | \n", + "
| \n", + " | \n", + " | count | \n", + "mean | \n", + "std | \n", + "min | \n", + "max | \n", + "
|---|---|---|---|---|---|---|
| model | \n", + "method | \n", + "\n", + " | \n", + " | \n", + " | \n", + " | \n", + " |
| gpt-3.5-turbo | \n", + "narrative_synopsis | \n", + "142.000 | \n", + "250.000 | \n", + "197.720 | \n", + "0.000 | \n", + "743.000 | \n", + "
| no_synopsis | \n", + "142.000 | \n", + "292.690 | \n", + "213.086 | \n", + "3.000 | \n", + "962.000 | \n", + "|
| ontological_synopsis | \n", + "142.000 | \n", + "192.803 | \n", + "177.135 | \n", + "2.000 | \n", + "832.000 | \n", + "|
| text-davinci-003 | \n", + "narrative_synopsis | \n", + "142.000 | \n", + "312.120 | \n", + "250.861 | \n", + "0.000 | \n", + "1257.000 | \n", + "
| no_synopsis | \n", + "142.000 | \n", + "298.479 | \n", + "251.715 | \n", + "0.000 | \n", + "1122.000 | \n", + "|
| ontological_synopsis | \n", + "142.000 | \n", + "330.331 | \n", + "264.180 | \n", + "0.000 | \n", + "1137.000 | \n", + "
| \n", + " | NAME | \n", + "narrative_synopsis | \n", + "no_synopsis | \n", + "ontological_synopsis | \n", + "
|---|---|---|---|---|
| 0 | \n", + "regulation of collagen metabolic process | \n", + "[EDS] | \n", + "NaN | \n", + "NaN | \n", + "
| 1 | \n", + "post-translational protein modification | \n", + "[EDS] | \n", + "NaN | \n", + "NaN | \n", + "
| 2 | \n", + "protein folding | \n", + "[EDS-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 3 | \n", + "positive regulation of fatty acid beta-oxidation | \n", + "NaN | \n", + "[HALLMARK_ADIPOGENESIS] | \n", + "NaN | \n", + "
| 4 | \n", + "obsolete electron transport | \n", + "[HALLMARK_FATTY_ACID_METABOLISM] | \n", + "NaN | \n", + "[HALLMARK_OXIDATIVE_PHOSPHORYLATION-1] | \n", + "
| 5 | \n", + "cell growth | \n", + "[HALLMARK_ADIPOGENESIS-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 6 | \n", + "obsolete transcription factor activity, protein binding | \n", + "[tf-downreg-colorectal] | \n", + "[tf-downreg-colorectal-1] | \n", + "[tf-downreg-colorectal-1] | \n", + "
| 7 | \n", + "interleukin-2 production | \n", + "[HALLMARK_ALLOGRAFT_REJECTION] | \n", + "NaN | \n", + "NaN | \n", + "
| 8 | \n", + "type II interferon production | \n", + "[HALLMARK_ALLOGRAFT_REJECTION] | \n", + "NaN | \n", + "NaN | \n", + "
| 9 | \n", + "regulation of protein stability | \n", + "NaN | \n", + "[HALLMARK_ANDROGEN_RESPONSE] | \n", + "NaN | \n", + "
| 10 | \n", + "platelet degranulation | \n", + "[amigo-example] | \n", + "[HALLMARK_ANGIOGENESIS] | \n", + "NaN | \n", + "
| 11 | \n", + "regulation of bone development | \n", + "NaN | \n", + "[HALLMARK_ANGIOGENESIS] | \n", + "NaN | \n", + "
| 12 | \n", + "proteoglycan metabolic process | \n", + "[amigo-example-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 13 | \n", + "regulation of transforming growth factor beta receptor signaling pathway | \n", + "NaN | \n", + "[HALLMARK_ANGIOGENESIS-1] | \n", + "NaN | \n", + "
| 14 | \n", + "regulation of mitotic nuclear division | \n", + "[HALLMARK_ANGIOGENESIS-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 15 | \n", + "obsolete calcium-dependent cell adhesion molecule activity | \n", + "[HALLMARK_APICAL_JUNCTION-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 16 | \n", + "regulation of signal transduction by p53 class mediator | \n", + "[HALLMARK_APICAL_SURFACE] | \n", + "NaN | \n", + "NaN | \n", + "
| 17 | \n", + "modulation by virus of host process | \n", + "[HALLMARK_APICAL_SURFACE] | \n", + "NaN | \n", + "NaN | \n", + "
| 18 | \n", + "regulation of glucose metabolic process | \n", + "NaN | \n", + "[HALLMARK_APICAL_SURFACE-1] | \n", + "NaN | \n", + "
| 19 | \n", + "protein kinase C signaling | \n", + "NaN | \n", + "[HALLMARK_APICAL_SURFACE-1] | \n", + "NaN | \n", + "
| 20 | \n", + "positive regulation of MAP kinase activity | \n", + "NaN | \n", + "[HALLMARK_APICAL_SURFACE-1] | \n", + "NaN | \n", + "
| 21 | \n", + "regulation of B cell receptor signaling pathway | \n", + "NaN | \n", + "[HALLMARK_APOPTOSIS] | \n", + "NaN | \n", + "
| 22 | \n", + "obsolete cytochrome P450 | \n", + "[HALLMARK_BILE_ACID_METABOLISM-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 23 | \n", + "obsolete cell surface binding | \n", + "NaN | \n", + "[HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION] | \n", + "NaN | \n", + "
| 24 | \n", + "calcium-dependent protein kinase activity | \n", + "NaN | \n", + "[HALLMARK_ESTROGEN_RESPONSE_EARLY] | \n", + "NaN | \n", + "
| 25 | \n", + "calcium-dependent ATPase activity | \n", + "NaN | \n", + "[HALLMARK_ESTROGEN_RESPONSE_EARLY] | \n", + "NaN | \n", + "
| 26 | \n", + "acetyl-CoA catabolic process | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_FATTY_ACID_METABOLISM] | \n", + "
| 27 | \n", + "coenzyme A metabolic process | \n", + "[HALLMARK_FATTY_ACID_METABOLISM-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 28 | \n", + "UDP-D-galactose metabolic process | \n", + "[HALLMARK_GLYCOLYSIS] | \n", + "NaN | \n", + "NaN | \n", + "
| 29 | \n", + "glucose transmembrane transport | \n", + "[HALLMARK_GLYCOLYSIS-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 30 | \n", + "UDP-galactose biosynthetic process | \n", + "[HALLMARK_GLYCOLYSIS-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 31 | \n", + "regulation of protein homodimerization activity | \n", + "NaN | \n", + "[HALLMARK_HEME_METABOLISM-1] | \n", + "NaN | \n", + "
| 32 | \n", + "regulation of response to reactive oxygen species | \n", + "NaN | \n", + "[HALLMARK_HYPOXIA] | \n", + "NaN | \n", + "
| 33 | \n", + "cellular response to interferon-alpha | \n", + "NaN | \n", + "[HALLMARK_INTERFERON_ALPHA_RESPONSE-1] | \n", + "NaN | \n", + "
| 34 | \n", + "antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent | \n", + "NaN | \n", + "[HALLMARK_INTERFERON_GAMMA_RESPONSE] | \n", + "NaN | \n", + "
| 35 | \n", + "P-type calcium transporter activity | \n", + "[HALLMARK_KRAS_SIGNALING_DN] | \n", + "NaN | \n", + "NaN | \n", + "
| 36 | \n", + "obsolete membrane part | \n", + "[HALLMARK_KRAS_SIGNALING_UP] | \n", + "NaN | \n", + "NaN | \n", + "
| 37 | \n", + "RNA splicing, via endonucleolytic cleavage and ligation | \n", + "[HALLMARK_MYC_TARGETS_V1] | \n", + "[HALLMARK_MYC_TARGETS_V2-1] | \n", + "[HALLMARK_MYC_TARGETS_V1-1] | \n", + "
| 38 | \n", + "spliceosomal complex | \n", + "NaN | \n", + "[HALLMARK_MYC_TARGETS_V2] | \n", + "NaN | \n", + "
| 39 | \n", + "translational initiation | \n", + "NaN | \n", + "[HALLMARK_MYC_TARGETS_V2] | \n", + "NaN | \n", + "
| 40 | \n", + "muscle thin filament assembly | \n", + "NaN | \n", + "[HALLMARK_MYOGENESIS] | \n", + "NaN | \n", + "
| 41 | \n", + "chemical synaptic transmission | \n", + "NaN | \n", + "[HALLMARK_NOTCH_SIGNALING] | \n", + "NaN | \n", + "
| 42 | \n", + "obsolete transcription activator activity | \n", + "[HALLMARK_NOTCH_SIGNALING] | \n", + "NaN | \n", + "[HALLMARK_UV_RESPONSE_DN-1] | \n", + "
| 43 | \n", + "cysteine-type endopeptidase activity involved in apoptotic process | \n", + "[HALLMARK_NOTCH_SIGNALING] | \n", + "NaN | \n", + "NaN | \n", + "
| 44 | \n", + "obsolete hydrogen-translocating F-type ATPase activity | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_OXIDATIVE_PHOSPHORYLATION-1] | \n", + "
| 45 | \n", + "peroxisome proliferator activated receptor signaling pathway | \n", + "NaN | \n", + "[HALLMARK_PEROXISOME] | \n", + "NaN | \n", + "
| 46 | \n", + "11-cis retinal binding | \n", + "[HALLMARK_PEROXISOME] | \n", + "NaN | \n", + "NaN | \n", + "
| 47 | \n", + "negative regulation of receptor internalization | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_PROTEIN_SECRETION] | \n", + "
| 48 | \n", + "obsolete vesicle transport | \n", + "[HALLMARK_PROTEIN_SECRETION] | \n", + "NaN | \n", + "NaN | \n", + "
| 49 | \n", + "protein targeting to membrane | \n", + "NaN | \n", + "[HALLMARK_PROTEIN_SECRETION-1] | \n", + "NaN | \n", + "
| 50 | \n", + "negative regulation of reactive oxygen species metabolic process | \n", + "NaN | \n", + "[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1] | \n", + "NaN | \n", + "
| 51 | \n", + "regulation of DNA repair | \n", + "NaN | \n", + "[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1] | \n", + "NaN | \n", + "
| 52 | \n", + "positive regulation of protein binding | \n", + "NaN | \n", + "[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1] | \n", + "NaN | \n", + "
| 53 | \n", + "regulation of kinetochore assembly | \n", + "NaN | \n", + "[HALLMARK_SPERMATOGENESIS-1] | \n", + "NaN | \n", + "
| 54 | \n", + "positive regulation of mitotic spindle organization | \n", + "NaN | \n", + "[HALLMARK_SPERMATOGENESIS-1] | \n", + "NaN | \n", + "
| 55 | \n", + "glycoprotein transport | \n", + "[HALLMARK_TGF_BETA_SIGNALING-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 56 | \n", + "None | \n", + "NaN | \n", + "[HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1] | \n", + "NaN | \n", + "
| 57 | \n", + "MAP kinase activity | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_TNFA_SIGNALING_VIA_NFKB-1] | \n", + "
| 58 | \n", + "chemokine production | \n", + "[HALLMARK_TNFA_SIGNALING_VIA_NFKB-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 59 | \n", + "regulation of phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands | \n", + "NaN | \n", + "[HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1] | \n", + "NaN | \n", + "
| 60 | \n", + "protein localization to plasma membrane | \n", + "NaN | \n", + "[HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1] | \n", + "NaN | \n", + "
| 61 | \n", + "negative regulation of protein ubiquitination | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_WNT_BETA_CATENIN_SIGNALING-1] | \n", + "
| 62 | \n", + "obsolete lectin | \n", + "[T cell proliferation] | \n", + "NaN | \n", + "NaN | \n", + "
| 63 | \n", + "COP9 signalosome | \n", + "[T cell proliferation] | \n", + "NaN | \n", + "NaN | \n", + "
| 64 | \n", + "cell population proliferation | \n", + "NaN | \n", + "[Yamanaka-TFs] | \n", + "NaN | \n", + "
| 65 | \n", + "stem cell differentiation | \n", + "[Yamanaka-TFs-1] | \n", + "[Yamanaka-TFs-1] | \n", + "NaN | \n", + "
| 66 | \n", + "obsolete lipoprotein binding | \n", + "NaN | \n", + "NaN | \n", + "[amigo-example] | \n", + "
| 67 | \n", + "obsolete collagen | \n", + "[amigo-example] | \n", + "NaN | \n", + "NaN | \n", + "
| 68 | \n", + "keratan sulfate metabolic process | \n", + "[amigo-example-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 69 | \n", + "tissue regeneration | \n", + "[amigo-example-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 70 | \n", + "regulation of muscle filament sliding speed | \n", + "[bicluster_RNAseqDB_1002] | \n", + "NaN | \n", + "NaN | \n", + "
| 71 | \n", + "positive regulation of phosphoprotein phosphatase activity | \n", + "[bicluster_RNAseqDB_1002] | \n", + "NaN | \n", + "NaN | \n", + "
| 72 | \n", + "energy homeostasis | \n", + "[bicluster_RNAseqDB_1002-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 73 | \n", + "regulation of neurotransmitter secretion | \n", + "NaN | \n", + "[go-postsynapse-calcium-transmembrane-1] | \n", + "NaN | \n", + "
| 74 | \n", + "G protein-coupled neurotransmitter receptor activity | \n", + "NaN | \n", + "[term-GO:0007212-1] | \n", + "NaN | \n", + "
| 75 | \n", + "regulation of cytosolic calcium ion concentration | \n", + "NaN | \n", + "NaN | \n", + "[term-GO:0007212-1] | \n", + "
| 76 | \n", + "second-messenger-mediated signaling | \n", + "[term-GO:0007212-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 77 | \n", + "bone development | \n", + "[endocytosis] | \n", + "NaN | \n", + "NaN | \n", + "
| 78 | \n", + "protein localization to endosome | \n", + "NaN | \n", + "[endocytosis-1] | \n", + "NaN | \n", + "
| 79 | \n", + "protein kinase activity | \n", + "NaN | \n", + "[go-postsynapse-calcium-transmembrane-1] | \n", + "NaN | \n", + "
| 80 | \n", + "O-glycan processing | \n", + "NaN | \n", + "[hydrolase activity, hydrolyzing O-glycosyl compounds] | \n", + "NaN | \n", + "
| 81 | \n", + "glycolytic process | \n", + "NaN | \n", + "[hydrolase activity, hydrolyzing O-glycosyl compounds-1] | \n", + "NaN | \n", + "
| 82 | \n", + "immunoglobulin production | \n", + "NaN | \n", + "[ig-receptor-binding-2022-1] | \n", + "[ig-receptor-binding-2022-1] | \n", + "
| 83 | \n", + "B cell activation | \n", + "NaN | \n", + "[ig-receptor-binding-2022-1] | \n", + "NaN | \n", + "
| 84 | \n", + "positive regulation of humoral immune response | \n", + "[ig-receptor-binding-2022] | \n", + "NaN | \n", + "NaN | \n", + "
| 85 | \n", + "germ cell proliferation | \n", + "NaN | \n", + "[meiosis I] | \n", + "NaN | \n", + "
| 86 | \n", + "obsolete iron ion homeostasis | \n", + "NaN | \n", + "[molecular sequestering-1] | \n", + "NaN | \n", + "
| 87 | \n", + "protein stabilization | \n", + "NaN | \n", + "[molecular sequestering-1] | \n", + "NaN | \n", + "
| 88 | \n", + "RNA splicing | \n", + "NaN | \n", + "NaN | \n", + "[mtorc1-1] | \n", + "
| 89 | \n", + "protein import | \n", + "[peroxisome-1] | \n", + "NaN | \n", + "[peroxisome-1] | \n", + "
| 90 | \n", + "peroxisome fission | \n", + "NaN | \n", + "[peroxisome-1] | \n", + "NaN | \n", + "
| 91 | \n", + "obsolete aging | \n", + "NaN | \n", + "[progeria] | \n", + "[progeria-1] | \n", + "
| 92 | \n", + "protein homodimerization activity | \n", + "NaN | \n", + "[regulation of presynaptic membrane potential-1] | \n", + "NaN | \n", + "
| 93 | \n", + "obsolete covalent chromatin modification | \n", + "NaN | \n", + "[tf-downreg-colorectal] | \n", + "NaN | \n", + "
| 94 | \n", + "obsolete RNA polymerase II transcription factor activity | \n", + "NaN | \n", + "NaN | \n", + "[tf-downreg-colorectal-1] | \n", + "
| \n", + " | NAME | \n", + "narrative_synopsis | \n", + "ontological_synopsis | \n", + "no_synopsis | \n", + "
|---|---|---|---|---|
| 0 | \n", + "obsolete Gly-X carboxypeptidase activity | \n", + "[EDS-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 1 | \n", + "phosphorylation | \n", + "[FA] | \n", + "NaN | \n", + "NaN | \n", + "
| 2 | \n", + "Holliday junction resolvase complex | \n", + "NaN | \n", + "[FA-1] | \n", + "NaN | \n", + "
| 3 | \n", + "double-stranded telomeric DNA binding | \n", + "NaN | \n", + "[FA-1] | \n", + "NaN | \n", + "
| 4 | \n", + "histone acetylation | \n", + "NaN | \n", + "[FA-1] | \n", + "NaN | \n", + "
| 5 | \n", + "protein tag | \n", + "NaN | \n", + "[FA-1] | \n", + "NaN | \n", + "
| 6 | \n", + "cysteine-type endopeptidase inhibitor activity | \n", + "NaN | \n", + "[HALLMARK_TGF_BETA_SIGNALING-1] | \n", + "NaN | \n", + "
| 7 | \n", + "obsolete electron transport | \n", + "[HALLMARK_OXIDATIVE_PHOSPHORYLATION-1] | \n", + "[HALLMARK_OXIDATIVE_PHOSPHORYLATION] | \n", + "NaN | \n", + "
| 8 | \n", + "cytosolic transport | \n", + "[HALLMARK_ADIPOGENESIS] | \n", + "NaN | \n", + "NaN | \n", + "
| 9 | \n", + "endopeptidase activity | \n", + "NaN | \n", + "[HALLMARK_ADIPOGENESIS-1] | \n", + "NaN | \n", + "
