diff --git a/examples/usecases/PCS/01_PCS_graph_workflow.ipynb b/examples/usecases/PCS/01_PCS_graph_workflow.ipynb index 49d6b48..4ccd535 100644 --- a/examples/usecases/PCS/01_PCS_graph_workflow.ipynb +++ b/examples/usecases/PCS/01_PCS_graph_workflow.ipynb @@ -1086,9 +1086,10 @@ ")\n", "\n", "if not os.path.exists(opentargets_dc_pickle_path):\n", - " opentargets_disease_compound_df, opentargets_disease_compound_metadata = (\n", - " opentargets.get_disease_compound_interactions(disease_mapping_df, cache_pubchem_cid=True)\n", - " )\n", + " (\n", + " opentargets_disease_compound_df,\n", + " opentargets_disease_compound_metadata,\n", + " ) = opentargets.get_disease_compound_interactions(disease_mapping_df, cache_pubchem_cid=True)\n", "\n", " opentargets_disease_compound_df.to_pickle(opentargets_dc_pickle_path)\n", " with open(opentargets_dc_metadata_path, \"wb\") as file:\n", @@ -1218,9 +1219,10 @@ ")\n", "\n", "if not os.path.exists(opentargets_gc_pickle_path):\n", - " opentargets_gene_compound_df, opentargets_gene_compound_metadata = (\n", - " opentargets.get_gene_compound_interactions(bridgedb_df)\n", - " )\n", + " (\n", + " opentargets_gene_compound_df,\n", + " opentargets_gene_compound_metadata,\n", + " ) = opentargets.get_gene_compound_interactions(bridgedb_df)\n", "\n", " opentargets_gene_compound_df.to_pickle(opentargets_gc_pickle_path)\n", " with open(opentargets_gc_metadata_path, \"wb\") as file:\n", diff --git a/examples/usecases/mito/graph_generation_human.ipynb b/examples/usecases/mito/graph_generation_human.ipynb new file mode 100644 index 0000000..5220169 --- /dev/null +++ b/examples/usecases/mito/graph_generation_human.ipynb @@ -0,0 +1,66125 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Explore mitochondrial impairment in tumars " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "**Aim**: in this notebook, you will see all the steps for collecting data and constructing a KG to explore mitochondrial impairment in tumer (both in human and mice)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Import required libraries" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "# Import modules\n", + "import gzip\n", + "import os\n", + "import pickle\n", + "from io import BytesIO\n", + "\n", + "import numpy as np\n", + "import pandas as pd\n", + "import requests\n", + "from gprofiler.gprofiler import GProfiler\n", + "\n", + "from pyBiodatafuse import id_mapper\n", + "from pyBiodatafuse.annotators import (\n", + " bgee,\n", + " disgenet,\n", + " minerva,\n", + " molmedb,\n", + " opentargets,\n", + " pubchem,\n", + " stringdb,\n", + " wikipathways,\n", + ")\n", + "from pyBiodatafuse.constants import BGEE_GENE_EXPRESSION_LEVELS_COL, DISGENET_DISEASE_COL\n", + "from pyBiodatafuse.graph import generator\n", + "from pyBiodatafuse.utils import (\n", + " combine_sources,\n", + " create_harmonized_input_file,\n", + " create_or_append_to_metadata,\n", + " get_identifier_of_interest,\n", + ")\n", + "\n", + "os.makedirs(\"data\", exist_ok=True)\n", + "base_dir = os.path.abspath(os.getcwd())" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Load the input files" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Number of genes: 12322\n" + ] + }, + { + "data": { + "text/html": [ + "
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identifierGENE_SYMBOLbaseMeanlog2FoldChangelfcSEstatpvaluepadjminus_log10_pvalue
6ENSG00000001084GCLC412.4493450.4540350.13023.4872220.0004880.0186593.311521
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" + ], + "text/plain": [ + " identifier GENE_SYMBOL baseMean log2FoldChange lfcSE stat \\\n", + "6 ENSG00000001084 GCLC 412.449345 0.454035 0.1302 3.487222 \n", + "\n", + " pvalue padj minus_log10_pvalue \n", + "6 0.000488 0.018659 3.311521 " + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Read only specific columns and skip the first row\n", + "all_genes_human = pd.read_excel(\"datasets/cachexia_vs_control_all_genes.xlsx\")\n", + "all_genes_human.rename(\n", + " columns={\"Unnamed: 0\": \"identifier\", \"Unnamed: 1\": \"GENE_SYMBOL\"}, inplace=True\n", + ")\n", + "deg_human = all_genes_human[all_genes_human[\"padj\"] < 0.05]\n", + "print(\"Number of genes:\", len(all_genes_human[\"identifier\"].unique()))\n", + "deg_human.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifierGENE_SYMBOLbaseMeanlog2FoldChangelfcSEstatpvaluepadjminus_log10_pvalue
7049ENSG00000159713TPPP3665.538751.4361980.3602263.9869340.0000670.0053444.174362
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" + ], + "text/plain": [ + " identifier GENE_SYMBOL baseMean log2FoldChange lfcSE \\\n", + "7049 ENSG00000159713 TPPP3 665.53875 1.436198 0.360226 \n", + "\n", + " stat pvalue padj minus_log10_pvalue \n", + "7049 3.986934 0.000067 0.005344 4.174362 " + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "deg_human[deg_human[\"identifier\"] == \"ENSG00000159713\"] # does not exist in the deg table shared" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Entity resolution with BridgeDB" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "pickle_path_human = os.path.join(base_dir, \"data/human/bridgedb_df_human.pkl\")\n", + "metadata_path_human = os.path.join(base_dir, \"data/human/bridgedb_metadata_human.pkl\")\n", + "\n", + "if not os.path.exists(pickle_path_human):\n", + " bridgedb_df_human, bridgedb_metadata_human = id_mapper.bridgedb_xref(\n", + " identifiers=all_genes_human,\n", + " input_species=\"Human\",\n", + " input_datasource=\"Ensembl\",\n", + " output_datasource=\"All\",\n", + " )\n", + " bridgedb_df_human.to_pickle(pickle_path_human)\n", + " with open(metadata_path_human, \"wb\") as file:\n", + " pickle.dump(bridgedb_metadata_human, file)\n", + "else:\n", + " bridgedb_df_human = pd.read_pickle(pickle_path_human)\n", + " with open(metadata_path_human, \"rb\") as file:\n", + " bridgedb_metadata_human = pickle.load(file)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Number of genes with mapping in BridgeDb: 12310\n" + ] + }, + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_deapadj_deaminus_log10_pvalue_dea
0ENSG00000000003EnsemblHGNC:11858HGNC Accession NumberTSPAN6106.899174-0.4016590.143909-2.7910570.0052540.07792.279542
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" + ], + "text/plain": [ + " identifier identifier.source target target.source \\\n", + "0 ENSG00000000003 Ensembl HGNC:11858 HGNC Accession Number \n", + "\n", + " GENE_SYMBOL_dea baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea \\\n", + "0 TSPAN6 106.899174 -0.401659 0.143909 -2.791057 \n", + "\n", + " pvalue_dea padj_dea minus_log10_pvalue_dea \n", + "0 0.005254 0.0779 2.279542 " + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "print(\"Number of genes with mapping in BridgeDb:\", len(bridgedb_df_human[\"identifier\"].unique()))\n", + "bridgedb_df_human.head(1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Extract \"NCBI Gene\" ids for adding transcription factor (TF) and target interaction " + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "# from pyBiodatafuse.annotators.tflink import get_tf_target\n", + "\n", + "# tflink_df, tflink_metadata = get_tf_target(\n", + "# tf_file=\"data/human/TFLink_Homo_sapiens_interactions_All_simpleFormat_v1.0.tsv.gz\",\n", + "# filename=\"data/human/tflink_human.tsv.gz\",\n", + "# filter_deg=True,\n", + "# bridgedb_df=bridgedb_df_human,\n", + "# )" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [], + "source": [ + "# from pyBiodatafuse.annotators.gprofiler import get_gene_enrichment\n", + "\n", + "# gprofiler_df, gprofiler_metadata = get_gene_enrichment(\n", + "# bridgedb_df=bridgedb_df_human)" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [], + "source": [ + "# gprofiler_df.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_deapadj_deaminus_log10_pvalue_dea
0ENSG00000000003Ensembl7105NCBI GeneTSPAN6106.899174-0.4016590.143909-2.7910570.0052540.07792.279542
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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "0 ENSG00000000003 Ensembl 7105 NCBI Gene TSPAN6 \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea \\\n", + "0 106.899174 -0.401659 0.143909 -2.791057 0.005254 \n", + "\n", + " padj_dea minus_log10_pvalue_dea \n", + "0 0.0779 2.279542 " + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_df_human = get_identifier_of_interest(bridgedb_df_human, \"NCBI Gene\")\n", + "ncbi_to_ensembl = dict(zip(ncbi_df_human['target'], ncbi_df_human['identifier']))\n", + "ncbi_df_human.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_deapadj_deaminus_log10_pvalue_dea
105693ENSG00000287047Ensembl105378473NCBI GeneNaN108.208973-0.815570.391216-2.0847060.0370960.218081.430673
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" + ], + "text/plain": [ + " identifier identifier.source target target.source \\\n", + "105693 ENSG00000287047 Ensembl 105378473 NCBI Gene \n", + "\n", + " GENE_SYMBOL_dea baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea \\\n", + "105693 NaN 108.208973 -0.81557 0.391216 -2.084706 \n", + "\n", + " pvalue_dea padj_dea minus_log10_pvalue_dea \n", + "105693 0.037096 0.21808 1.430673 " + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "bridgedb_df_human[bridgedb_df_human[\"target\"] == \"105378473\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Number of humman genes with mapping for NCBI Gene: 11792\n" + ] + } + ], + "source": [ + "print(\"Number of humman genes with mapping for NCBI Gene:\", len(ncbi_df_human[\"target\"].unique()))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Download TF-target interactions\n", + "\n", + "You can download the Gene-TF interactions dataset from **TFLink**. Please visit the following page for the download:\n", + "\n", + "[TFLink Download Page](https://tflink.net/download/)\n", + "\n", + "The datasets you need can be downloaded from the following links:\n", + "\n", + "**For Humans (Homo sapiens):**\n", + "- [TFLink_Homo_sapiens_interactions_All_simpleFormat_v1.0.tsv.gz](https://cdn.netbiol.org/tflink/download_files/TFLink_Homo_sapiens_interactions_All_simpleFormat_v1.0.tsv.gz)\n", + "\n", + "**For Mice (Mus musculus):**\n", + "- [TFLink_Mus_musculus_interactions_All_simpleFormat_v1.0.tsv.gz](https://cdn.netbiol.org/tflink/download_files/TFLink_Mus_musculus_interactions_All_simpleFormat_v1.0.tsv.gz)\n", + "\n", + "These files contain the TF-target interaction data in a simple format for each species.\n" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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UniprotID.TFUniprotID.TargetNCBI.GeneID.TFNCBI.GeneID.TargetName.TFName.TargetDetection.methodPubmedIDOrganismSource.databaseSmall-scale.evidenceTF.TFLink.orthoTF.nonTFLink.orthoTarget.TFLink.orthoTarget.nonTFLink.ortho
1P37231P1082654685915PPARGRARBchromatin immunoprecipitation assay;inferred b...17202159;12839938;29087512;27924024Homo sapiensGTRD;TRED;TRRUSTYes--Mm:P22605;Rn:D3ZFD9-