| 10 | \n", + "phosphatidylserine decarboxylase activity | \n", + "NaN | \n", + "[HALLMARK_ADIPOGENESIS-1] | \n", + "NaN | \n", + "
| 11 | \n", + "obsolete transcription activator activity | \n", + "NaN | \n", + "[tf-downreg-colorectal-1] | \n", + "NaN | \n", + "
| 12 | \n", + "C-X-C chemokine binding | \n", + "NaN | \n", + "[HALLMARK_ALLOGRAFT_REJECTION] | \n", + "NaN | \n", + "
| 13 | \n", + "DNA replication | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_PEROXISOME-1] | \n", + "
| 14 | \n", + "obsolete lectin | \n", + "[HALLMARK_APICAL_JUNCTION] | \n", + "NaN | \n", + "NaN | \n", + "
| 15 | \n", + "phosphatidylinositol trisphosphate phosphatase activity | \n", + "NaN | \n", + "[HALLMARK_ANDROGEN_RESPONSE-1] | \n", + "NaN | \n", + "
| 16 | \n", + "obsolete serpin | \n", + "[HALLMARK_COMPLEMENT] | \n", + "NaN | \n", + "NaN | \n", + "
| 17 | \n", + "obsolete extracellular matrix glycoprotein | \n", + "[HALLMARK_UV_RESPONSE_DN] | \n", + "NaN | \n", + "NaN | \n", + "
| 18 | \n", + "obsolete calcium-dependent cell adhesion molecule activity | \n", + "[HALLMARK_APICAL_JUNCTION-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 19 | \n", + "cytokine production | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_APICAL_JUNCTION-1] | \n", + "
| 20 | \n", + "obsolete vesicle transport | \n", + "[HALLMARK_PROTEIN_SECRETION] | \n", + "[endocytosis-1] | \n", + "NaN | \n", + "
| 21 | \n", + "receptor-mediated endocytosis | \n", + "[HALLMARK_APICAL_SURFACE] | \n", + "NaN | \n", + "NaN | \n", + "
| 22 | \n", + "obsolete transcription factor activity, protein binding | \n", + "[tf-downreg-colorectal-1] | \n", + "[molecular sequestering-1] | \n", + "[Yamanaka-TFs] | \n", + "
| 23 | \n", + "limb development | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_BILE_ACID_METABOLISM] | \n", + "
| 24 | \n", + "obsolete cytochrome P450 | \n", + "[HALLMARK_BILE_ACID_METABOLISM] | \n", + "NaN | \n", + "NaN | \n", + "
| 25 | \n", + "translation | \n", + "[HALLMARK_BILE_ACID_METABOLISM-1] | \n", + "NaN | \n", + "[bicluster_RNAseqDB_0-1] | \n", + "
| 26 | \n", + "glycoprotein biosynthetic process | \n", + "[HALLMARK_CHOLESTEROL_HOMEOSTASIS] | \n", + "NaN | \n", + "NaN | \n", + "
| 27 | \n", + "sterol catabolic process | \n", + "[HALLMARK_CHOLESTEROL_HOMEOSTASIS] | \n", + "NaN | \n", + "NaN | \n", + "
| 28 | \n", + "bile acid biosynthetic process | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_CHOLESTEROL_HOMEOSTASIS-1] | \n", + "
| 29 | \n", + "obsolete plasma protein | \n", + "[HALLMARK_COAGULATION] | \n", + "NaN | \n", + "NaN | \n", + "
| 30 | \n", + "obsolete matrilysin activity | \n", + "[HALLMARK_COAGULATION] | \n", + "NaN | \n", + "NaN | \n", + "
| 31 | \n", + "obsolete RNA | \n", + "[HALLMARK_KRAS_SIGNALING_DN-1] | \n", + "[HALLMARK_COMPLEMENT] | \n", + "NaN | \n", + "
| 32 | \n", + "DNA replication-dependent chromatin assembly | \n", + "[HALLMARK_MYC_TARGETS_V2] | \n", + "NaN | \n", + "[HALLMARK_DNA_REPAIR] | \n", + "
| 33 | \n", + "obsolete small nuclear ribonucleoprotein | \n", + "[HALLMARK_MYC_TARGETS_V1] | \n", + "NaN | \n", + "NaN | \n", + "
| 34 | \n", + "obsolete covalent chromatin modification | \n", + "[tf-downreg-colorectal-1] | \n", + "NaN | \n", + "[tf-downreg-colorectal-1] | \n", + "
| 35 | \n", + "obsolete ATP catabolic process | \n", + "NaN | \n", + "[HALLMARK_SPERMATOGENESIS-1] | \n", + "NaN | \n", + "
| 36 | \n", + "epidermal growth factor receptor activity | \n", + "NaN | \n", + "[HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION-1] | \n", + "NaN | \n", + "
| 37 | \n", + "obsolete collagen | \n", + "[HALLMARK_MYOGENESIS-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 38 | \n", + "cell growth | \n", + "[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1] | \n", + "NaN | \n", + "[Yamanaka-TFs] | \n", + "
| 39 | \n", + "protein processing | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_ESTROGEN_RESPONSE_EARLY] | \n", + "
| 40 | \n", + "inward rectifier potassium channel activity | \n", + "NaN | \n", + "[HALLMARK_ESTROGEN_RESPONSE_LATE] | \n", + "NaN | \n", + "
| 41 | \n", + "activin receptor activity | \n", + "NaN | \n", + "[HALLMARK_ESTROGEN_RESPONSE_LATE] | \n", + "NaN | \n", + "
| 42 | \n", + "nucleotide transport | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_FATTY_ACID_METABOLISM] | \n", + "
| 43 | \n", + "metalloendopeptidase activity | \n", + "NaN | \n", + "[HALLMARK_FATTY_ACID_METABOLISM] | \n", + "NaN | \n", + "
| 44 | \n", + "biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity | \n", + "NaN | \n", + "[HALLMARK_FATTY_ACID_METABOLISM] | \n", + "NaN | \n", + "
| 45 | \n", + "obsolete coenzyme metabolic process | \n", + "[HALLMARK_FATTY_ACID_METABOLISM] | \n", + "NaN | \n", + "NaN | \n", + "
| 46 | \n", + "actin filament | \n", + "NaN | \n", + "[HALLMARK_G2M_CHECKPOINT] | \n", + "NaN | \n", + "
| 47 | \n", + "adenyl-nucleotide exchange factor activity | \n", + "NaN | \n", + "[HALLMARK_G2M_CHECKPOINT-1] | \n", + "NaN | \n", + "
| 48 | \n", + "microtubule polymerization | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_GLYCOLYSIS-1] | \n", + "
| 49 | \n", + "activation of GTPase activity | \n", + "NaN | \n", + "[HALLMARK_HEDGEHOG_SIGNALING] | \n", + "NaN | \n", + "
| 50 | \n", + "structural constituent of ribosome | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_HEME_METABOLISM] | \n", + "
| 51 | \n", + "cell cycle checkpoint signaling | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_HEME_METABOLISM] | \n", + "
| 52 | \n", + "mitotic prophase | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_HEME_METABOLISM] | \n", + "
| 53 | \n", + "nucleoside metabolic process | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_HEME_METABOLISM] | \n", + "
| 54 | \n", + "obsolete transcription repressor activity | \n", + "NaN | \n", + "[tf-downreg-colorectal-1] | \n", + "NaN | \n", + "
| 55 | \n", + "cytokinesis | \n", + "[HALLMARK_HEME_METABOLISM] | \n", + "NaN | \n", + "NaN | \n", + "
| 56 | \n", + "histone deacetylation | \n", + "[HALLMARK_HEME_METABOLISM] | \n", + "NaN | \n", + "NaN | \n", + "
| 57 | \n", + "obsolete DNA | \n", + "[HALLMARK_HEME_METABOLISM] | \n", + "[T cell proliferation-1] | \n", + "NaN | \n", + "
| 58 | \n", + "growth | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_HEME_METABOLISM-1] | \n", + "
| 59 | \n", + "glycolytic process | \n", + "[HALLMARK_HEME_METABOLISM-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 60 | \n", + "obsolete membrane-associated guanylate kinase | \n", + "[HALLMARK_UV_RESPONSE_DN-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 61 | \n", + "acetyltransferase activity | \n", + "NaN | \n", + "[HALLMARK_HYPOXIA-1] | \n", + "NaN | \n", + "
| 62 | \n", + "1-phosphatidylinositol-3-kinase activity | \n", + "NaN | \n", + "[HALLMARK_HYPOXIA-1] | \n", + "NaN | \n", + "
| 63 | \n", + "NAD+-dinitrogen-reductase ADP-D-ribosyltransferase activity | \n", + "[HALLMARK_INTERFERON_ALPHA_RESPONSE-1] | \n", + "[HALLMARK_INTERFERON_ALPHA_RESPONSE-1] | \n", + "NaN | \n", + "
| 64 | \n", + "cyclin-dependent protein serine/threonine kinase activity | \n", + "NaN | \n", + "[HALLMARK_HYPOXIA-1] | \n", + "NaN | \n", + "
| 65 | \n", + "lipoprotein metabolic process | \n", + "[HALLMARK_HYPOXIA-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 66 | \n", + "obsolete movement of cell or subcellular component | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_INFLAMMATORY_RESPONSE-1] | \n", + "
| 67 | \n", + "neutrophil mediated immunity | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_INTERFERON_ALPHA_RESPONSE-1] | \n", + "
| 68 | \n", + "obsolete tumor suppressor | \n", + "[HALLMARK_INTERFERON_ALPHA_RESPONSE-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 69 | \n", + "protein methylation | \n", + "[HALLMARK_INTERFERON_ALPHA_RESPONSE-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 70 | \n", + "obsolete transcription regulator activity | \n", + "NaN | \n", + "[HALLMARK_INTERFERON_GAMMA_RESPONSE] | \n", + "NaN | \n", + "
| 71 | \n", + "histone methylation | \n", + "[HALLMARK_KRAS_SIGNALING_UP-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 72 | \n", + "dextransucrase activity | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_MITOTIC_SPINDLE] | \n", + "
| 73 | \n", + "NF-kappaB binding | \n", + "NaN | \n", + "[HALLMARK_MITOTIC_SPINDLE-1] | \n", + "NaN | \n", + "
| 74 | \n", + "pyruvate dehydrogenase activity | \n", + "NaN | \n", + "[mtorc1] | \n", + "NaN | \n", + "
| 75 | \n", + "ncRNA-mediated post-transcriptional gene silencing | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_MTORC1_SIGNALING-1] | \n", + "
| 76 | \n", + "RNA splicing, via endonucleolytic cleavage and ligation | \n", + "[HALLMARK_MYC_TARGETS_V1-1] | \n", + "NaN | \n", + "[HALLMARK_MYC_TARGETS_V1-1] | \n", + "
| 77 | \n", + "ribosome | \n", + "NaN | \n", + "[HALLMARK_MYC_TARGETS_V2-1] | \n", + "NaN | \n", + "
| 78 | \n", + "calcium-mediated signaling | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_NOTCH_SIGNALING] | \n", + "
| 79 | \n", + "obsolete hydrogen-translocating F-type ATPase activity | \n", + "[mtorc1-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 80 | \n", + "P-type proton-exporting transporter activity | \n", + "NaN | \n", + "[HALLMARK_PROTEIN_SECRETION-1] | \n", + "NaN | \n", + "
| 81 | \n", + "G protein activity | \n", + "NaN | \n", + "[HALLMARK_OXIDATIVE_PHOSPHORYLATION-1] | \n", + "NaN | \n", + "
| 82 | \n", + "post-translational protein modification | \n", + "NaN | \n", + "[bicluster_RNAseqDB_1002] | \n", + "[bicluster_RNAseqDB_0-1] | \n", + "
| 83 | \n", + "cellular senescence | \n", + "NaN | \n", + "[HALLMARK_PANCREAS_BETA_CELLS] | \n", + "NaN | \n", + "
| 84 | \n", + "obsolete peptide hormone | \n", + "[HALLMARK_PANCREAS_BETA_CELLS-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 85 | \n", + "actin filament polymerization | \n", + "NaN | \n", + "[HALLMARK_PANCREAS_BETA_CELLS-1] | \n", + "NaN | \n", + "
| 86 | \n", + "detection of glucose | \n", + "NaN | \n", + "[HALLMARK_PANCREAS_BETA_CELLS-1] | \n", + "NaN | \n", + "
| 87 | \n", + "long-term synaptic potentiation | \n", + "NaN | \n", + "[HALLMARK_PANCREAS_BETA_CELLS-1] | \n", + "NaN | \n", + "
| 88 | \n", + "obsolete insulin | \n", + "[HALLMARK_PANCREAS_BETA_CELLS-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 89 | \n", + "mRNA transcription | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_PEROXISOME] | \n", + "
| 90 | \n", + "respiratory gaseous exchange by respiratory system | \n", + "NaN | \n", + "[HALLMARK_PEROXISOME] | \n", + "NaN | \n", + "
| 91 | \n", + "stearoyl-CoA 9-desaturase activity | \n", + "[HALLMARK_PEROXISOME] | \n", + "NaN | \n", + "NaN | \n", + "
| 92 | \n", + "glutamate metabolic process | \n", + "[HALLMARK_PEROXISOME-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 93 | \n", + "11-cis retinal binding | \n", + "[HALLMARK_PEROXISOME-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 94 | \n", + "glycosylation | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_PI3K_AKT_MTOR_SIGNALING-1] | \n", + "
| 95 | \n", + "obsolete clathrin adaptor | \n", + "[HALLMARK_PROTEIN_SECRETION-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 96 | \n", + "protein glutathionylation | \n", + "NaN | \n", + "[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY] | \n", + "NaN | \n", + "
| 97 | \n", + "obsolete glutaredoxin | \n", + "[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY] | \n", + "NaN | \n", + "NaN | \n", + "
| 98 | \n", + "myosin-light-chain-phosphatase activity | \n", + "[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY] | \n", + "NaN | \n", + "NaN | \n", + "
| 99 | \n", + "chloramphenicol O-acetyltransferase activity | \n", + "NaN | \n", + "[HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1] | \n", + "NaN | \n", + "
| 100 | \n", + "adenylate cyclase activity | \n", + "[HALLMARK_SPERMATOGENESIS] | \n", + "NaN | \n", + "NaN | \n", + "
| 101 | \n", + "vasodilation | \n", + "[HALLMARK_SPERMATOGENESIS-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 102 | \n", + "obsolete aging | \n", + "[HALLMARK_SPERMATOGENESIS-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 103 | \n", + "anaphase-promoting complex | \n", + "[HALLMARK_TGF_BETA_SIGNALING] | \n", + "NaN | \n", + "NaN | \n", + "
| 104 | \n", + "MAP kinase activity | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_TNFA_SIGNALING_VIA_NFKB] | \n", + "
| 105 | \n", + "transcription initiation at RNA polymerase II promoter | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_TNFA_SIGNALING_VIA_NFKB-1] | \n", + "
| 106 | \n", + "protein kinase A signaling | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_TNFA_SIGNALING_VIA_NFKB-1] | \n", + "
| 107 | \n", + "protein ubiquitination | \n", + "NaN | \n", + "NaN | \n", + "[HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1] | \n", + "
| 108 | \n", + "ubiquitin-protein transferase activity | \n", + "[HALLMARK_WNT_BETA_CATENIN_SIGNALING-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 109 | \n", + "stem cell development | \n", + "NaN | \n", + "NaN | \n", + "[Yamanaka-TFs-1] | \n", + "
| 110 | \n", + "stem cell differentiation | \n", + "NaN | \n", + "NaN | \n", + "[Yamanaka-TFs-1] | \n", + "
| 111 | \n", + "BMP signaling pathway involved in heart induction | \n", + "NaN | \n", + "[Yamanaka-TFs-1] | \n", + "NaN | \n", + "
| 112 | \n", + "cell cycle | \n", + "[Yamanaka-TFs-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 113 | \n", + "platelet aggregation | \n", + "NaN | \n", + "NaN | \n", + "[amigo-example-1] | \n", + "
| 114 | \n", + "nuclear migration | \n", + "NaN | \n", + "NaN | \n", + "[bicluster_RNAseqDB_1002] | \n", + "
| 115 | \n", + "phosphoprotein binding | \n", + "[bicluster_RNAseqDB_1002] | \n", + "NaN | \n", + "NaN | \n", + "
| 116 | \n", + "negative regulation of phosphoprotein phosphatase activity | \n", + "[bicluster_RNAseqDB_1002] | \n", + "NaN | \n", + "NaN | \n", + "
| 117 | \n", + "cell motility | \n", + "[bicluster_RNAseqDB_1002] | \n", + "NaN | \n", + "NaN | \n", + "
| 118 | \n", + "protein serine/threonine phosphatase activity | \n", + "[bicluster_RNAseqDB_1002] | \n", + "NaN | \n", + "NaN | \n", + "
| 119 | \n", + "obsolete striated muscle fiber development | \n", + "NaN | \n", + "NaN | \n", + "[bicluster_RNAseqDB_1002-1] | \n", + "
| 120 | \n", + "nerve development | \n", + "NaN | \n", + "NaN | \n", + "[bicluster_RNAseqDB_1002-1] | \n", + "
| 121 | \n", + "muscle thin filament assembly | \n", + "NaN | \n", + "[bicluster_RNAseqDB_1002-1] | \n", + "NaN | \n", + "
| 122 | \n", + "calcineurin-NFAT signaling cascade | \n", + "[bicluster_RNAseqDB_1002-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 123 | \n", + "pentose-phosphate shunt | \n", + "NaN | \n", + "NaN | \n", + "[glycolysis-gocam-1] | \n", + "
| 124 | \n", + "glucose transmembrane transport | \n", + "NaN | \n", + "[glycolysis-gocam-1] | \n", + "NaN | \n", + "