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" + ], + "text/plain": [ + " UniprotID.TF UniprotID.Target NCBI.GeneID.TF NCBI.GeneID.Target Name.TF \\\n", + "1 P37231 P10826 5468 5915 PPARG \n", + "\n", + " Name.Target Detection.method \\\n", + "1 RARB chromatin immunoprecipitation assay;inferred b... \n", + "\n", + " PubmedID Organism Source.database \\\n", + "1 17202159;12839938;29087512;27924024 Homo sapiens GTRD;TRED;TRRUST \n", + "\n", + " Small-scale.evidence TF.TFLink.ortho TF.nonTFLink.ortho \\\n", + "1 Yes - - \n", + "\n", + " Target.TFLink.ortho Target.nonTFLink.ortho \n", + "1 Mm:P22605;Rn:D3ZFD9 - " + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# URLs for the TF datasets\n", + "url_human = \"https://cdn.netbiol.org/tflink/download_files/TFLink_Homo_sapiens_interactions_All_simpleFormat_v1.0.tsv.gz\"\n", + "\n", + "# Function to download and read a gzipped file into a dataframe\n", + "def download_save_and_read(url, filename):\n", + " if not os.path.exists(filename):\n", + " response = requests.get(url)\n", + " with open(filename, \"wb\") as file:\n", + " file.write(response.content)\n", + " else:\n", + " print(f\"{filename} already exists, skipping download.\")\n", + "\n", + " with gzip.open(filename, \"rt\") as f:\n", + " df = pd.read_csv(f, sep=\"\\t\")\n", + " return df\n", + "\n", + "# Download and read the mouse and human datasets\n", + "tf_df_human = download_save_and_read(url_human, \"data/human/tflink_human.tsv.gz\")\n", + "\n", + "# Keep rows where both TF and target exist in our dataset\n", + "tf_df_human = tf_df_human[tf_df_human[\"NCBI.GeneID.TF\"].isin(ncbi_df_human[\"target\"])]\n", + "tf_df_human = tf_df_human[tf_df_human[\"NCBI.GeneID.Target\"].isin(ncbi_df_human[\"target\"])]\n", + "\n", + "tf_df_human.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(4067478, 15)" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tf_df_human.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(is_target\n", + " True 11283\n", + " False 534\n", + " Name: count, dtype: int64,\n", + " is_tf\n", + " False 10633\n", + " True 1184\n", + " Name: count, dtype: int64)" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Extract the TF and the TF targets\n", + "tf_list_human = list(tf_df_human[\"NCBI.GeneID.TF\"])\n", + "target_list_human = list(tf_df_human[\"NCBI.GeneID.Target\"])\n", + "\n", + "# Add 'is_tf' and 'is_target' columns\n", + "ncbi_df_human[\"is_tf\"] = ncbi_df_human[\"target\"].isin(tf_list_human)\n", + "ncbi_df_human[\"is_target\"] = ncbi_df_human[\"target\"].isin(target_list_human)\n", + "\n", + "ncbi_df_human[\"is_target\"].value_counts(), ncbi_df_human[\"is_tf\"].value_counts()" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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UniprotID.TFUniprotID.TargetNCBI.GeneID.TFNCBI.GeneID.TargetName.TFName.TargetDetection.methodPubmedIDOrganismSource.databaseSmall-scale.evidenceTF.TFLink.orthoTF.nonTFLink.orthoTarget.TFLink.orthoTarget.nonTFLink.orthoEnsembl.GeneID.TFEnsembl.GeneID.Target
6P13631P0541259163725RARGJUNinferred by curator17202159Homo sapiensTREDYesDr:Q91392;Mm:P18911Rn:D3ZF61Dr:Q6NZT5;Mm:P05627;Rn:P17325-ENSG00000172819ENSG00000177606
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" + ], + "text/plain": [ + " UniprotID.TF UniprotID.Target NCBI.GeneID.TF NCBI.GeneID.Target Name.TF \\\n", + "6 P13631 P05412 5916 3725 RARG \n", + "\n", + " Name.Target Detection.method PubmedID Organism Source.database \\\n", + "6 JUN inferred by curator 17202159 Homo sapiens TRED \n", + "\n", + " Small-scale.evidence TF.TFLink.ortho TF.nonTFLink.ortho \\\n", + "6 Yes Dr:Q91392;Mm:P18911 Rn:D3ZF61 \n", + "\n", + " Target.TFLink.ortho Target.nonTFLink.ortho Ensembl.GeneID.TF \\\n", + "6 Dr:Q6NZT5;Mm:P05627;Rn:P17325 - ENSG00000172819 \n", + "\n", + " Ensembl.GeneID.Target \n", + "6 ENSG00000177606 " + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# kepp only rows where the target is a DEG\n", + "tf_sig_df_human = tf_df_human[tf_df_human[\"NCBI.GeneID.Target\"].isin(ncbi_df_human[ncbi_df_human[\"padj_dea\"] <= 0.05][\"target\"])]\n", + "# add ensembl gene id for the TF and target\n", + "tf_sig_df_human['Ensembl.GeneID.TF'] = tf_sig_df_human['NCBI.GeneID.TF'].map(ncbi_to_ensembl)\n", + "tf_sig_df_human['Ensembl.GeneID.Target'] = tf_sig_df_human['NCBI.GeneID.Target'].map(ncbi_to_ensembl)\n", + "tf_sig_df_human.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array(['PKM', 'TGFB3', 'TUBG1', 'HERPUD1', 'PMVK', 'IGF2R', 'TMPO',\n", + " 'AKR1A1', 'MCM7', 'PPIF', 'GAPDH', 'NDUFS1', 'ETFDH', 'GCLC',\n", + " 'FECH', 'ZPR1', 'JUN', 'PARP1', 'DCAF11', 'AXIN2', 'MYC', 'ETS2',\n", + " 'CD38', 'AP4M1', 'DUSP1', 'GADD45A', 'EIF3B', 'CDCA7', 'TFRC',\n", + " 'NOP56', 'NDUFV1', 'IFNAR1', 'ACO2', 'ABCB6', 'CDKN1A', 'DAXX',\n", + " 'ETFA', 'UNG', 'PRDX3', 'ARHGEF9', 'EFCAB7', 'CHSY1', 'SLC30A9',\n", + " 'ECHDC1', 'MT-CO2', 'COQ6', 'GNG2', 'AGO4', 'GOLGA6L9', 'AOPEP',\n", + " 'ECHS1', 'NFE2L2', 'ZFP36', 'ACKR1', 'PM20D2', 'MYLK4', 'SRRT',\n", + " 'ING2', 'DBT', 'NUCKS1', 'CERT1', 'TBL2', 'GDI1', 'CIAO2A',\n", + " 'HABP4', 'RMDN3', 'FABP3', 'LTBP1', 'INSIG1', 'PAAF1', 'ZNF367',\n", + " 'FIBIN', 'NDUFA9', 'COQ9', 'FAM210A', 'LYSMD4', 'SC5D', 'ATP6V0D1',\n", + " 'CD2BP2', 'HNRNPAB', 'FTH1', 'DOP1B', 'PNPLA4', 'OLFML3', 'CEP112',\n", + " 'CLTCL1', 'OTUD1', 'PLAAT1', 'RBM19', 'IBTK', 'FOXO1', 'ALDH1A2',\n", + " 'ADAMTS1', 'TP53BP1', 'LACTB', 'BCL6', 'SPRYD4', 'DCAF6', 'DGKG',\n", + " 'NSF', 'FHL1', 'SUCLG1', 'EIF4EBP1', 