| 125 | \n", + "substantia nigra development | \n", + "NaN | \n", + "[glycolysis-gocam-1] | \n", + "NaN | \n", + "
| 126 | \n", + "angiogenesis | \n", + "[glycolysis-gocam-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 127 | \n", + "regulation of cytosolic calcium ion concentration | \n", + "NaN | \n", + "[term-GO:0007212] | \n", + "NaN | \n", + "
| 128 | \n", + "cellular response to glucose stimulus | \n", + "NaN | \n", + "[term-GO:0007212-1] | \n", + "NaN | \n", + "
| 129 | \n", + "positive regulation of lamellipodium morphogenesis | \n", + "NaN | \n", + "[term-GO:0007212-1] | \n", + "NaN | \n", + "
| 130 | \n", + "nuclear export | \n", + "[endocytosis] | \n", + "NaN | \n", + "NaN | \n", + "
| 131 | \n", + "mitotic nuclear division | \n", + "[endocytosis-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 132 | \n", + "regulation of presynaptic cytosolic calcium ion concentration | \n", + "NaN | \n", + "[go-postsynapse-calcium-transmembrane] | \n", + "NaN | \n", + "
| 133 | \n", + "regulation of synaptic vesicle exocytosis | \n", + "NaN | \n", + "[go-postsynapse-calcium-transmembrane] | \n", + "NaN | \n", + "
| 134 | \n", + "obsolete neuroprotection | \n", + "NaN | \n", + "NaN | \n", + "[go-reg-autophagy-pkra-1] | \n", + "
| 135 | \n", + "obsolete Goodpasture-antigen-binding protein kinase activity | \n", + "[go-reg-autophagy-pkra-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 136 | \n", + "peroxisome | \n", + "NaN | \n", + "NaN | \n", + "[hydrolase activity, hydrolyzing O-glycosyl compounds] | \n", + "
| 137 | \n", + "limb morphogenesis | \n", + "NaN | \n", + "NaN | \n", + "[hydrolase activity, hydrolyzing O-glycosyl compounds] | \n", + "
| 138 | \n", + "chitin biosynthetic process | \n", + "NaN | \n", + "NaN | \n", + "[hydrolase activity, hydrolyzing O-glycosyl compounds-1] | \n", + "
| 139 | \n", + "protein kinase activity | \n", + "NaN | \n", + "[hydrolase activity, hydrolyzing O-glycosyl compounds-1] | \n", + "NaN | \n", + "
| 140 | \n", + "carbohydrate transmembrane transporter activity | \n", + "NaN | \n", + "[hydrolase activity, hydrolyzing O-glycosyl compounds-1] | \n", + "NaN | \n", + "
| 141 | \n", + "indole-3-glycerol-phosphate lyase activity | \n", + "NaN | \n", + "NaN | \n", + "[ig-receptor-binding-2022] | \n", + "
| 142 | \n", + "immunoglobulin production | \n", + "[sensory ataxia] | \n", + "NaN | \n", + "NaN | \n", + "
| 143 | \n", + "blood coagulation | \n", + "NaN | \n", + "NaN | \n", + "[ig-receptor-binding-2022-1] | \n", + "
| 144 | \n", + "fibrinogen complex | \n", + "NaN | \n", + "NaN | \n", + "[ig-receptor-binding-2022-1] | \n", + "
| 145 | \n", + "regulation of immunoglobulin production | \n", + "NaN | \n", + "NaN | \n", + "[ig-receptor-binding-2022-1] | \n", + "
| 146 | \n", + "chronic inflammatory response | \n", + "NaN | \n", + "NaN | \n", + "[ig-receptor-binding-2022-1] | \n", + "
| 147 | \n", + "cell-matrix adhesion | \n", + "NaN | \n", + "[ig-receptor-binding-2022-1] | \n", + "NaN | \n", + "
| 148 | \n", + "cell-cell adhesion | \n", + "NaN | \n", + "[ig-receptor-binding-2022-1] | \n", + "NaN | \n", + "
| 149 | \n", + "calcium ion transport | \n", + "NaN | \n", + "NaN | \n", + "[molecular sequestering] | \n", + "
| 150 | \n", + "mRNA base-pairing translational repressor activity | \n", + "NaN | \n", + "[molecular sequestering] | \n", + "NaN | \n", + "
| 151 | \n", + "ubiquitin-dependent protein catabolic process | \n", + "[molecular sequestering] | \n", + "NaN | \n", + "NaN | \n", + "
| 152 | \n", + "proteasome-mediated ubiquitin-dependent protein catabolic process | \n", + "[molecular sequestering] | \n", + "NaN | \n", + "NaN | \n", + "
| 153 | \n", + "obsolete initiation of signal transduction | \n", + "[mtorc1-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 154 | \n", + "protein import | \n", + "[peroxisome-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 155 | \n", + "RNA metabolic process | \n", + "NaN | \n", + "NaN | \n", + "[progeria] | \n", + "
| 156 | \n", + "regulation of telomere maintenance | \n", + "NaN | \n", + "[progeria] | \n", + "NaN | \n", + "
| 157 | \n", + "nucleosome assembly | \n", + "NaN | \n", + "NaN | \n", + "[progeria-1] | \n", + "
| 158 | \n", + "regulation of cell cycle | \n", + "NaN | \n", + "NaN | \n", + "[progeria-1] | \n", + "
| 159 | \n", + "apoptotic process | \n", + "NaN | \n", + "[progeria-1] | \n", + "NaN | \n", + "
| 160 | \n", + "regulation of cellular senescence | \n", + "NaN | \n", + "[progeria-1] | \n", + "NaN | \n", + "
| 161 | \n", + "DNA-templated transcription | \n", + "[progeria-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 162 | \n", + "cell division | \n", + "[progeria-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 163 | \n", + "RNA modification | \n", + "[regulation of presynaptic membrane potential-1] | \n", + "NaN | \n", + "NaN | \n", + "
| 164 | \n", + "muscle contraction | \n", + "NaN | \n", + "NaN | \n", + "[sensory ataxia] | \n", + "
| 165 | \n", + "glycosaminoglycan catabolic process | \n", + "NaN | \n", + "[sensory ataxia] | \n", + "NaN | \n", + "
| 166 | \n", + "transmission of nerve impulse | \n", + "NaN | \n", + "[sensory ataxia] | \n", + "NaN | \n", + "
| 167 | \n", + "RNA splicing | \n", + "NaN | \n", + "[sensory ataxia] | \n", + "NaN | \n", + "
| 168 | \n", + "cytoskeletal motor activity | \n", + "NaN | \n", + "[sensory ataxia] | \n", + "NaN | \n", + "
| 169 | \n", + "nucleic acid transport | \n", + "NaN | \n", + "NaN | \n", + "[sensory ataxia-1] | \n", + "
| 170 | \n", + "nuclear lamina | \n", + "NaN | \n", + "NaN | \n", + "[tf-downreg-colorectal] | \n", + "
| \n", + " | NAME | \n", + "narrative_synopsis | \n", + "no_synopsis | \n", + "ontological_synopsis | \n", + "
|---|---|---|---|---|
| 0 | \n", + "regulation of collagen metabolic process | \n", + "[(EDS, regulation of metabolic process)] | \n", + "NaN | \n", + "NaN | \n", + "
| 1 | \n", + "post-translational protein modification | \n", + "[(EDS, regulation of protein modification process)] | \n", + "NaN | \n", + "NaN | \n", + "
| 2 | \n", + "protein folding | \n", + "[(EDS-1, protein processing)] | \n", + "NaN | \n", + "NaN | \n", + "
| 3 | \n", + "positive regulation of fatty acid beta-oxidation | \n", + "NaN | \n", + "[(HALLMARK_ADIPOGENESIS, very long-chain fatty acid beta-oxidation)] | \n", + "NaN | \n", + "
| 4 | \n", + "obsolete electron transport | \n", + "[(HALLMARK_FATTY_ACID_METABOLISM, respiratory electron transport chain)] | \n", + "NaN | \n", + "[(HALLMARK_OXIDATIVE_PHOSPHORYLATION-1, respiratory electron transport chain)] | \n", + "
| 5 | \n", + "cell growth | \n", + "[(HALLMARK_ADIPOGENESIS-1, cell)] | \n", + "NaN | \n", + "NaN | \n", + "
| 6 | \n", + "obsolete transcription factor activity, protein binding | \n", + "[(tf-downreg-colorectal, DNA-binding transcription factor binding)] | \n", + "[(tf-downreg-colorectal-1, DNA-binding transcription factor binding)] | \n", + "[(tf-downreg-colorectal-1, DNA-binding transcription factor binding)] | \n", + "
| 7 | \n", + "interleukin-2 production | \n", + "[(HALLMARK_ALLOGRAFT_REJECTION, interleukin-2 binding)] | \n", + "NaN | \n", + "NaN | \n", + "
| 8 | \n", + "type II interferon production | \n", + "[(HALLMARK_ALLOGRAFT_REJECTION, type III interferon production)] | \n", + "NaN | \n", + "NaN | \n", + "
| 9 | \n", + "regulation of protein stability | \n", + "NaN | \n", + "[(HALLMARK_ANDROGEN_RESPONSE, regulation of mRNA stability)] | \n", + "NaN | \n", + "
| 10 | \n", + "platelet degranulation | \n", + "[(amigo-example, platelet)] | \n", + "[(HALLMARK_ANGIOGENESIS, platelet)] | \n", + "NaN | \n", + "
| 11 | \n", + "regulation of bone development | \n", + "NaN | \n", + "[(HALLMARK_ANGIOGENESIS, regulation of cell development)] | \n", + "NaN | \n", + "
| 12 | \n", + "proteoglycan metabolic process | \n", + "[(amigo-example-1, aminoglycan metabolic process)] | \n", + "NaN | \n", + "NaN | \n", + "
| 13 | \n", + "regulation of transforming growth factor beta receptor signaling pathway | \n", + "NaN | \n", + "[(HALLMARK_ANGIOGENESIS-1, regulation of transforming growth factor beta activation)] | \n", + "NaN | \n", + "
| 14 | \n", + "regulation of mitotic nuclear division | \n", + "[(HALLMARK_ANGIOGENESIS-1, regulation of nuclear division)] | \n", + "NaN | \n", + "NaN | \n", + "
| 15 | \n", + "obsolete calcium-dependent cell adhesion molecule activity | \n", + "[(HALLMARK_APICAL_JUNCTION-1, substrate adhesion-dependent cell spreading)] | \n", + "NaN | \n", + "NaN | \n", + "
| 16 | \n", + "regulation of signal transduction by p53 class mediator | \n", + "[(HALLMARK_APICAL_SURFACE, regulation of signal transduction)] | \n", + "NaN | \n", + "NaN | \n", + "
| 17 | \n", + "modulation by virus of host process | \n", + "[(HALLMARK_APICAL_SURFACE, regulation of metabolic process)] | \n", + "NaN | \n", + "NaN | \n", + "
| 18 | \n", + "regulation of glucose metabolic process | \n", + "NaN | \n", + "[(HALLMARK_APICAL_SURFACE-1, regulation of metabolic process)] | \n", + "NaN | \n", + "
| 19 | \n", + "protein kinase C signaling | \n", + "NaN | \n", + "[(HALLMARK_APICAL_SURFACE-1, protein kinase C binding)] | \n", + "NaN | \n", + "
| 20 | \n", + "positive regulation of MAP kinase activity | \n", + "NaN | \n", + "[(HALLMARK_APICAL_SURFACE-1, positive regulation of kinase activity)] | \n", + "NaN | \n", + "
| 21 | \n", + "regulation of B cell receptor signaling pathway | \n", + "NaN | \n", + "[(HALLMARK_APOPTOSIS, regulation of T cell receptor signaling pathway)] | \n", + "NaN | \n", + "
| 22 | \n", + "obsolete cytochrome P450 | \n", + "[(HALLMARK_BILE_ACID_METABOLISM-1, axon cytoplasm)] | \n", + "NaN | \n", + "NaN | \n", + "
| 23 | \n", + "obsolete cell surface binding | \n", + "NaN | \n", + "[(HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION, protein localization to cell surface)] | \n", + "NaN | \n", + "
| 24 | \n", + "calcium-dependent protein kinase activity | \n", + "NaN | \n", + "[(HALLMARK_ESTROGEN_RESPONSE_EARLY, calcium-dependent protein binding)] | \n", + "NaN | \n", + "
| 25 | \n", + "calcium-dependent ATPase activity | \n", + "NaN | \n", + "[(HALLMARK_ESTROGEN_RESPONSE_EARLY, calcium channel activity)] | \n", + "NaN | \n", + "
| 26 | \n", + "acetyl-CoA catabolic process | \n", + "NaN | \n", + "NaN | \n", + "[(HALLMARK_FATTY_ACID_METABOLISM, acetyl-CoA metabolic process)] | \n", + "
| 27 | \n", + "coenzyme A metabolic process | \n", + "[(HALLMARK_FATTY_ACID_METABOLISM-1, amine metabolic process)] | \n", + "NaN | \n", + "NaN | \n", + "
| 28 | \n", + "UDP-D-galactose metabolic process | \n", + "[(HALLMARK_GLYCOLYSIS, galactose metabolic process)] | \n", + "NaN | \n", + "NaN | \n", + "
| 29 | \n", + "glucose transmembrane transport | \n", + "[(HALLMARK_GLYCOLYSIS-1, protein transmembrane transport)] | \n", + "NaN | \n", + "NaN | \n", + "
| 30 | \n", + "UDP-galactose biosynthetic process | \n", + "[(HALLMARK_GLYCOLYSIS-1, lactose biosynthetic process)] | \n", + "NaN | \n", + "NaN | \n", + "
| 31 | \n", + "regulation of protein homodimerization activity | \n", + "NaN | \n", + "[(HALLMARK_HEME_METABOLISM-1, protein homodimerization activity)] | \n", + "NaN | \n", + "
| 32 | \n", + "regulation of response to reactive oxygen species | \n", + "NaN | \n", + "[(HALLMARK_HYPOXIA, regulation of reactive oxygen species metabolic process)] | \n", + "NaN | \n", + "
| 33 | \n", + "cellular response to interferon-alpha | \n", + "NaN | \n", + "[(HALLMARK_INTERFERON_ALPHA_RESPONSE-1, cellular response to interferon-beta)] | \n", + "NaN | \n", + "
| 34 | \n", + "antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent | \n", + "NaN | \n", + "[(HALLMARK_INTERFERON_GAMMA_RESPONSE, antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent)] | \n", + "NaN | \n", + "
| 35 | \n", + "P-type calcium transporter activity | \n", + "[(HALLMARK_KRAS_SIGNALING_DN, P-type sodium transporter activity)] | \n", + "NaN | \n", + "NaN | \n", + "
| 36 | \n", + "obsolete membrane part | \n", + "[(HALLMARK_KRAS_SIGNALING_UP, outer membrane)] | \n", + "NaN | \n", + "NaN | \n", + "
| 37 | \n", + "RNA splicing, via endonucleolytic cleavage and ligation | \n", + "[(HALLMARK_MYC_TARGETS_V1, RNA phosphodiester bond hydrolysis, endonucleolytic)] | \n", + "[(HALLMARK_MYC_TARGETS_V2-1, RNA phosphodiester bond hydrolysis, endonucleolytic)] | \n", + "[(HALLMARK_MYC_TARGETS_V1-1, RNA phosphodiester bond hydrolysis, endonucleolytic)] | \n", + "
| 38 | \n", + "spliceosomal complex | \n", + "NaN | \n", + "[(HALLMARK_MYC_TARGETS_V2, CMG complex)] | \n", + "NaN | \n", + "
| 39 | \n", + "translational initiation | \n", + "NaN | \n", + "[(HALLMARK_MYC_TARGETS_V2, transcription initiation at mitochondrial promoter)] | \n", + "NaN | \n", + "
| 40 | \n", + "muscle thin filament assembly | \n", + "NaN | \n", + "[(HALLMARK_MYOGENESIS, muscle filament sliding)] | \n", + "NaN | \n", + "
| 41 | \n", + "chemical synaptic transmission | \n", + "NaN | \n", + "[(HALLMARK_NOTCH_SIGNALING, modulation of chemical synaptic transmission)] | \n", + "NaN | \n", + "
| 42 | \n", + "obsolete transcription activator activity | \n", + "[(HALLMARK_NOTCH_SIGNALING, DNA-binding transcription activator activity)] | \n", + "NaN | \n", + "[(HALLMARK_UV_RESPONSE_DN-1, DNA-binding transcription activator activity)] | \n", + "
| 43 | \n", + "cysteine-type endopeptidase activity involved in apoptotic process | \n", + "[(HALLMARK_NOTCH_SIGNALING, aspartic-type endopeptidase activity)] | \n", + "NaN | \n", + "NaN | \n", + "
| 44 | \n", + "obsolete hydrogen-translocating F-type ATPase activity | \n", + "NaN | \n", + "NaN | \n", + "[(HALLMARK_OXIDATIVE_PHOSPHORYLATION-1, serine-type peptidase activity)] | \n", + "
| 45 | \n", + "peroxisome proliferator activated receptor signaling pathway | \n", + "NaN | \n", + "[(HALLMARK_PEROXISOME, peroxisome)] | \n", + "NaN | \n", + "
| 46 | \n", + "11-cis retinal binding | \n", + "[(HALLMARK_PEROXISOME, retinal binding)] | \n", + "NaN | \n", + "NaN | \n", + "
| 47 | \n", + "negative regulation of receptor internalization | \n", + "NaN | \n", + "NaN | \n", + "[(HALLMARK_PROTEIN_SECRETION, positive regulation of receptor internalization)] | \n", + "
| 48 | \n", + "obsolete vesicle transport | \n", + "[(HALLMARK_PROTEIN_SECRETION, synaptic vesicle transport)] | \n", + "NaN | \n", + "NaN | \n", + "
| 49 | \n", + "protein targeting to membrane | \n", + "NaN | \n", + "[(HALLMARK_PROTEIN_SECRETION-1, protein localization to membrane)] | \n", + "NaN | \n", + "
| 50 | \n", + "negative regulation of reactive oxygen species metabolic process | \n", + "NaN | \n", + "[(HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1, positive regulation of reactive oxygen species metabolic process)] | \n", + "NaN | \n", + "
| 51 | \n", + "regulation of DNA repair | \n", + "NaN | \n", + "[(HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1, regulation of DNA binding)] | \n", + "NaN | \n", + "