'CAMTA1', 'AUP1', 'CPSF4',\n", + " 'BTG2', 'NFKBIA', 'PCCA', 'COL1A2', 'KCNE4', 'SCN7A', 'GGPS1',\n", + " 'NR1H3', 'ARHGEF6', 'NIPSNAP3B', 'TMED1', 'PPRC1', 'HSCB', 'PAN2',\n", + " 'DMAC2', 'ARHGAP18', 'GCSH', 'TMEM185A', 'MT-ND3', 'UBE2D4',\n", + " 'AGBL1', 'SRXN1', 'GSTZ1', 'CLYBL', 'NOP2', 'MCF2L2', 'ANAPC1',\n", + " 'EIF4EBP3', 'CYP4V2', 'ACADSB', 'FBN1', 'THY1', 'MYL3', 'ANK2',\n", + " 'HMG20A', 'HIBADH', 'ENTR1', 'CAPRIN2', 'CCS', 'SLC36A1', 'FGL2',\n", + " 'AGL', 'TAB2', 'ATP5MC3', 'TNFRSF12A', 'LRP2BP', 'MT-CO3',\n", + " 'TMEM159', 'ZNF608', 'NUP210', 'FNDC5', 'ACIN1', 'TAF1',\n", + " 'KIDINS220', 'INHBB', 'PEX7', 'CDK11A', 'NDUFA10', 'ACAT1',\n", + " 'NDUFS2', 'GDNF', 'NAV1', 'TSPYL2', 'RBP1', 'GRSF1', 'RET',\n", + " 'HACD2', 'CA14', 'OSBPL8', 'CKMT2', 'MRPL16', 'SLC25A12',\n", + " 'EPB41L2', 'C1RL', 'SDHC', 'MARK4', 'UQCC1', 'TOR3A', 'ADPRH',\n", + " 'PRRX1', 'FAM174B', 'XBP1', 'ETV5', 'OPN3', 'MYG1', 'PCNT',\n", + " 'RBFOX1', 'KHDRBS1', 'DHRS12', 'GNL2', 'SIRT5', 'BOLA1', 'HERC1',\n", + " 'SLCO5A1', 'TSTA3', 'NRG4', 'RFTN1', 'HAPLN3', 'POLDIP3', 'MFSD6',\n", + " 'SMIM20', 'LRPAP1', 'GATB', 'NMT1', 'RASD1', 'MT-CO1', 'SLCO4A1',\n", + " 'ARHGAP10', 'TMEM50B', 'MFN2', 'ST3GAL5', 'NTAN1', 'KCTD9', 'CA11',\n", + " 'NARS2', 'RANBP10', 'BHLHB9', 'GAB2', 'SHISA4', 'CYB5D2', 'NDUFS3',\n", + " 'IARS2', 'ZDHHC7', 'TIMELESS', 'LDLRAD4', 'MT1X', 'PGAM2', 'BLCAP',\n", + " 'KIF22', 'APBA1', 'SYNJ2BP', 'KRTCAP2', 'MICU1', 'CMC4', 'RCAN3',\n", + " 'DLD', 'ADA2', 'CHRNG', 'C1orf122', 'PKD1L1', 'CSAD', 'RAB9B',\n", + " 'NEDD1', 'BRAWNIN', 'HLTF', 'PPP2R5D', 'FSTL1', 'MKKS', 'MOSPD1',\n", + " 'VLDLR', 'IDH2', 'PDHB', 'SIL1', 'DNASE1', 'MT-ND5', 'PKIA',\n", + " 'DDX41', 'NUP85', 'MEMO1', 'AMOTL1', 'OXNAD1', 'PTP4A2', 'EEF2KMT',\n", + " 'ALDOA', 'SLC38A4', 'BNIP3', 'NMNAT3', 'DECR1', 'PLN', 'CSRNP1',\n", + " 'MAP3K7CL', 'GRIPAP1', 'PRKAG2', 'GSE1', 'CDH13', 'DDIT4', 'PARP4',\n", + " 'GUF1', 'MTMR2', 'ASTN2', 'DDX27', 'CCDC80', 'AUH', 'CCDC107',\n", + " 'SIRT4', 'ANKRD2', 'PTRHD1', 'GALNT1', 'ANKRD1', 'COQ10A', 'SCRN3',\n", + " 'ZC3H10', 'MFGE8', 'SSRP1', 'LRRC41', 'EMD', 'PCBD1', 'TECRL',\n", + " 'TIGD1', 'MT-ND2', 'RAPGEF2', 'ACTR1A', 'TACO1', 'BRMS1',\n", + " 'SELENOM', 'PLA2G12A', 'APOD', 'AIG1', 'PRDX5', 'TXNL4A', 'ZCRB1',\n", + " 'ABCA5', 'SNTB1', 'BTRC', 'RRP1', 'GADD45G', 'LRP4', 'VPS53',\n", + " 'PHYH', 'TMLHE', 'CFAP61', 'ABCA1', 'CKAP2', 'PPP1R27', 'GOT2',\n", + " 'PHPT1', 'CCN1', 'TRO', 'XIRP1', 'COX7B', 'CPT2', 'CCDC28B',\n", + " 'SOCS3', 'MRPS24', 'PPP1R10', 'MRPL45', 'APRT', 'NDUFAB1', 'HSPB1',\n", + " 'ARMCX4', 'USP54', 'MRPL44', 'RAB15', 'MB', 'FRAS1', 'BBS10',\n", + " 'ANK1', 'RRAGD', 'MAP3K4', 'CDC42EP3', 'NIPSNAP2', 'SDF2L1',\n", + " 'SLC35D1', 'PLCE1', 'APBB3', 'ICAM3', 'GNG5', 'P4HB', 'MT2A',\n", + " 'GPX4', 'ADRM1', 'KRI1', 'PHKG2', 'MT-CYB', 'NXF1', 'FDXR',\n", + " 'GLUD1', 'SPARC', 'CFAP44', 'ANGPT2', 'CEBPD', 'HMGCL', 'ATP6V1E2',\n", + " 'CCDC167', 'CCNL2', 'ACBD5', 'NNT', 'PHKB', 'SFRP4', 'CKB', 'AATF',\n", + " 'ADD3', 'WWP1', 'TMEM144', 'NADK2', 'CELF2', 'ABHD3', 'NUDT16',\n", + " 'METTL15', 'NELFE', 'PRKACB', 'ARPP21', 'SLC35E3', 'SLC14A1',\n", + " 'MBD5', 'PMP22', 'FAM149A', 'KCTD3', 'CARNMT1', 'CCDC124',\n", + " 'PPP1R1C', 'AACS', 'PGRMC2', 'PAQR9', 'CHRAC1', 'PRICKLE2',\n", + " 'ARMH3', 'DUT', 'RGN', 'LACTB2', 'RHOB', 'PSTPIP2', 'NNMT', 'BYSL',\n", + " 'KCNQ5', 'SIRT3', 'SUCLG2', 'DHTKD1', 'AAMDC', 'RNPS1', 'UGCG',\n", + " 'ATPAF1', 'ETFRF1', 'HSBP1L1', 'ZNRD2', 'TP63', 'RNF144A',\n", + " 'ATP5F1B', 'KLHL7', 'CTPS1', 'SH3KBP1', 'PDHX', 'TTL', 'PTGDS',\n", + " 'PPP1R12B', 'SPTB', 'KLF6', 'ALAS1', 'DCP1A', 'SUPV3L1', 'MT-ATP6',\n", + " 'ARID5B', 'MT-ND4', 'TPPP3', 'HNRNPU', 'ABLIM2', 'C19orf12',\n", + " 'SCP2', 'RNF5', 'NDUFAF5', 'LYRM7', 'DLST', 'KCTD2', 'ENC1',\n", + " 'GSTK1', 'S100A1', 'IGFBP3', 'ACOT1', 'VPS16', 'KLF4', 'WASHC3',\n", + " 'SLC22A3', 'IER5', 'UTRN', 'SLC7A6', 'APOOL', 'LRP1B', 'TPI1',\n", + " 'PFKP', 'FBXO9', 'THSD4', 'SLC16A1', 'NUDT6', 'ATP5F1A', 'LOXL4',\n", + " 'CYFIP2', 'RNF168', 'PPARA', 'GPX3', 'XPC', 'HIBCH', 'FAM171A1',\n", + " 'SUCLA2', 'DNAJC19', 'MRM3', 'NTPCR', 'PRDX2', 'FUNDC2',\n", + " 'TBC1D22B', 'IGSF3', 'DCUN1D5', 'SDHB', 'MYH6', 'MYORG', 'PSMG3',\n", + " 'OXSM', 'B4GALT6', 'FERMT2', 'RNLS', 'DGLUCY', 'CPSF7', 'SCN3B',\n", + " 'CNOT10', 'BLOC1S1', 'CCDC69', 'SMPD3', 'ARHGAP21', 'COX8A',\n", + " 'KAZALD1', 'NREP', 'TMEM65', 'MT-ND1', 'SF3A1', 'SPPL2A', 'ARSG',\n", + " 'EXOSC4', 'THSD1', 'CTNS', 'PLXDC1', 'SETD9', 'MT1E', 'UQCRC1',\n", + " 'NGRN', 'NOXA1', 'BCKDHB', 'YARS2', 'CHRNA1', 'GTPBP8', 'MEA1',\n", + " 'LIN37', 'ZCCHC2', 'CADM2', 'SYNPO2'], dtype=object)" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tf_sig_df_human[tf_sig_df_human[\"Name.TF\"] == \"MYC\"][\"Name.Target\"].unique()" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "2509282 AAMDC\n", + "5125177 ACADSB\n", + "1950997 ACBD5\n", + "831514 ACTR1A\n", + "3941183 AGO4\n", + " ... \n", + "2962146 WASHC3\n", + "3733022 YARS2\n", + "707720 ZC3H10\n", + "972910 ZCRB1\n", + "2592332 ZNRD2\n", + "Name: Name.Target, Length: 77, dtype: object" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tf_sig_df_human[tf_sig_df_human[\"Name.TF\"] == \"PDHX\"][\"Name.Target\"].sort_values()" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(192033, 17)" + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tf_sig_df_human.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Processing targets. (11817, 15)\n", + "Processed 2000 rows (targets).