| 52 | \n", + "positive regulation of protein binding | \n", + "NaN | \n", + "[(HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY-1, positive regulation of binding)] | \n", + "NaN | \n", + "
| 53 | \n", + "regulation of kinetochore assembly | \n", + "NaN | \n", + "[(HALLMARK_SPERMATOGENESIS-1, regulation of attachment of spindle microtubules to kinetochore)] | \n", + "NaN | \n", + "
| 54 | \n", + "positive regulation of mitotic spindle organization | \n", + "NaN | \n", + "[(HALLMARK_SPERMATOGENESIS-1, positive regulation of mitotic cell cycle)] | \n", + "NaN | \n", + "
| 55 | \n", + "glycoprotein transport | \n", + "[(HALLMARK_TGF_BETA_SIGNALING-1, glycoprotein metabolic process)] | \n", + "NaN | \n", + "NaN | \n", + "
| 56 | \n", + "None | \n", + "NaN | \n", + "[(HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1, protein secretion)] | \n", + "NaN | \n", + "
| 57 | \n", + "MAP kinase activity | \n", + "NaN | \n", + "NaN | \n", + "[(HALLMARK_TNFA_SIGNALING_VIA_NFKB-1, MAP kinase kinase activity)] | \n", + "
| 58 | \n", + "chemokine production | \n", + "[(HALLMARK_TNFA_SIGNALING_VIA_NFKB-1, chemokine activity)] | \n", + "NaN | \n", + "NaN | \n", + "
| 59 | \n", + "regulation of phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands | \n", + "NaN | \n", + "[(HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1, regulation of phosphatase activity)] | \n", + "NaN | \n", + "
| 60 | \n", + "protein localization to plasma membrane | \n", + "NaN | \n", + "[(HALLMARK_UNFOLDED_PROTEIN_RESPONSE-1, protein localization to membrane)] | \n", + "NaN | \n", + "
| 61 | \n", + "negative regulation of protein ubiquitination | \n", + "NaN | \n", + "NaN | \n", + "[(HALLMARK_WNT_BETA_CATENIN_SIGNALING-1, positive regulation of protein ubiquitination)] | \n", + "
| 62 | \n", + "obsolete lectin | \n", + "[(T cell proliferation, response to lectin)] | \n", + "NaN | \n", + "NaN | \n", + "
| 63 | \n", + "COP9 signalosome | \n", + "[(T cell proliferation, endosome)] | \n", + "NaN | \n", + "NaN | \n", + "
| 64 | \n", + "cell population proliferation | \n", + "NaN | \n", + "[(Yamanaka-TFs, cell)] | \n", + "NaN | \n", + "
| 65 | \n", + "stem cell differentiation | \n", + "[(Yamanaka-TFs-1, fat cell differentiation)] | \n", + "[(Yamanaka-TFs-1, fat cell differentiation)] | \n", + "NaN | \n", + "
| 66 | \n", + "obsolete lipoprotein binding | \n", + "NaN | \n", + "NaN | \n", + "[(amigo-example, low-density lipoprotein particle receptor binding)] | \n", + "
| 67 | \n", + "obsolete collagen | \n", + "[(amigo-example, banded collagen fibril)] | \n", + "NaN | \n", + "NaN | \n", + "
| 68 | \n", + "keratan sulfate metabolic process | \n", + "[(amigo-example-1, RNA metabolic process)] | \n", + "NaN | \n", + "NaN | \n", + "
| 69 | \n", + "tissue regeneration | \n", + "[(amigo-example-1, tissue)] | \n", + "NaN | \n", + "NaN | \n", + "
| 70 | \n", + "regulation of muscle filament sliding speed | \n", + "[(bicluster_RNAseqDB_1002, regulation of muscle contraction)] | \n", + "NaN | \n", + "NaN | \n", + "
| 71 | \n", + "positive regulation of phosphoprotein phosphatase activity | \n", + "[(bicluster_RNAseqDB_1002, positive regulation of calcium-dependent ATPase activity)] | \n", + "NaN | \n", + "NaN | \n", + "
| 72 | \n", + "energy homeostasis | \n", + "[(bicluster_RNAseqDB_1002-1, chemical homeostasis)] | \n", + "NaN | \n", + "NaN | \n", + "
| 73 | \n", + "regulation of neurotransmitter secretion | \n", + "NaN | \n", + "[(go-postsynapse-calcium-transmembrane-1, regulation of neurotransmitter levels)] | \n", + "NaN | \n", + "
| 74 | \n", + "G protein-coupled neurotransmitter receptor activity | \n", + "NaN | \n", + "[(term-GO:0007212-1, G protein-coupled receptor activity)] | \n", + "NaN | \n", + "
| 75 | \n", + "regulation of cytosolic calcium ion concentration | \n", + "NaN | \n", + "NaN | \n", + "[(term-GO:0007212-1, positive regulation of cytosolic calcium ion concentration)] | \n", + "
| 76 | \n", + "second-messenger-mediated signaling | \n", + "[(term-GO:0007212-1, cytokine-mediated signaling pathway)] | \n", + "NaN | \n", + "NaN | \n", + "
| 77 | \n", + "bone development | \n", + "[(endocytosis, brain development)] | \n", + "NaN | \n", + "NaN | \n", + "
| 78 | \n", + "protein localization to endosome | \n", + "NaN | \n", + "[(endocytosis-1, protein localization to membrane)] | \n", + "NaN | \n", + "
| 79 | \n", + "protein kinase activity | \n", + "NaN | \n", + "[(go-postsynapse-calcium-transmembrane-1, protein kinase B signaling)] | \n", + "NaN | \n", + "
| 80 | \n", + "O-glycan processing | \n", + "NaN | \n", + "[(hydrolase activity, hydrolyzing O-glycosyl compounds, N-glycan processing)] | \n", + "NaN | \n", + "
| 81 | \n", + "glycolytic process | \n", + "NaN | \n", + "[(hydrolase activity, hydrolyzing O-glycosyl compounds-1, glycolipid metabolic process)] | \n", + "NaN | \n", + "
| 82 | \n", + "immunoglobulin production | \n", + "NaN | \n", + "[(ig-receptor-binding-2022-1, immunoglobulin complex)] | \n", + "[(ig-receptor-binding-2022-1, immunoglobulin complex)] | \n", + "
| 83 | \n", + "B cell activation | \n", + "NaN | \n", + "[(ig-receptor-binding-2022-1, T cell activation)] | \n", + "NaN | \n", + "
| 84 | \n", + "positive regulation of humoral immune response | \n", + "[(ig-receptor-binding-2022, positive regulation of immune response)] | \n", + "NaN | \n", + "NaN | \n", + "
| 85 | \n", + "germ cell proliferation | \n", + "NaN | \n", + "[(meiosis I, germ cell)] | \n", + "NaN | \n", + "
| 86 | \n", + "obsolete iron ion homeostasis | \n", + "NaN | \n", + "[(molecular sequestering-1, intracellular iron ion homeostasis)] | \n", + "NaN | \n", + "
| 87 | \n", + "protein stabilization | \n", + "NaN | \n", + "[(molecular sequestering-1, protein targeting)] | \n", + "NaN | \n", + "
| 88 | \n", + "RNA splicing | \n", + "NaN | \n", + "NaN | \n", + "[(mtorc1-1, RNA processing)] | \n", + "
| 89 | \n", + "protein import | \n", + "[(peroxisome-1, protein stabilization)] | \n", + "NaN | \n", + "[(peroxisome-1, protein stabilization)] | \n", + "
| 90 | \n", + "peroxisome fission | \n", + "NaN | \n", + "[(peroxisome-1, peroxisome)] | \n", + "NaN | \n", + "
| 91 | \n", + "obsolete aging | \n", + "NaN | \n", + "[(progeria, telomere maintenance via semi-conservative replication)] | \n", + "[(progeria-1, telomere maintenance via semi-conservative replication)] | \n", + "
| 92 | \n", + "protein homodimerization activity | \n", + "NaN | \n", + "[(regulation of presynaptic membrane potential-1, protein heterodimerization activity)] | \n", + "NaN | \n", + "
| 93 | \n", + "obsolete covalent chromatin modification | \n", + "NaN | \n", + "[(tf-downreg-colorectal, structural constituent of chromatin)] | \n", + "NaN | \n", + "
| 94 | \n", + "obsolete RNA polymerase II transcription factor activity | \n", + "NaN | \n", + "NaN | \n", + "[(tf-downreg-colorectal-1, DNA-binding transcription factor activity, RNA polymerase II-specific)] | \n", + "
| \n", + " | id | \n", + "label | \n", + "redundant | \n", + "standard | \n", + "standard no ontology | \n", + "turbo ontological synopsis | \n", + "dav narrative synopsis | \n", + "dav ontological synopsis | \n", + "turbo no synopsis | \n", + "turbo narrative synopsis | \n", + "dav no synopsis | \n", + "rank based | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", + "GO:0006907 | \n", + "pinocytosis | \n", + "False | \n", + "0.0 | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 1 | \n", + "GO:0006897 | \n", + "endocytosis | \n", + "True | \n", + "1.0 | \n", + "6.0 | \n", + "0.0 | \n", + "0.0 | \n", + "5.0 | \n", + "0.0 | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 2 | \n", + "GO:0044351 | \n", + "macropinocytosis | \n", + "True | \n", + "2.0 | \n", + "0.0 | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 3 | \n", + "GO:0016192 | \n", + "vesicle-mediated transport | \n", + "True | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 4 | \n", + "GO:0030100 | \n", + "regulation of endocytosis | \n", + "False | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 5 | \n", + "GO:0006810 | \n", + "transport | \n", + "True | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 6 | \n", + "GO:0051234 | \n", + "establishment of localization | \n", + "True | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 7 | \n", + "GO:0045807 | \n", + "positive regulation of endocytosis | \n", + "True | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 8 | \n", + "GO:0060627 | \n", + "regulation of vesicle-mediated transport | \n", + "True | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 9 | \n", + "GO:0051179 | \n", + "localization | \n", + "True | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 10 | \n", + "GO:0031410 | \n", + "cytoplasmic vesicle | \n", + "False | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 11 | \n", + "GO:0097708 | \n", + "intracellular vesicle | \n", + "True | \n", + "11.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 12 | \n", + "GO:0050766 | \n", + "positive regulation of phagocytosis | \n", + "True | \n", + "12.0 | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 13 | \n", + "GO:0048518 | \n", + "positive regulation of biological process | \n", + "True | \n", + "13.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 14 | \n", + "GO:0050764 | \n", + "regulation of phagocytosis | \n", + "True | \n", + "14.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 15 | \n", + "GO:0051128 | \n", + "regulation of cellular component organization | \n", + "True | \n", + "15.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 16 | \n", + "GO:0031982 | \n", + "vesicle | \n", + "True | \n", + "16.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 17 | \n", + "GO:0150094 | \n", + "amyloid-beta clearance by cellular catabolic process | \n", + "False | \n", + "17.0 | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 18 | \n", + "GO:0006909 | \n", + "phagocytosis | \n", + "True | \n", + "18.0 | \n", + "17.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 19 | \n", + "GO:0051049 | \n", + "regulation of transport | \n", + "True | \n", + "19.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 20 | \n", + "GO:0006898 | \n", + "receptor-mediated endocytosis | \n", + "True | \n", + "20.0 | \n", + "2.0 | \n", + "2.0 | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 21 | \n", + "GO:0051050 | \n", + "positive regulation of transport | \n", + "True | \n", + "21.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 22 | \n", + "GO:0005041 | \n", + "low-density lipoprotein particle receptor activity | \n", + "True | \n", + "22.0 | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 23 | \n", + "GO:0030139 | \n", + "endocytic vesicle | \n", + "True | \n", + "23.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 24 | \n", + "GO:0030228 | \n", + "lipoprotein particle receptor activity | \n", + "True | \n", + "24.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 25 | \n", + "GO:0030666 | \n", + "endocytic vesicle membrane | \n", + "True | \n", + "25.0 | \n", + "18.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 26 | \n", + "GO:0097242 | \n", + "amyloid-beta clearance | \n", + "True | \n", + "26.0 | \n", + "22.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 27 | \n", + "GO:0051130 | \n", + "positive regulation of cellular component organization | \n", + "True | \n", + "27.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 28 | \n", + "GO:0060907 | \n", + "positive regulation of macrophage cytokine production | \n", + "True | \n", + "28.0 | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 29 | \n", + "GO:0032879 | \n", + "regulation of localization | \n", + "True | \n", + "29.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 30 | \n", + "GO:0048522 | \n", + "positive regulation of cellular process | \n", + "True | \n", + "30.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 31 | \n", + "GO:0002277 | \n", + "myeloid dendritic cell activation involved in immune response | \n", + "False | \n", + "31.0 | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 32 | \n", + "GO:0030659 | \n", + "cytoplasmic vesicle membrane | \n", + "True | \n", + "32.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 33 | \n", + "GO:0012506 | \n", + "vesicle membrane | \n", + "True | \n", + "33.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 34 | \n", + "GO:0061081 | \n", + "positive regulation of myeloid leukocyte cytokine production involved in immune response | \n", + "True | \n", + "34.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 35 | \n", + "GO:0010935 | \n", + "regulation of macrophage cytokine production | \n", + "True | \n", + "35.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 36 | \n", + "GO:0048583 | \n", + "regulation of response to stimulus | \n", + "False | \n", + "36.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 37 | \n", + "GO:1905167 | \n", + "positive regulation of lysosomal protein catabolic process | \n", + "True | \n", + "37.0 | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 38 | \n", + "GO:0009894 | \n", + "regulation of catabolic process | \n", + "True | \n", + "38.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 39 | \n", + "GO:0023051 | \n", + "regulation of signaling | \n", + "False | \n", + "39.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 40 | \n", + "GO:0051641 | \n", + "cellular localization | \n", + "True | \n", + "40.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 41 | \n", + "GO:1904352 | \n", + "positive regulation of protein catabolic process in the vacuole | \n", + "True | \n", + "41.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 42 | \n", + "GO:0070508 | \n", + "cholesterol import | \n", + "True | \n", + "42.0 | \n", + "13.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 43 | \n", + "GO:0031347 | \n", + "regulation of defense response | \n", + "True | \n", + "43.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 44 | \n", + "GO:0005794 | \n", + "Golgi apparatus | \n", + "False | \n", + "44.0 | \n", + "14.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 45 | \n", + "GO:1901700 | \n", + "response to oxygen-containing compound | \n", + "False | \n", + "45.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 46 | \n", + "GO:0061024 | \n", + "membrane organization | \n", + "False | \n", + "46.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 47 | \n", + "GO:0009966 | \n", + "regulation of signal transduction | \n", + "True | \n", + "47.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 48 | \n", + "GO:0015031 | \n", + "protein transport | \n", + "True | \n", + "48.0 | \n", + "NaN | \n", + "1.0 | \n", + "1.0 | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 49 | \n", + "GO:0048523 | \n", + "negative regulation of cellular process | \n", + "False | \n", + "49.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 50 | \n", + "GO:0032429 | \n", + "regulation of phospholipase A2 activity | \n", + "False | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 51 | \n", + "GO:0034381 | \n", + "plasma lipoprotein particle clearance | \n", + "False | \n", + "NaN | \n", + "11.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 52 | \n", + "GO:0031623 | \n", + "receptor internalization | \n", + "False | \n", + "NaN | \n", + "12.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 53 | \n", + "GO:0009931 | \n", + "calcium-dependent protein serine/threonine kinase activity | \n", + "False | \n", + "NaN | \n", + "15.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 54 | \n", + "GO:0005905 | \n", + "clathrin-coated pit | \n", + "False | \n", + "NaN | \n", + "16.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 55 | \n", + "GO:0032050 | \n", + "clathrin heavy chain binding | \n", + "False | \n", + "NaN | \n", + "19.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 56 | \n", + "GO:0030299 | \n", + "intestinal cholesterol absorption | \n", + "False | \n", + "NaN | \n", + "20.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 57 | \n", + "GO:0001540 | \n", + "amyloid-beta binding | \n", + "False | \n", + "NaN | \n", + "21.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 58 | \n", + "GO:0034383 | \n", + "low-density lipoprotein particle clearance | \n", + "False | \n", + "NaN | \n", + "23.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 59 | \n", + "GO:0032760 | \n", + "positive regulation of tumor necrosis factor production | \n", + "False | \n", + "NaN | \n", + "24.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 60 | \n", + "GO:0071404 | \n", + "cellular response to low-density lipoprotein particle stimulus | \n", + "False | \n", + "NaN | \n", + "25.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 61 | \n", + "GO:0042953 | \n", + "lipoprotein transport | \n", + "False | \n", + "NaN | \n", + "26.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 62 | \n", + "GO:0030169 | \n", + "low-density lipoprotein particle binding | \n", + "False | \n", + "NaN | \n", + "27.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 63 | \n", + "GO:0051639 | \n", + "actin filament network formation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 64 | \n", + "endoplasmic reticulum and recycling endosome membrane organization | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 65 | \n", + "GO:0016043 | \n", + "cellular component organization | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 66 | \n", + "intracellular signaling | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 67 | \n", + "GO:0051260 | \n", + "protein homooligomerization | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 68 | \n", + "protein signaling | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 69 | \n", + "GO:0006468 | \n", + "protein phosphorylation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 70 | \n", + "GO:0016567 | \n", + "protein ubiquitination | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 71 | \n", + "GO:0030030 | \n", + "cell projection organization | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 72 | \n", + "GO:0035091 | \n", + "phosphatidylinositol binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 73 | \n", + "GO:0001766 | \n", + "membrane raft polarization | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 74 | \n", + "GO:0097320 | \n", + "plasma membrane tubulation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 75 | \n", + "GO:0007041 | \n", + "lysosomal transport | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 76 | \n", + "GO:0007032 | \n", + "endosome organization | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 77 | \n", + "GO:0030163 | \n", + "protein catabolic process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 78 | \n", + "intracellular trafficking | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 79 | \n", + "cytoskeleton reorganization | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 80 | \n", + "GO:0007165 | \n", + "signal transduction | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "
| 81 | \n", + "vesicle/lipid trafficking | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "
| 82 | \n", + "cellular adhesion | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "
| 83 | \n", + "nutrient regulation | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "
| 84 | \n", + "cell metabolism | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "
| 85 | \n", + "cytoskeletal organization | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "
| 86 | \n", + "endocytosis/exocytosis | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "
| 87 | \n", + "intercellular adhesion/motility | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "
| 88 | \n", + "GO:0005654 | \n", + "nucleoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "
| 89 | \n", + "GO:0005634 | \n", + "nucleus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "
| 90 | \n", + "GO:0046872 | \n", + "metal ion binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "
| 91 | \n", + "GO:0005886 | \n", + "plasma membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "
| 92 | \n", + "GO:0005524 | \n", + "ATP binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "
| 93 | \n", + "GO:0045944 | \n", + "positive regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "
| 94 | \n", + "GO:0070062 | \n", + "extracellular exosome | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "
| 95 | \n", + "GO:0005576 | \n", + "extracellular region | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "
| 96 | \n", + "GO:0042802 | \n", + "identical protein binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "8.0 | \n", + "
| 97 | \n", + "GO:0005829 | \n", + "cytosol | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "9.0 | \n", + "
| 98 | \n", + "GO:0006357 | \n", + "regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "10.0 | \n", + "
| 99 | \n", + "GO:0005739 | \n", + "mitochondrion | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "11.0 | \n", + "
| 100 | \n", + "GO:0005737 | \n", + "cytoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "12.0 | \n", + "
| 101 | \n", + "GO:0016020 | \n", + "membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "13.0 | \n", + "
| 102 | \n", + "GO:0003723 | \n", + "RNA binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "14.0 | \n", + "
| 103 | \n", + "GO:0005615 | \n", + "extracellular space | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "15.0 | \n", + "
| \n", + " | has top term | \n", + "in top 5 | \n", + "in top 10 | \n", + "size overlap | \n", + "similarity | \n", + "num terms | \n", + "num GO terms | \n", + "nr size overlap | \n", + "nr similarity | \n", + "mean p value | \n", + "min p value | \n", + "max p value | \n", + "proportion significant | \n", + "num unannotated | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2188 | \n", + "True | \n", + "True | \n", + "True | \n", + "26 | \n", + "1.00 | \n", + "26 | \n", + "26 | \n", + "10 | \n", + "1.00e+00 | \n", + "0.02 | \n", + "1.83e-93 | \n", + "0.05 | \n", + "1.00 | \n", + "0 | \n", + "
| 2189 | \n", + "True | \n", + "True | \n", + "True | \n", + "9 | \n", + "0.28 | \n", + "15 | \n", + "15 | \n", + "2 | \n", + "1.05e-01 | \n", + "0.41 | \n", + "1.83e-93 | \n", + "1.00 | \n", + "0.60 | \n", + "0 | \n", + "
| 2179 | \n", + "True | \n", + "True | \n", + "True | \n", + "2 | \n", + "0.07 | \n", + "6 | \n", + "4 | \n", + "1 | \n", + "8.33e-02 | \n", + "0.50 | \n", + "1.83e-93 | \n", + "1.00 | \n", + "0.50 | \n", + "0 | \n", + "
| 2178 | \n", + "False | \n", + "False | \n", + "False | \n", + "1 | \n", + "0.04 | \n", + "8 | \n", + "3 | \n", + "0 | \n", + "0.00e+00 | \n", + "0.67 | \n", + "1.97e-03 | \n", + "1.00 | \n", + "0.33 | \n", + "0 | \n", + "
| 2184 | \n", + "True | \n", + "False | \n", + "True | \n", + "1 | \n", + "0.03 | \n", + "19 | \n", + "6 | \n", + "0 | \n", + "0.00e+00 | \n", + "0.83 | \n", + "1.83e-93 | \n", + "1.00 | \n", + "0.17 | \n", + "1 | \n", + "
| 2185 | \n", + "False | \n", + "False | \n", + "False | \n", + "1 | \n", + "0.03 | \n", + "10 | \n", + "6 | \n", + "0 | \n", + "0.00e+00 | \n", + "0.83 | \n", + "2.83e-38 | \n", + "1.00 | \n", + "0.17 | \n", + "0 | \n", + "
| 2176 | \n", + "False | \n", + "False | \n", + "False | \n", + "1 | \n", + "0.03 | \n", + "8 | \n", + "8 | \n", + "1 | \n", + "6.25e-02 | \n", + "0.88 | \n", + "4.66e-04 | \n", + "1.00 | \n", + "0.12 | \n", + "0 | \n", + "
| 2191 | \n", + "False | \n", + "False | \n", + "False | \n", + "1 | \n", + "0.02 | \n", + "30 | \n", + "30 | \n", + "0 | \n", + "0.00e+00 | \n", + "0.97 | \n", + "4.71e-02 | \n", + "1.00 | \n", + "0.03 | \n", + "1 | \n", + "
| 2192 | \n", + "True | \n", + "False | \n", + "False | \n", + "26 | \n", + "0.01 | \n", + "2570 | \n", + "2526 | \n", + "1 | \n", + "3.23e-03 | \n", + "0.99 | \n", + "1.83e-93 | \n", + "1.00 | \n", + "0.01 | \n", + "0 | \n", + "
| 2183 | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "6 | \n", + "2 | \n", + "0 | \n", + "0.00e+00 | \n", + "1.00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "1 | \n", + "
| 2177 | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "7 | \n", + "7 | \n", + "0 | \n", + "0.00e+00 | \n", + "1.00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "0 | \n", + "
| 2182 | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "5 | \n", + "2 | \n", + "0 | \n", + "0.00e+00 | \n", + "1.00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "0 | \n", + "
| 2186 | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "19 | \n", + "9 | \n", + "0 | \n", + "0.00e+00 | \n", + "1.00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "1 | \n", + "
| 2187 | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "13 | \n", + "8 | \n", + "0 | \n", + "0.00e+00 | \n", + "1.00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "1 | \n", + "
| 2181 | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "3 | \n", + "3 | \n", + "0 | \n", + "0.00e+00 | \n", + "1.00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "0 | \n", + "
| 2180 | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "3 | \n", + "2 | \n", + "0 | \n", + "0.00e+00 | \n", + "1.00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "0 | \n", + "
| 2190 | \n", + "False | \n", + "False | \n", + "False | \n", + "0 | \n", + "0.00 | \n", + "29 | \n", + "29 | \n", + "0 | \n", + "0.00e+00 | \n", + "1.00 | \n", + "1.00e+00 | \n", + "1.00 | \n", + "0.00 | \n", + "17 | \n", + "
| \n", + " | id | \n", + "label | \n", + "redundant | \n", + "standard | \n", + "standard no ontology | \n", + "dav ontological synopsis | \n", + "turbo no synopsis | \n", + "turbo ontological synopsis | \n", + "rank based | \n", + "dav no synopsis | \n", + "dav narrative synopsis | \n", + "turbo narrative synopsis | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", + "GO:0140313 | \n", + "molecular sequestering activity | \n", + "False | \n", + "0.0 | \n", + "1.0 | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 1 | \n", + "GO:0140311 | \n", + "protein sequestering activity | \n", + "True | \n", + "1.0 | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 2 | \n", + "GO:0140487 | \n", + "metal ion sequestering activity | \n", + "True | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 3 | \n", + "GO:0048519 | \n", + "negative regulation of biological process | \n", + "False | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 4 | \n", + "GO:0006950 | \n", + "response to stress | \n", + "False | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 5 | \n", + "GO:0048523 | \n", + "negative regulation of cellular process | \n", + "True | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 6 | \n", + "GO:0140678 | \n", + "molecular function inhibitor activity | \n", + "False | \n", + "6.0 | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 7 | \n", + "GO:0048585 | \n", + "negative regulation of response to stimulus | \n", + "True | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 8 | \n", + "GO:0036316 | \n", + "SREBP-SCAP complex retention in endoplasmic reticulum | \n", + "True | \n", + "8.0 | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 9 | \n", + "GO:0140315 | \n", + "iron ion sequestering activity | \n", + "True | \n", + "9.0 | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 10 | \n", + "GO:0140486 | \n", + "zinc ion sequestering activity | \n", + "True | \n", + "10.0 | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 11 | \n", + "GO:0140610 | \n", + "RNA sequestering activity | \n", + "True | \n", + "11.0 | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 12 | \n", + "GO:0005488 | \n", + "binding | \n", + "False | \n", + "12.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 13 | \n", + "GO:0051235 | \n", + "maintenance of location | \n", + "True | \n", + "13.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 14 | \n", + "GO:0002682 | \n", + "regulation of immune system process | \n", + "False | \n", + "14.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 15 | \n", + "GO:0010629 | \n", + "negative regulation of gene expression | \n", + "True | \n", + "15.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 16 | \n", + "GO:0032937 | \n", + "SREBP-SCAP-Insig complex | \n", + "False | \n", + "16.0 | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 17 | \n", + "GO:2000639 | \n", + "negative regulation of SREBP signaling pathway | \n", + "True | \n", + "17.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 18 | \n", + "GO:0009968 | \n", + "negative regulation of signal transduction | \n", + "True | \n", + "18.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 19 | \n", + "GO:0000041 | \n", + "transition metal ion transport | \n", + "False | \n", + "19.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 20 | \n", + "GO:1901222 | \n", + "regulation of NIK/NF-kappaB signaling | \n", + "False | \n", + "20.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 21 | \n", + "GO:0051651 | \n", + "maintenance of location in cell | \n", + "True | \n", + "21.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 22 | \n", + "GO:0010648 | \n", + "negative regulation of cell communication | \n", + "True | \n", + "22.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 23 | \n", + "GO:0023057 | \n", + "negative regulation of signaling | \n", + "True | \n", + "23.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 24 | \n", + "GO:0042802 | \n", + "identical protein binding | \n", + "True | \n", + "24.0 | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "24.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 25 | \n", + "GO:0071417 | \n", + "cellular response to organonitrogen compound | \n", + "False | \n", + "25.