\n", + "Processed 4000 rows (targets).\n", + "Processed 6000 rows (targets).\n", + "Processed 8000 rows (targets).\n", + "Processed 10000 rows (targets).\n", + "Processing TFs...\n", + "Processed 2000 rows (TFs).\n", + "Processed 4000 rows (TFs).\n", + "Processed 6000 rows (TFs).\n", + "Processed 8000 rows (TFs).\n", + "Processed 10000 rows (TFs).\n" + ] + } + ], + "source": [ + "# Function to add targets and TFs to each row (gene)\n", + "def add_target_and_tf_interaction(ncbi_df, tf_df, filename):\n", + " if not os.path.exists(filename):\n", + " ncbi_df[\"its_target\"] = None\n", + " print(f\"Processing targets. {ncbi_df.shape}\")\n", + " for index, row in ncbi_df.iterrows():\n", + " if index % 2000 == 0 and index > 0:\n", + " print(f\"Processed {index} rows (targets).\")\n", + " if row[\"is_tf\"]:\n", + " targets = tf_df[tf_df[\"NCBI.GeneID.TF\"] == row[\"target\"]]\n", + " if not targets.empty:\n", + " target_info_list = targets[[\"NCBI.GeneID.Target\",\n", + " \"Ensembl.GeneID.Target\",\n", + " \"Name.Target\",\n", + " \"UniprotID.Target\",\n", + " \"Target.TFLink.ortho\",\n", + " \"Target.nonTFLink.ortho\",\n", + " \"Detection.method\",\n", + " \"PubmedID\",\n", + " \"Source.database\",\n", + " \"Small-scale.evidence\",\n", + " ]].to_dict(orient=\"records\")\n", + " ncbi_df.at[index, \"its_target\"] = target_info_list\n", + " else:\n", + " ncbi_df.at[index, \"its_target\"] = []\n", + "\n", + " ncbi_df[\"its_tf\"] = None\n", + " print(\"Processing TFs...\")\n", + " for index, row in ncbi_df.iterrows():\n", + " if index % 2000 == 0 and index > 0:\n", + " print(f\"Processed {index} rows (TFs).\")\n", + " if row[\"is_target\"] and row[\"padj_dea\"] <= 0.05:\n", + " tf = tf_df[tf_df[\"NCBI.GeneID.Target\"] == row[\"target\"]]\n", + " if not tf.empty:\n", + " tf_info_list = tf[[\"NCBI.GeneID.TF\",\n", + " \"Ensembl.GeneID.TF\",\n", + " \"Name.TF\",\n", + " \"UniprotID.TF\",\n", + " \"TF.TFLink.ortho\",\n", + " \"TF.nonTFLink.ortho\",\n", + " \"Detection.method\",\n", + " \"PubmedID\",\n", + " \"Source.database\",\n", + " \"Small-scale.evidence\",\n", + " ]].to_dict(orient=\"records\")\n", + " ncbi_df.at[index, \"its_tf\"] = tf_info_list\n", + " else:\n", + " # if row[\"padj_dea\"] <= 0.05:\n", + " # ncbi_df.at[index, \"its_tf\"] = None\n", + " # else:\n", + " ncbi_df.at[index, \"its_tf\"] = []\n", + "\n", + " ncbi_df.to_pickle(filename)\n", + "\n", + " else:\n", + " with open(filename, 'rb') as f:\n", + " ncbi_df = pickle.load(f)\n", + "\n", + " return ncbi_df\n", + "\n", + "# Add target and TF\n", + "ncbi_tf_df_human = add_target_and_tf_interaction(ncbi_df_human, tf_sig_df_human, filename=\"data/human/ncbi_tf_df_human.pkl\")" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_deapadj_deaminus_log10_pvalue_deais_tfis_targetits_targetits_tf
0ENSG00000000003Ensembl7105NCBI GeneTSPAN6106.899174-0.4016590.143909-2.7910570.0052540.0779002.279542FalseTrueNoneNone
1ENSG00000000419Ensembl8813NCBI GeneDPM1601.924666-0.1046540.161936-0.6462700.5181050.7833770.285582FalseTrueNoneNone
2ENSG00000000457Ensembl57147NCBI GeneSCYL3244.623536-0.2854180.118343-2.4117840.0158750.1419511.799295FalseTrueNoneNone
3ENSG00000000938Ensembl2268NCBI GeneFGR91.9587670.5993040.3421101.7517860.0798110.3286481.097940FalseTrueNoneNone
4ENSG00000000971Ensembl3075NCBI GeneCFH499.5831250.0794480.2553760.3111010.7557240.9073400.121637FalseTrueNoneNone
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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "0 ENSG00000000003 Ensembl 7105 NCBI Gene TSPAN6 \n", + "1 ENSG00000000419 Ensembl 8813 NCBI Gene DPM1 \n", + "2 ENSG00000000457 Ensembl 57147 NCBI Gene SCYL3 \n", + "3 ENSG00000000938 Ensembl 2268 NCBI Gene FGR \n", + "4 ENSG00000000971 Ensembl 3075 NCBI Gene CFH \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea \\\n", + "0 106.899174 -0.401659 0.143909 -2.791057 0.005254 \n", + "1 601.924666 -0.104654 0.161936 -0.646270 0.518105 \n", + "2 244.623536 -0.285418 0.118343 -2.411784 0.015875 \n", + "3 91.958767 0.599304 0.342110 1.751786 0.079811 \n", + "4 499.583125 0.079448 0.255376 0.311101 0.755724 \n", + "\n", + " padj_dea minus_log10_pvalue_dea is_tf is_target its_target its_tf \n", + "0 0.077900 2.279542 False True None None \n", + "1 0.783377 0.285582 False True None None \n", + "2 0.141951 1.799295 False True None None \n", + "3 0.328648 1.097940 False True None None \n", + "4 0.907340 0.121637 False True None None " + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_df_human.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_deapadj_deaminus_log10_pvalue_deais_tfis_targetits_targetits_tf
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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "7 ENSG00000001167 Ensembl 4800 NCBI Gene NFYA \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea \\\n", + "7 198.963515 0.339027 0.133075 2.547627 0.010846 \n", + "\n", + " padj_dea minus_log10_pvalue_dea is_tf is_target \\\n", + "7 0.114127 1.964737 True True \n", + "\n", + " its_target its_tf \n", + "7 [{'NCBI.GeneID.Target': '1647', 'Ensembl.GeneI... None " + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_df_human[ncbi_tf_df_human['its_target'].notna()].head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_deapadj_deaminus_log10_pvalue_deais_tfis_targetits_targetits_tf
3343ENSG00000116717Ensembl1647NCBI GeneGADD45A448.208281.4321840.3776283.7925790.0001490.0088323.826549FalseTrueNone[{'NCBI.GeneID.TF': '672', 'Ensembl.GeneID.TF'...