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 26 | \n", + "GO:0060363 | \n", + "cranial suture morphogenesis | \n", + "False | \n", + "NaN | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 27 | \n", + "GO:0010894 | \n", + "negative regulation of steroid biosynthetic process | \n", + "False | \n", + "NaN | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 28 | \n", + "GO:0090402 | \n", + "oncogene-induced cell senescence | \n", + "False | \n", + "NaN | \n", + "11.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 29 | \n", + "GO:0034198 | \n", + "cellular response to amino acid starvation | \n", + "False | \n", + "NaN | \n", + "12.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 30 | \n", + "GO:0008142 | \n", + "oxysterol binding | \n", + "False | \n", + "NaN | \n", + "13.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 31 | \n", + "GO:0032933 | \n", + "SREBP signaling pathway | \n", + "False | \n", + "NaN | \n", + "14.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 32 | \n", + "molecular sequestering | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 33 | \n", + "protein binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 34 | \n", + "transport of metal ions | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 35 | \n", + "response to infection and stress | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 36 | \n", + "GO:0010468 | \n", + "regulation of gene expression | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 37 | \n", + "GO:0019722 | \n", + "calcium-mediated signaling | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 38 | \n", + "regulation of transcription | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 39 | \n", + "calcium ion binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 40 | \n", + "identical protein binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 41 | \n", + "GO:0004252 | \n", + "serine-type endopeptidase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 42 | \n", + "GO:0140314 | \n", + "calcium ion sequestering activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 43 | \n", + "calcium-dependent protein binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 44 | \n", + "arginine binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 45 | \n", + "enzyme binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 46 | \n", + "GO:0019887 | \n", + "protein kinase regulator activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 47 | \n", + "nf-κb binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 48 | \n", + "nuclear localization sequence binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 49 | \n", + "oxysterol binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "11.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 50 | \n", + "rage receptor binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "12.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 51 | \n", + "ubiquitin protein ligase binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "13.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 52 | \n", + "actin binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "14.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 53 | \n", + "rig-i binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "15.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 54 | \n", + "GO:0003713 | \n", + "transcription coactivator activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "16.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 55 | \n", + "zinc ion binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "17.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 56 | \n", + "GO:1903231 | \n", + "mRNA base-pairing translational repressor activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "18.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 57 | \n", + "GO:0002376 | \n", + "immune system process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 58 | \n", + "GO:0006457 | \n", + "protein folding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 59 | \n", + "GO:0051641 | \n", + "cellular localization | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 60 | \n", + "GO:0006396 | \n", + "RNA processing | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 61 | \n", + "GO:0006829 | \n", + "zinc ion transport | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 62 | \n", + "GO:0010467 | \n", + "gene expression | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 63 | \n", + "GO:0007165 | \n", + "signal transduction | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "21.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 64 | \n", + "GO:0003723 | \n", + "RNA binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 65 | \n", + "GO:0005730 | \n", + "nucleolus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 66 | \n", + "GO:0005783 | \n", + "endoplasmic reticulum | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 67 | \n", + "GO:0000122 | \n", + "negative regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 68 | \n", + "GO:0005829 | \n", + "cytosol | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 69 | \n", + "GO:0070062 | \n", + "extracellular exosome | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 70 | \n", + "GO:0000981 | \n", + "DNA-binding transcription factor activity, RNA polymerase II-specific | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 71 | \n", + "GO:0008270 | \n", + "zinc ion binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 72 | \n", + "GO:0048471 | \n", + "perinuclear region of cytoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 73 | \n", + "GO:0005886 | \n", + "plasma membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 74 | \n", + "GO:0005615 | \n", + "extracellular space | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 75 | \n", + "GO:0005576 | \n", + "extracellular region | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "11.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 76 | \n", + "GO:0005737 | \n", + "cytoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "12.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 77 | \n", + "GO:0043231 | \n", + "intracellular membrane-bounded organelle | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "13.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 78 | \n", + "GO:0005789 | \n", + "endoplasmic reticulum membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "14.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 79 | \n", + "GO:0005524 | \n", + "ATP binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "15.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 80 | \n", + "GO:0007186 | \n", + "G protein-coupled receptor signaling pathway | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "16.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 81 | \n", + "GO:0000978 | \n", + "RNA polymerase II cis-regulatory region sequence-specific DNA binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "17.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 82 | \n", + "GO:0005739 | \n", + "mitochondrion | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "18.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 83 | \n", + "GO:0006357 | \n", + "regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "19.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 84 | \n", + "GO:0000785 | \n", + "chromatin | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "20.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 85 | \n", + "GO:0016020 | \n", + "membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "22.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 86 | \n", + "GO:0045944 | \n", + "positive regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "23.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 87 | \n", + "GO:0003677 | \n", + "DNA binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "25.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 88 | \n", + "GO:0005794 | \n", + "Golgi apparatus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "26.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 89 | \n", + "GO:0046872 | \n", + "metal ion binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "27.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 90 | \n", + "GO:0005634 | \n", + "nucleus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "28.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 91 | \n", + "GO:0005654 | \n", + "nucleoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "29.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 92 | \n", + "GO:0000075 | \n", + "cell cycle checkpoint signaling | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 93 | \n", + "cell adhesion/motility complex | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 94 | \n", + "transcriptional complex | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 95 | \n", + "GO:0036211 | \n", + "protein modification process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 96 | \n", + "rna processing complex | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 97 | \n", + "this list of genes encodes proteins involved in a range of cellular processes such as cell cycle progression | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "
| 98 | \n", + "GO:0006897 | \n", + "endocytosis | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "
| 99 | \n", + "iron storage and regulation | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "
| 100 | \n", + "cellular response to stress and inflammation | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "
| 101 | \n", + "GO:0006915 | \n", + "apoptotic process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "17.0 | \n", + "NaN | \n", + "
| 102 | \n", + "transcriptional regulation | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "
| 103 | \n", + "GO:0046907 | \n", + "intracellular transport | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "
| 104 | \n", + "GO:0016567 | \n", + "protein ubiquitination | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "
| 105 | \n", + "and toxic metal and cytosolic signaling. enriched terms include protein binding | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "8.0 | \n", + "NaN | \n", + "
| 106 | \n", + "lipid and hormone transport | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "9.0 | \n", + "NaN | \n", + "
| 107 | \n", + "GO:0003779 | \n", + "actin binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "10.0 | \n", + "NaN | \n", + "
| 108 | \n", + "GO:0003724 | \n", + "RNA helicase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "11.0 | \n", + "NaN | \n", + "
| 109 | \n", + "GO:0006511 | \n", + "ubiquitin-dependent protein catabolic process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "12.0 | \n", + "NaN | \n", + "
| 110 | \n", + "cell cycle progression | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "13.0 | \n", + "NaN | \n", + "
| 111 | \n", + "and negative regulation of nitrogen compound metabolic process. mechanism: these genes are involved in a wide range of processes related to regulating cell growth | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "14.0 | \n", + "NaN | \n", + "
| 112 | \n", + "GO:0032502 | \n", + "developmental process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "15.0 | \n", + "NaN | \n", + "
| 113 | \n", + "and homeostasis. they play a role in pathways such as the cell cycle | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "16.0 | \n", + "NaN | \n", + "
| 114 | \n", + "inflammatory metabolic processes | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "18.0 | \n", + "NaN | \n", + "
| 115 | \n", + "GO:0005515 | \n", + "protein binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "
| 116 | \n", + "GO:0006955 | \n", + "immune response | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "
| 117 | \n", + "intracellular transport\\n\\nmechanism/ | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "
| \n", + " | id | \n", + "label | \n", + "redundant | \n", + "standard | \n", + "standard no ontology | \n", + "rank based | \n", + "dav narrative synopsis | \n", + "turbo ontological synopsis | \n", + "turbo narrative synopsis | \n", + "dav no synopsis | \n", + "dav ontological synopsis | \n", + "turbo no synopsis | \n", + "
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", + "GO:0019814 | \n", + "immunoglobulin complex | \n", + "False | \n", + "0.0 | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 1 | \n", + "GO:0009897 | \n", + "external side of plasma membrane | \n", + "False | \n", + "1.0 | \n", + "0.0 | \n", + "89.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 2 | \n", + "GO:0098552 | \n", + "side of membrane | \n", + "True | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 3 | \n", + "GO:0002250 | \n", + "adaptive immune response | \n", + "False | \n", + "3.0 | \n", + "1.0 | \n", + "16.0 | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 4 | \n", + "GO:0009986 | \n", + "cell surface | \n", + "True | \n", + "4.0 | \n", + "NaN | \n", + "68.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 5 | \n", + "GO:0006955 | \n", + "immune response | \n", + "True | \n", + "5.0 | \n", + "6.0 | \n", + "52.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 6 | \n", + "GO:0002376 | \n", + "immune system process | \n", + "True | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 7 | \n", + "GO:0005886 | \n", + "plasma membrane | \n", + "True | \n", + "7.0 | \n", + "NaN | \n", + "64.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 8 | \n", + "GO:0071944 | \n", + "cell periphery | \n", + "True | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 9 | \n", + "GO:0003823 | \n", + "antigen binding | \n", + "False | \n", + "9.0 | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 10 | \n", + "GO:0005576 | \n", + "extracellular region | \n", + "False | \n", + "10.0 | \n", + "3.0 | \n", + "65.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 11 | \n", + "GO:0016020 | \n", + "membrane | \n", + "True | \n", + "11.0 | \n", + "NaN | \n", + "43.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 12 | \n", + "GO:0071735 | \n", + "IgG immunoglobulin complex | \n", + "True | \n", + "12.0 | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 13 | \n", + "GO:0032991 | \n", + "protein-containing complex | \n", + "True | \n", + "13.0 | \n", + "NaN | \n", + "63.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 14 | \n", + "GO:0050853 | \n", + "B cell receptor signaling pathway | \n", + "True | \n", + "14.0 | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 15 | \n", + "GO:0034987 | \n", + "immunoglobulin receptor binding | \n", + "False | \n", + "15.0 | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 16 | \n", + "GO:0050851 | \n", + "antigen receptor-mediated signaling pathway | \n", + "True | \n", + "16.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 17 | \n", + "GO:0050896 | \n", + "response to stimulus | \n", + "True | \n", + "17.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 18 | \n", + "PR:000050567 | \n", + "protein-containing material entity | \n", + "True | \n", + "18.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 19 | \n", + "GO:0072562 | \n", + "blood microparticle | \n", + "True | \n", + "19.0 | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 20 | \n", + "GO:0071745 | \n", + "IgA immunoglobulin complex | \n", + "True | \n", + "20.0 | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 21 | \n", + "GO:0002768 | \n", + "immune response-regulating cell surface receptor signaling pathway | \n", + "True | \n", + "21.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 22 | \n", + "GO:0002429 | \n", + "immune response-activating cell surface receptor signaling pathway | \n", + "True | \n", + "22.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 23 | \n", + "GO:0071753 | \n", + "IgM immunoglobulin complex | \n", + "True | \n", + "23.0 | \n", + "11.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 24 | \n", + "GO:0002764 | \n", + "immune response-regulating signaling pathway | \n", + "True | \n", + "24.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 25 | \n", + "GO:0002757 | \n", + "immune response-activating signaling pathway | \n", + "True | \n", + "25.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 26 | \n", + "GO:0071738 | \n", + "IgD immunoglobulin complex | \n", + "True | \n", + "26.0 | \n", + "12.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 27 | \n", + "GO:0071742 | \n", + "IgE immunoglobulin complex | \n", + "True | \n", + "27.0 | \n", + "13.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 28 | \n", + "GO:0002253 | \n", + "activation of immune response | \n", + "True | \n", + "28.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 29 | \n", + "GO:0050778 | \n", + "positive regulation of immune response | \n", + "True | \n", + "29.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 30 | \n", + "GO:0050776 | \n", + "regulation of immune response | \n", + "True | \n", + "30.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 31 | \n", + "GO:0042571 | \n", + "immunoglobulin complex, circulating | \n", + "True | \n", + "31.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 32 | \n", + "GO:0002684 | \n", + "positive regulation of immune system process | \n", + "True | \n", + "32.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 33 | \n", + "GO:0071752 | \n", + "secretory dimeric IgA immunoglobulin complex | \n", + "True | \n", + "33.0 | \n", + "14.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 34 | \n", + "GO:0071750 | \n", + "dimeric IgA immunoglobulin complex | \n", + "True | \n", + "34.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 35 | \n", + "GO:0071748 | \n", + "monomeric IgA immunoglobulin complex | \n", + "True | \n", + "35.0 | \n", + "15.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 36 | \n", + "GO:0071751 | \n", + "secretory IgA immunoglobulin complex | \n", + "True | \n", + "36.0 | \n", + "16.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 37 | \n", + "GO:0071749 | \n", + "polymeric IgA immunoglobulin complex | \n", + "True | \n", + "37.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 38 | \n", + "GO:0071746 | \n", + "IgA immunoglobulin complex, circulating | \n", + "True | \n", + "38.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 39 | \n", + "GO:0002682 | \n", + "regulation of immune system process | \n", + "True | \n", + "39.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 40 | \n", + "GO:0060267 | \n", + "positive regulation of respiratory burst | \n", + "False | \n", + "40.0 | \n", + "18.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 41 | \n", + "GO:0001895 | \n", + "retina homeostasis | \n", + "False | \n", + "41.0 | \n", + "17.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 42 | \n", + "GO:0071756 | \n", + "pentameric IgM immunoglobulin complex | \n", + "True | \n", + "42.0 | \n", + "20.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 43 | \n", + "GO:0071754 | \n", + "IgM immunoglobulin complex, circulating | \n", + "True | \n", + "43.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 44 | \n", + "GO:0034988 | \n", + "Fc-gamma receptor I complex binding | \n", + "True | \n", + "44.0 | \n", + "21.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 45 | \n", + "GO:0060263 | \n", + "regulation of respiratory burst | \n", + "True | \n", + "45.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 46 | \n", + "GO:0019731 | \n", + "antibacterial humoral response | \n", + "False | \n", + "NaN | \n", + "19.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 47 | \n", + "GO:0003094 | \n", + "glomerular filtration | \n", + "False | \n", + "NaN | \n", + "22.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 48 | \n", + "GO:0005615 | \n", + "extracellular space | \n", + "False | \n", + "NaN | \n", + "23.0 | \n", + "39.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 49 | \n", + "GO:0003674 | \n", + "molecular_function | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 50 | \n", + "GO:0010628 | \n", + "positive regulation of gene expression | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 51 | \n", + "GO:0005737 | \n", + "cytoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 52 | \n", + "GO:0030425 | \n", + "dendrite | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 53 | \n", + "GO:0006355 | \n", + "regulation of DNA-templated transcription | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 54 | \n", + "GO:0005813 | \n", + "centrosome | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 55 | \n", + "GO:0016604 | \n", + "nuclear body | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 56 | \n", + "GO:0003700 | \n", + "DNA-binding transcription factor activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 57 | \n", + "GO:0016607 | \n", + "nuclear speck | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "8.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 58 | \n", + "GO:0046872 | \n", + "metal ion binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "9.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 59 | \n", + "GO:0006954 | \n", + "inflammatory response | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "10.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 60 | \n", + "GO:0005856 | \n", + "cytoskeleton | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "11.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 61 | \n", + "GO:0030154 | \n", + "cell differentiation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "12.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 62 | \n", + "GO:0003677 | \n", + "DNA binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "13.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 63 | \n", + "GO:0000981 | \n", + "DNA-binding transcription factor activity, RNA polymerase II-specific | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "14.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 64 | \n", + "GO:0005730 | \n", + "nucleolus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "15.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 65 | \n", + "GO:0005509 | \n", + "calcium ion binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "17.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 66 | \n", + "GO:0005765 | \n", + "lysosomal membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "18.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 67 | \n", + "GO:0005743 | \n", + "mitochondrial inner membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "19.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 68 | \n", + "GO:0019899 | \n", + "enzyme binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "20.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 69 | \n", + "GO:0006468 | \n", + "protein phosphorylation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "21.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 70 | \n", + "GO:0050911 | \n", + "detection of chemical stimulus involved in sensory perception of smell | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "22.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 71 | \n", + "GO:0000785 | \n", + "chromatin | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "23.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 72 | \n", + "GO:0005759 | \n", + "mitochondrial matrix | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "24.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 73 | \n", + "GO:0106310 | \n", + "protein serine kinase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "25.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 74 | \n", + "GO:0003682 | \n", + "chromatin binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "26.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 75 | \n", + "GO:0007155 | \n", + "cell adhesion | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "27.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 76 | \n", + "GO:0004984 | \n", + "olfactory receptor activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "28.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 77 | \n", + "GO:0007165 | \n", + "signal transduction | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "29.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 78 | \n", + "GO:0061630 | \n", + "ubiquitin protein ligase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "30.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 79 | \n", + "GO:0005654 | \n", + "nucleoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "31.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 80 | \n", + "GO:0005829 | \n", + "cytosol | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "32.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 81 | \n", + "GO:0005575 | \n", + "cellular_component | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "33.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 82 | \n", + "GO:0000122 | \n", + "negative regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "34.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 83 | \n", + "GO:0042802 | \n", + "identical protein binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "35.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 84 | \n", + "GO:0008284 | \n", + "positive regulation of cell population proliferation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "36.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 85 | \n", + "GO:0007186 | \n", + "G protein-coupled receptor signaling pathway | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "37.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 86 | \n", + "GO:0005783 | \n", + "endoplasmic reticulum | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "38.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 87 | \n", + "GO:0001228 | \n", + "DNA-binding transcription activator activity, RNA polymerase II-specific | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "40.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 88 | \n", + "GO:0008270 | \n", + "zinc ion binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "41.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 89 | \n", + "GO:0000139 | \n", + "Golgi membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "42.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 90 | \n", + "GO:0003723 | \n", + "RNA binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "44.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 91 | \n", + "GO:0005789 | \n", + "endoplasmic reticulum membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "45.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 92 | \n", + "GO:0005525 | \n", + "GTP binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "46.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 93 | \n", + "GO:0005102 | \n", + "signaling receptor binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "47.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 94 | \n", + "GO:0005794 | \n", + "Golgi apparatus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "48.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 95 | \n", + "GO:0043231 | \n", + "intracellular membrane-bounded organelle | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "49.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 96 | \n", + "GO:0005739 | \n", + "mitochondrion | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "50.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 97 | \n", + "GO:0051301 | \n", + "cell division | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "51.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 98 | \n", + "GO:0006357 | \n", + "regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "53.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 99 | \n", + "GO:0048471 | \n", + "perinuclear region of cytoplasm | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "54.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 100 | \n", + "GO:1990837 | \n", + "sequence-specific double-stranded DNA binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "55.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 101 | \n", + "GO:0042803 | \n", + "protein homodimerization activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "56.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 102 | \n", + "GO:0007399 | \n", + "nervous system development | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "57.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 103 | \n", + "GO:0070062 | \n", + "extracellular exosome | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "58.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 104 | \n", + "GO:0006915 | \n", + "apoptotic process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "59.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 105 | \n", + "GO:0098978 | \n", + "glutamatergic synapse | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "60.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 106 | \n", + "GO:0043066 | \n", + "negative regulation of apoptotic process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "61.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 107 | \n", + "GO:0004674 | \n", + "protein serine/threonine kinase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "62.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 108 | \n", + "GO:0045087 | \n", + "innate immune response | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "66.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 109 | \n", + "GO:0005634 | \n", + "nucleus | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "67.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 110 | \n", + "GO:0005925 | \n", + "focal adhesion | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "69.