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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "3343 ENSG00000116717 Ensembl 1647 NCBI Gene GADD45A \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea \\\n", + "3343 448.20828 1.432184 0.377628 3.792579 0.000149 \n", + "\n", + " padj_dea minus_log10_pvalue_dea is_tf is_target its_target \\\n", + "3343 0.008832 3.826549 False True None \n", + "\n", + " its_tf \n", + "3343 [{'NCBI.GeneID.TF': '672', 'Ensembl.GeneID.TF'... " + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_df_human[ncbi_tf_df_human['target']==\"1647\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{3343: [{'NCBI.GeneID.TF': '672',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000012048',\n", + " 'Name.TF': 'BRCA1',\n", + " 'UniprotID.TF': 'P38398',\n", + " 'TF.TFLink.ortho': 'Mm:P48754;Rn:G3V8S5',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay;inferred by curator',\n", + " 'PubmedID': '17428466;12647291;18350249;11777930;10962562;27924024;18025037;17202159;29087512',\n", + " 'Source.database': 'GTRD;TRED;TRRUST',\n", + " 'Small-scale.evidence': 'Yes'},\n", + " {'NCBI.GeneID.TF': '4790',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000109320',\n", + " 'Name.TF': 'NFKB1',\n", + " 'UniprotID.TF': 'P19838',\n", + " 'TF.TFLink.ortho': 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immunoprecipitation assay',\n", + " 'PubmedID': '29126285',\n", + " 'Source.database': 'ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '26959',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000105856',\n", + " 'Name.TF': 'HBP1',\n", + " 'UniprotID.TF': 'O60381',\n", + " 'TF.TFLink.ortho': 'Dr:F1QK54;Mm:E9Q1A8;Rn:Z4YNI2',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'}]}" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_df_human[ncbi_tf_df_human['target']==\"1647\"][\"its_tf\"].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{3343: [{'NCBI.GeneID.TF': '672',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000012048',\n", + " 'Name.TF': 'BRCA1',\n", + " 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{'NCBI.GeneID.TF': '4824',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000167034',\n", + " 'Name.TF': 'NKX3-1',\n", + " 'UniprotID.TF': 'Q99801',\n", + " 'TF.TFLink.ortho': 'Mm:P97436',\n", + " 'TF.nonTFLink.ortho': 'Dr:Q68EL7;Rn:Q497B7',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285',\n", + " 'Source.database': 'ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '7728',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000105497',\n", + " 'Name.TF': 'ZNF175',\n", + " 'UniprotID.TF': 'Q9Y473',\n", + " 'TF.TFLink.ortho': '-',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285',\n", + " 'Source.database': 'ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '26959',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000105856',\n", + " 'Name.TF': 'HBP1',\n", + " 'UniprotID.TF': 'O60381',\n", + " 'TF.TFLink.ortho': 'Dr:F1QK54;Mm:E9Q1A8;Rn:Z4YNI2',\n", 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{'NCBI.GeneID.Target': '6309',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000109929',\n", + " 'Name.Target': 'SC5D',\n", + " 'UniprotID.Target': 'O75845',\n", + " 'Target.TFLink.ortho': 'Dr:F1QG97;Mm:O88822;Rn:Q9EQS5;Sc:P32353',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '9114',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000159720',\n", + " 'Name.Target': 'ATP6V0D1',\n", + " 'UniprotID.Target': 'P61421',\n", + " 'Target.TFLink.ortho': '-',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '10421',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000169217',\n", + " 'Name.Target': 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'Dm:Q9VZE2;Mm:Q9D1X9;Rn:Q5BJS6',\n", + " 'Target.nonTFLink.ortho': 'Ce:Q9N2X7',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '9927',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000116688',\n", + " 'Name.Target': 'MFN2',\n", + " 'UniprotID.Target': 'O95140',\n", + " 'Target.TFLink.ortho': 'Dr:A8WIN6;Mm:Q80U63',\n", + " 'Target.nonTFLink.ortho': 'Rn:F7FHF7',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '8869',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000115525',\n", + " 'Name.Target': 'ST3GAL5',\n", + " 'UniprotID.Target': 'Q9UNP4',\n", + " 'Target.TFLink.ortho': 'Rn:Q68G12',\n", + " 'Target.nonTFLink.ortho': 'Dr:F1RCA6;Mm:A0A0U1RNK2',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '123803',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000157045',\n", + " 'Name.Target': 'NTAN1',\n", + " 'UniprotID.Target': 'Q96AB6',\n", + " 'Target.TFLink.ortho': 'Dm:Q7KIS4;Mm:Q64311;Rn:A0A0G2JWG0',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '54793',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000104756',\n", + " 'Name.Target': 'KCTD9',\n", + " 'UniprotID.Target': 'Q7L273',\n", + " 'Target.TFLink.ortho': 'Dm:B9A0N7;Dr:A8DZF0;Rn:D3ZE91',\n", + " 'Target.nonTFLink.ortho': 'Dr:B0V3Q8;Mm:E9PUA6',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '770',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000063180',\n", + " 'Name.Target': 'CA11',\n", + " 'UniprotID.Target': 'O75493',\n", + " 'Target.TFLink.ortho': 'Mm:O70354;Rn:Q811X3',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '79731',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000137513',\n", + " 'Name.Target': 'NARS2',\n", + " 'UniprotID.Target': 'Q96I59',\n", + " 'Target.TFLink.ortho': 'Ce:Q95PZ8;Dm:Q7JZR5;Mm:Q8BGV0;Sc:P25345',\n", + " 'Target.nonTFLink.ortho': 'Rn:A0A0G2K7D7',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '57610',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000141084',\n", + " 'Name.Target': 'RANBP10',\n", + " 'UniprotID.Target': 'Q6VN20',\n", + " 'Target.TFLink.ortho': '-',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '80823',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000198908',\n", + " 'Name.Target': 'BHLHB9',\n", + " 'UniprotID.Target': 'Q6PI77',\n", + " 'Target.TFLink.ortho': '-',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '9846',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000033327',\n", + " 'Name.Target': 'GAB2',\n", + " 'UniprotID.Target': 'Q9UQC2',\n", + " 'Target.TFLink.ortho': 'Mm:Q3ZB57;Rn:F1LSR2',\n", + " 'Target.nonTFLink.ortho': 'Dr:A0A0R4I9X7',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '149345',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000198892',\n", + " 'Name.Target': 'SHISA4',\n", + " 'UniprotID.Target': 'Q96DD7',\n", + " 'Target.TFLink.ortho': 'Dr:A5WUR8;Mm:Q8CA71;Rn:A0MV40',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '124936',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000167740',\n", + " 'Name.Target': 'CYB5D2',\n", + " 'UniprotID.Target': 'Q8WUJ1',\n", + " 'Target.TFLink.ortho': 'Ce:Q9XXA7;Dm:Q9W376;Mm:Q5SSH8;Rn:Q6AY62',\n", + " 'Target.nonTFLink.ortho': 'Dr:A2CES0',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '4722',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000213619',\n", + " 'Name.Target': 'NDUFS3',\n", + " 'UniprotID.Target': 'O75489',\n", + " 'Target.TFLink.ortho': 'Dm:Q9VZU4;Dr:F1R4C8;Mm:Q9DCT2;Rn:D3ZG43',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '55699',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000067704',\n", + " 'Name.Target': 'IARS2',\n", + " 'UniprotID.Target': 'Q9NSE4',\n", + " 'Target.TFLink.ortho': 'Dm:Q9VUY4;Dr:F1QUQ0;Mm:Q8BIJ6;Rn:A0A0G2K261;Sc:P48526',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '55625',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000153786',\n", + " 'Name.Target': 'ZDHHC7',\n", + " 'UniprotID.Target': 'Q9NXF8',\n", + " 'Target.TFLink.ortho': 'Dr:Q6DHI1;Mm:Q91WU6;Rn:Q923G5',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '2597',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000111640',\n", + " 'Name.Target': 'GAPDH',\n", + " 'UniprotID.Target': 'P04406',\n", + " 'Target.TFLink.ortho': 'Ce:P17331;Ce:P04970;Ce:P17330;Ce:P17329;Dm:P07486;Dm:P07487;Mm:S4R1W1;Rn:P04797',\n", + " 'Target.nonTFLink.ortho': 'Mm:S4R1W8;Mm:A0A1D5RLD8;Rn:D3ZGY4;Rn:M0R590',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '8914',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000111602',\n", + " 'Name.Target': 'TIMELESS',\n", + " 'UniprotID.Target': 'Q9UNS1',\n", + " 'Target.TFLink.ortho': 'Ce:G5EDN3;Dm:Q8INH7;Dr:E7FGL0;Mm:Q9R1X4;Rn:E9PTS7',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '753',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000168675',\n", + " 'Name.Target': 'LDLRAD4',\n", + " 'UniprotID.Target': 'O15165',\n", + " 'Target.TFLink.ortho': 'Dr:E9QGX8;Mm:Q8BWJ4',\n", + " 'Target.nonTFLink.ortho': 'Rn:F1LZA8',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '4501',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000187193',\n", + " 'Name.Target': 'MT1X',\n", + " 'UniprotID.Target': 'P80297',\n", + " 'Target.TFLink.ortho': '-',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '5224',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000164708',\n", + " 'Name.Target': 'PGAM2',\n", + " 'UniprotID.Target': 'P15259',\n", + " 'Target.TFLink.ortho': 'Mm:O70250',\n", + " 'Target.nonTFLink.ortho': 'Dr:Q7T3G4;Rn:P16290',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '10904',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000166619',\n", + " 'Name.Target': 'BLCAP',\n", + " 'UniprotID.Target': 'P62952',\n", + " 'Target.TFLink.ortho': 'Ce:G5EE03;Dm:Q9V3L0;Dr:Q9IB61;Mm:P62951;Rn:P62950',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '3835',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000079616',\n", + " 'Name.Target': 'KIF22',\n", + " 'UniprotID.Target': 'Q14807',\n", + " 'Target.TFLink.ortho': 'Dr:B7ZV80;Mm:Q3V300;Rn:Q5I0E8',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '320',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000107282',\n", + " 'Name.Target': 'APBA1',\n", + " 'UniprotID.Target': 'Q02410',\n", + " 'Target.TFLink.ortho': 'Mm:B2RUJ5;Rn:F1LR60',\n", + " 'Target.nonTFLink.ortho': 'Dr:A0A2R9YJM9',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '55333',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000213463',\n", + " 'Name.Target': 'SYNJ2BP',\n", + " 'UniprotID.Target': 'P57105',\n", + " 'Target.TFLink.ortho': 'Dr:Q7ZV59;Mm:Q9D6K5;Rn:Q9WVJ4',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '200185',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000163463',\n", + " 'Name.Target': 'KRTCAP2',\n", + " 'UniprotID.Target': 'Q8N6L1',\n", + " 'Target.TFLink.ortho': 'Dm:Q8INQ7;Dr:Q0P494;Mm:Q5RL79;Rn:B2RZC9',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '10367',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000107745',\n", + " 'Name.Target': 'MICU1',\n", + " 'UniprotID.Target': 'Q9BPX6',\n", + " 'Target.TFLink.ortho': 'Ce:Q95PZ2;Dm:A2VEI2;Mm:Q8VCX5;Rn:A0A0G2K0T5',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '100272147',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000182712',\n", + " 'Name.Target': 'CMC4',\n", + " 'UniprotID.Target': 'P56277',\n", + " 'Target.TFLink.ortho': 'Dm:B7YZN8;Dr:A0A0R4IZJ0;Mm:Q61908;Rn:A0A0G2K2W2',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '11123',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000117602',\n", + " 'Name.Target': 'RCAN3',\n", + " 'UniprotID.Target': 'Q9UKA8',\n", + " 'Target.TFLink.ortho': 'Mm:Q9JKK0;Rn:F7ENE7',\n", + " 'Target.nonTFLink.ortho': 'Dr:Q6DG39',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '4719',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000023228',\n", + " 'Name.Target': 'NDUFS1',\n", + " 'UniprotID.Target': 'P28331',\n", + " 'Target.TFLink.ortho': 'Ce:Q9N4Y8;Dm:Q94511;Mm:Q91VD9;Rn:Q66HF1',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '1738',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000091140',\n", + " 'Name.Target': 'DLD',\n", + " 'UniprotID.Target': 'P09622',\n", + " 'Target.TFLink.ortho': 'Ce:O17953;Dm:Q9VVL7;Dr:Q6TNU6;Mm:O08749;Rn:Q6P6R2;Sc:P09624',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '51816',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000093072',\n", + " 'Name.Target': 'ADA2',\n", + " 'UniprotID.Target': 'Q9NZK5',\n", + " 'Target.TFLink.ortho': 'Dm:Q9VVK4;Dm:Q9VVK5',\n", + " 'Target.nonTFLink.ortho': 'Dm:Q7KGG1;Dr:F1R9S0;Dr:F6NKG5',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'}]}" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_df_human[ncbi_tf_df_human['target']==\"3725\"][\"its_target\"].to_dict()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Enrichment analysis using g:Profiler\n", + "all the pathways and annotations are being added despite being significance." + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [], + "source": [ + "gp = GProfiler(return_dataframe=True)\n", + "filename_human = \"data/human/gprofiler_human.pkl\"\n", + "if not os.path.exists(filename_human):\n", + " gprofiler_human = gp.profile(\n", + " organism=\"hsapiens\",\n", + " all_results=True,\n", + " query=bridgedb_df_human[bridgedb_df_human[\"padj_dea\"] <= 0.05][\"identifier\"]\n", + " .unique()\n", + " .tolist(),\n", + " background=bridgedb_df_human[\"identifier\"].unique().tolist(),\n", + " no_evidences=False,\n", + " significance_threshold_method=\"fdr\",\n", + " user_threshold=0.05,\n", + " )\n", + " gprofiler_human.rename(columns={\"native\": \"id\"}, inplace=True)\n", + " gprofiler_human[\"datasource\"] = \"g:Profiler\"\n", + " gprofiler_human.to_pickle(filename_human)\n", + "else:\n", + " with open(filename_human, \"rb\") as f:\n", + " gprofiler_human = pickle.load(f)" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(25282, 17)\n" + ] + }, + { + "data": { + "text/html": [ + "
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sourceidnamep_valuesignificantdescriptionterm_sizequery_sizeintersection_sizeeffective_domain_sizeprecisionrecallqueryparentsintersectionsevidencesdatasource
0GO:CCGO:0005739mitochondrion1.242535e-16True\"A semiautonomous, self replicating organelle ...1429591145123030.2453470.10147query_1[GO:0005737, GO:0043231][ENSG00000001084, ENSG00000004779, ENSG0000000...[[IEA], [IDA, IPI, ISS, IBA, TAS, NAS, IEA], [...g:Profiler
\n", + "