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 111 | \n", + "GO:0019901 | \n", + "protein kinase binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "70.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 112 | \n", + "GO:0008150 | \n", + "biological_process | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "71.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 113 | \n", + "GO:0062023 | \n", + "collagen-containing extracellular matrix | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "72.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 114 | \n", + "GO:0007283 | \n", + "spermatogenesis | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "73.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 115 | \n", + "GO:0005524 | \n", + "ATP binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "74.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 116 | \n", + "GO:0045893 | \n", + "positive regulation of DNA-templated transcription | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "75.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 117 | \n", + "GO:0016887 | \n", + "ATP hydrolysis activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "76.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 118 | \n", + "GO:0035556 | \n", + "intracellular signal transduction | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "77.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 119 | \n", + "GO:0045892 | \n", + "negative regulation of DNA-templated transcription | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "78.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 120 | \n", + "GO:0008285 | \n", + "negative regulation of cell population proliferation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "79.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 121 | \n", + "GO:0043025 | \n", + "neuronal cell body | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "80.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 122 | \n", + "GO:0004930 | \n", + "G protein-coupled receptor activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "81.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 123 | \n", + "GO:0006508 | \n", + "proteolysis | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "82.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 124 | \n", + "GO:0000978 | \n", + "RNA polymerase II cis-regulatory region sequence-specific DNA binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "83.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 125 | \n", + "GO:0045202 | \n", + "synapse | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "84.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 126 | \n", + "GO:0045944 | \n", + "positive regulation of transcription by RNA polymerase II | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "85.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 127 | \n", + "GO:0044877 | \n", + "protein-containing complex binding | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "86.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 128 | \n", + "GO:0015031 | \n", + "protein transport | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "87.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 129 | \n", + "GO:0016324 | \n", + "apical plasma membrane | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "88.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 130 | \n", + "GO:0016567 | \n", + "protein ubiquitination | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "90.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 131 | \n", + "antigen binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "
| 132 | \n", + "immunoglobulin receptor binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "1.0 | \n", + "0.0 | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "
| 133 | \n", + "members of the immunoglobulin (ig) gene superfamily - specifically | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 134 | \n", + "igh | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 135 | \n", + "GO:0033984 | \n", + "indole-3-glycerol-phosphate lyase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 136 | \n", + "MESH:C014609 | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 137 | \n", + "response and maintenance of the adaptive immune system at different levels | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 138 | \n", + "likely via antigen binding | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 139 | \n", + "signal transduction and b cell activation | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "7.0 | \n", + "NaN | \n", + "NaN | \n", + "
| 140 | \n", + "GO:0002377 | \n", + "immunoglobulin production | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "0.0 | \n", + "
| 141 | \n", + "protein homodimerization | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 142 | \n", + "GO:0098542 | \n", + "defense response to other organism | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 143 | \n", + "GO:0002922 | \n", + "positive regulation of humoral immune response | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 144 | \n", + "b cell-mediated immunity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "
| 145 | \n", + "t cell receptor signaling | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "1.0 | \n", + "
| 146 | \n", + "GO:0042113 | \n", + "B cell activation | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "
| 147 | \n", + "t cell activation. \\n\\nhypotheses: this list of genes is heavily enriched in those involved in the function and development of b cells and t cells. specifically, they play a role in the production and function of immunoglobulins and t cell receptors, as well as the activation of these cell types. this suggests that these genes are integral to the proper functioning of the immune system | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "
| 148 | \n", + "fc-gamma receptor i complex binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "2.0 | \n", + "NaN | \n", + "
| 149 | \n", + "GO:0004715 | \n", + "non-membrane spanning protein tyrosine kinase activity | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "3.0 | \n", + "NaN | \n", + "
| 150 | \n", + "phosphotyrosine residue binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "4.0 | \n", + "NaN | \n", + "
| 151 | \n", + "peptidoglycan binding activity | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "5.0 | \n", + "NaN | \n", + "
| 152 | \n", + "phosphatidylcholine binding activity. mechanism: the genes listed appear to be involved in the regulation of the immune response. they likely aid in the recognition of pathogens, binding to the appropriate receptors, triggering a signal for an immune response. they may also play a role in enabling the recognition of self-antigens inhibiting a response to them | \n", + "None | \n", + "False | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "NaN | \n", + "6.0 | \n", + "NaN | \n", + "
| \n", + " | model | \n", + "geneset | \n", + "method | \n", + "summary | \n", + "
|---|---|---|---|---|
| 1680 | \n", + "None | \n", + "sensory ataxia-0 | \n", + "gpt-3.5-turbo.no_synopsis.v1 | \n", + "Summary: The enriched terms found among the listed human genes suggest a common involvement in cellular metabolism, particularly in mitochondrial function, protein folding and degradation, and transportation across cellular membranes.\\nMechanism: These genes may be involved in the maintenance of cellular homeostasis and energy production.\\n\\nHypothesis: Many of the enriched terms are related to cellular stress pathways, suggesting that these genes may be involved in the response to stress and cellular damage. Additionally, the involvement of several genes related to mitochondrial function suggests that there may be a common underlying mechanism related to energy production and metabolism. | \n", + "
| 1681 | \n", + "None | \n", + "sensory ataxia-0 | \n", + "gpt-3.5-turbo.no_synopsis.v2 | \n", + "Summary: Genes are involved in nervous system development and function. \\nMechanism: Myelination and axonal transport. \\n\\nHypothesis: The genes on the list are enriched for terms involved in nervous system development and function, including myelination, axon guidance, and neuron projection development. This suggests a role for these genes in the regulation of myelination and axonal transport, which are important processes for proper nervous system function. Dysfunction of these processes, due to mutations in genes such as PMP22 and SH3TC2, can lead to peripheral neuropathy and other neurological disorders. | \n", + "
| 1682 | \n", + "None | \n", + "sensory ataxia-0 | \n", + "gpt-3.5-turbo.ontological_synopsis.v1 | \n", + "Summary: Genes are primarily involved in the peripheral nervous system, myelination, and neurological disorders.\\nMechanism: The enriched terms suggest that these genes primarily function in the peripheral nervous system and myelination.\\n\\nHypothesis: These genes are all involved in the development and maintenance of the peripheral nervous system and myelination. Dysregulation or mutation of these genes likely leads to neuropathic disorders. | \n", + "
| 1683 | \n", + "None | \n", + "sensory ataxia-0 | \n", + "gpt-3.5-turbo.ontological_synopsis.v2 | \n", + "Summary: Genes are involved in various processes in the development and maintenance of the nervous system, specifically peripheral nerves and myelination, as well as nucleic acid and protein metabolism.\\n\\nMechanism: The enriched terms suggest a common underlying biological mechanism in the formation and maintenance of the peripheral nervous system and myelination, as well as in nucleic acid and protein metabolism.\\n\\n\\nHypothesis: The enrichment of terms related to Charcot-Marie-Tooth disease and myelination suggest that these genes play an important role in peripheral nervous system development and maintenance, specifically in the formation and maintenance of myelin. The enrichment of terms related to protein folding and nucleic acid metabolism suggest that these genes also have a role in maintaining and regulating the overall metabolic processes of cells. The involvement of genes in mitochondrial function suggests a possible link between peripheral nerve function and mitochondrial metabolism. | \n", + "
| 1684 | \n", + "None | \n", + "sensory ataxia-0 | \n", + "gpt-3.5-turbo.narrative_synopsis.v1 | \n", + "Summary: Myelin upkeep and neurological diseases\\n\\nHypothesis: Dysregulation of the myelin upkeep pathways can lead to mitochondrial dysfunction, accumulations of toxic metabolites, and impaired protein processing, which contribute to the development of neurological diseases. Dysfunction of the transporter proteins and nuclear membrane transporters can further exacerbate cell dysfunction and death. Treatment strategies aimed at restoring mitochondrial function and enhancing myelin synthesis and repair may alleviate symptoms of these diseases. | \n", + "
| 1685 | \n", + "None | \n", + "sensory ataxia-0 | \n", + "gpt-3.5-turbo.narrative_synopsis.v2 | \n", + "Summary: Peripheral nervous system myelination and neurodegenerative diseases are enriched in this set of genes. \\nMechanism: Maintenance of peripheral nervous system myelin structure and function through regulation of protein import, DNA replication, and degradation pathways in the endoplasmic reticulum and mitochondria. \\n | \n", + "
| 1686 | \n", + "None | \n", + "sensory ataxia-0 | \n", + "text-davinci-003.no_synopsis.v1 | \n", + "This list of genes is related to muscle, central and peripheral nervous system development, as well as protein and lipid transport and metabolism. \\nMechanism: The genes appear to be involved in regulatory pathways for growth and development of the skeletal and nervous systems via coordination of morphology, protein and lipid synthesis, and transport.\\n | \n", + "
| 1687 | \n", + "None | \n", + "sensory ataxia-0 | \n", + "text-davinci-003.no_synopsis.v2 | \n", + "These genes are mainly involved in protein synthesis, metabolism, ion channel transport, and muscle contraction or development.\\n\\nMechanism: These genes function as transcriptional regulators, enzymes in metabolic pathways, ion channels, or as key mediators of neuromuscular development and contraction.\\n\\n | \n", + "
| 1688 | \n", + "None | \n", + "sensory ataxia-0 | \n", + "text-davinci-003.ontological_synopsis.v1 | \n", + "The genes in the list are all involved in many functions including DNA-binding, RNA polymerase II-specific activity, metal ion binding, ubiquitin protein ligase binding, and positive regulation of transcription by RNA polymerase II. These genes are also likely to be involved in several processes including positive regulation of immunoglobulin production, regulation of ERBB signaling pathway, regulation of intracellular protein transport, monoatomic cation transport, nucleic acid metabolic process, protein hexamerization, glycosaminoglycan catabolic process, nervous system development, heme transport, and mitochondrial transport.\\n\\nMechanism: These genes likely coordinate a combination of transcription activities to maintain cell function, health, and development. They are also likely to be involved in transporting and processing essential molecules needed for maintaining normal neural and sensory functionality as well as involved in transporting and processing essential molecules for cell metabolism.\\n\\n | \n", + "
| 1689 | \n", + "None | \n", + "sensory ataxia-0 | \n", + "text-davinci-003.ontological_synopsis.v2 | \n", + "Analysis of the given list of genes suggests a common thread of involvement in the development and function of peripheral nerves, particularly with regard to varying forms of Charcot-Marie-Tooth disease, in addition to their role in nucleic acid and glycan metabolic pathways. \\n | \n", + "
| 1690 | \n", + "None | \n", + "sensory ataxia-0 | \n", + "text-davinci-003.narrative_synopsis.v1 | \n", + "\\nSummary: These genes are associated with functions related to development and maintenance of the nervous system, sensory systems, and erythropoiesis, as well as mitochodnrial mRNA synthesis and transcriptional regulation. \\n\\nMechanism: These genes regulate post-translational processes including ubiquitination and processing, protein synthesis, transcription and activity of transcription factors, and organization of the cytoskeleton and nucleus.\\n\\n | \n", + "
| 1691 | \n", + "None | \n", + "sensory ataxia-0 | \n", + "text-davinci-003.narrative_synopsis.v2 | \n", + "\\n\\nSummary: List of genes are involved in transcription factors, degradation heparan sulfate, moonlighting proteins, immunoglobulin secretion, adapter or docking molecule, heme transporter, myelin upkeep, nuclear pore complex, mitochondrial DNA polymerase, ubiquitin ligase, and aminoacyl-tRNA synthetase.\\n\\n | \n", + "