" + ], + "text/plain": [ + " source id name p_value significant \\\n", + "0 GO:CC GO:0005739 mitochondrion 1.242535e-16 True \n", + "\n", + " description term_size query_size \\\n", + "0 \"A semiautonomous, self replicating organelle ... 1429 591 \n", + "\n", + " intersection_size effective_domain_size precision recall query \\\n", + "0 145 12303 0.245347 0.10147 query_1 \n", + "\n", + " parents \\\n", + "0 [GO:0005737, GO:0043231] \n", + "\n", + " intersections \\\n", + "0 [ENSG00000001084, ENSG00000004779, ENSG0000000... \n", + "\n", + " evidences datasource \n", + "0 [[IEA], [IDA, IPI, ISS, IBA, TAS, NAS, IEA], [... g:Profiler " + ] + }, + "execution_count": 23, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "print(gprofiler_human.shape)\n", + "gprofiler_human.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([list(['ENSG00000001084', 'ENSG00000014824', 'ENSG00000022267', 'ENSG00000023228', 'ENSG00000040531', 'ENSG00000048740', 'ENSG00000055163', 'ENSG00000067704', 'ENSG00000073282', 'ENSG00000079616', 'ENSG00000087053', 'ENSG00000088682', 'ENSG00000093072', 'ENSG00000101247', 'ENSG00000101361', 'ENSG00000102119', 'ENSG00000102893', 'ENSG00000103657', 'ENSG00000106211', 'ENSG00000106617', 'ENSG00000106638', 'ENSG00000107537', 'ENSG00000107745', 'ENSG00000109099', 'ENSG00000109917', 'ENSG00000111669', 'ENSG00000112357', 'ENSG00000112640', 'ENSG00000113140', 'ENSG00000115840', 'ENSG00000116171', 'ENSG00000116688', 'ENSG00000117118', 'ENSG00000119699', 'ENSG00000120725', 'ENSG00000120802', 'ENSG00000122550', 'ENSG00000125863', 'ENSG00000128918', 'ENSG00000131174', 'ENSG00000131943', 'ENSG00000134313', 'ENSG00000134569', 'ENSG00000136143', 'ENSG00000137513', 'ENSG00000138435', 'ENSG00000139131', 'ENSG00000139180', 'ENSG00000141252', 'ENSG00000141759', 'ENSG00000143252', 'ENSG00000144354', 'ENSG00000147852', 'ENSG00000148677', 'ENSG00000149925', 'ENSG00000152904', 'ENSG00000153107', 'ENSG00000154518', 'ENSG00000156873', 'ENSG00000157184', 'ENSG00000158864', 'ENSG00000162688', 'ENSG00000163541', 'ENSG00000164708', 'ENSG00000165029', 'ENSG00000165672', 'ENSG00000165731', 'ENSG00000166147', 'ENSG00000167792', 'ENSG00000168542', 'ENSG00000173085', 'ENSG00000175198', 'ENSG00000179941', 'ENSG00000181192', 'ENSG00000196177', 'ENSG00000196811', 'ENSG00000197616', 'ENSG00000198125', 'ENSG00000198523', 'ENSG00000198712', 'ENSG00000198727', 'ENSG00000198763', 'ENSG00000198786', 'ENSG00000198804', 'ENSG00000198840', 'ENSG00000198886', 'ENSG00000198888', 'ENSG00000198899', 'ENSG00000198938', 'ENSG00000204406', 'ENSG00000205981', 'ENSG00000213619', 'ENSG00000215305', 'ENSG00000221838'])],\n", + " dtype=object)" + ] + }, + "execution_count": 24, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "gprofiler_human[gprofiler_human[\"id\"] == \"HP:0011805\"][\"intersections\"].values" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [], + "source": [ + "gprofiler_human = gprofiler_human[\n", + " ~gprofiler_human[\"parents\"].apply(lambda x: x == [])\n", + "] # rm the root terms" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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intersectionsg:Profiler_corumg:Profiler_go:bpg:Profiler_go:ccg:Profiler_go:mfg:Profiler_hpg:Profiler_hpag:Profiler_keggg:Profiler_mirnag:Profiler_reacg:Profiler_tfg:Profiler_wp
0ENSG00000001084[{'id': 'CORUM:7186', 'name': 'Glutamate-cyste...[{'id': 'GO:0044281', 'name': 'small molecule ...[{'id': 'GO:0005739', 'name': 'mitochondrion',...[{'id': 'GO:0003824', 'name': 'catalytic activ...[{'id': 'HP:0012337', 'name': 'Abnormal homeos...[{'id': 'HPA:0440341', 'name': 'skeletal muscl...[{'id': 'KEGG:01100', 'name': 'Metabolic pathw...[{'id': 'MIRNA:hsa-miR-30c-5p', 'name': 'hsa-m...[{'id': 'REAC:R-HSA-1430728', 'name': 'Metabol...[{'id': 'TF:M07428', 'name': 'Factor: Six-3; m...[{'id': 'WP:WP2882', 'name': 'Nuclear receptor...
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" + ], + "text/plain": [ + " intersections g:Profiler_corum \\\n", + "0 ENSG00000001084 [{'id': 'CORUM:7186', 'name': 'Glutamate-cyste... \n", + "\n", + " g:Profiler_go:bp \\\n", + "0 [{'id': 'GO:0044281', 'name': 'small molecule ... \n", + "\n", + " g:Profiler_go:cc \\\n", + "0 [{'id': 'GO:0005739', 'name': 'mitochondrion',... \n", + "\n", + " g:Profiler_go:mf \\\n", + "0 [{'id': 'GO:0003824', 'name': 'catalytic activ... \n", + "\n", + " g:Profiler_hp \\\n", + "0 [{'id': 'HP:0012337', 'name': 'Abnormal homeos... \n", + "\n", + " g:Profiler_hpa \\\n", + "0 [{'id': 'HPA:0440341', 'name': 'skeletal muscl... \n", + "\n", + " g:Profiler_kegg \\\n", + "0 [{'id': 'KEGG:01100', 'name': 'Metabolic pathw... \n", + "\n", + " g:Profiler_mirna \\\n", + "0 [{'id': 'MIRNA:hsa-miR-30c-5p', 'name': 'hsa-m... \n", + "\n", + " g:Profiler_reac \\\n", + "0 [{'id': 'REAC:R-HSA-1430728', 'name': 'Metabol... \n", + "\n", + " g:Profiler_tf \\\n", + "0 [{'id': 'TF:M07428', 'name': 'Factor: Six-3; m... \n", + "\n", + " g:Profiler_wp \n", + "0 [{'id': 'WP:WP2882', 'name': 'Nuclear receptor... " + ] + }, + "execution_count": 26, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from pyBiodatafuse.constants import GPROFILER\n", + "\n", + "\n", + "def create_path_info(row):\n", + " path_info = {\n", + " col: row[col] for col in gprofiler_human.columns if col not in [\"intersections\", \"source\"]\n", + " }\n", + " return path_info\n", + "\n", + "\n", + "gprofiler_human[\"gprofiler\"] = gprofiler_human.apply(create_path_info, axis=1)\n", + "gprofiler_human = gprofiler_human.drop(\n", + " columns=[\n", + " col\n", + " for col in gprofiler_human.columns\n", + " if col not in [\"source\", \"id\", \"intersections\", \"gprofiler\"]\n", + " ]\n", + ")\n", + "gprofiler_human = gprofiler_human.explode(\"intersections\").reset_index(drop=True)\n", + "unique_sources = sorted(gprofiler_human[\"source\"].unique())\n", + "gprofiler_human_final = pd.DataFrame()\n", + "gprofiler_human_final[\"intersections\"] = gprofiler_human[\"intersections\"].unique()\n", + "for source in unique_sources:\n", + " source_subset = gprofiler_human[gprofiler_human[\"source\"] == source]\n", + " source_dictionaries = source_subset.groupby(\"intersections\")[\"gprofiler\"].apply(list).to_dict()\n", + " gprofiler_human_final[f\"{GPROFILER}_{str.lower(source)}\"] = gprofiler_human_final[\n", + " \"intersections\"\n", + " ].map(source_dictionaries)\n", + "gprofiler_human_final.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'biomart': 'Ensembl',\n", + " 'biomart_version': '111',\n", + " 'display_name': 'Human',\n", + " 'genebuild': 'GRCh38.p14',\n", + " 'gprofiler_version': 'e111_eg58_p18_f463989d',\n", + " 'organism': 'hsapiens',\n", + " 'sources': {'CORUM': {'name': 'CORUM protein complexes',\n", + " 'version': '28.11.2022 Corum 4.1'},\n", + " 'GO:BP': {'name': 'biological process',\n", + " 'version': 'annotations: BioMart\\nclasses: releases/2024-01-17'},\n", + " 'GO:CC': {'name': 'cellular component',\n", + " 'version': 'annotations: BioMart\\nclasses: releases/2024-01-17'},\n", + " 'GO:MF': {'name': 'molecular function',\n", + " 'version': 'annotations: BioMart\\nclasses: releases/2024-01-17'},\n", + " 'HP': {'name': 'Human Phenotype Ontology',\n", + " 'version': 'annotations: 01.2024\\nclasses: None'},\n", + " 'HPA': {'name': 'Human Protein Atlas',\n", + " 'version': 'annotations: HPA website: 23-07-17\\nclasses: script: 24-01-02'},\n", + " 'KEGG': {'name': 'Kyoto Encyclopedia of Genes and Genomes',\n", + " 'version': 'KEGG FTP Release 2024-01-22'},\n", + " 'MIRNA': {'name': 'miRTarBase', 'version': 'Release 9.0'},\n", + " 'REAC': {'name': 'Reactome',\n", + " 'version': 'annotations: BioMart\\nclasses: 2024-1-25'},\n", + " 'TF': {'name': 'Transfac',\n", + " 'version': 'annotations: TRANSFAC Release 2023.2\\nclasses: v2'},\n", + " 'WP': {'name': 'WikiPathways', 'version': '20240101'}},\n", + " 'taxonomy_id': '9606'}" + ] + }, + "execution_count": 27, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "## get version\n", + "\n", + "\n", + "def get_data_versions(organism):\n", + " url = \"https://biit.cs.ut.ee/gprofiler/api/util/data_versions\"\n", + " params = {\"organism\": organism}\n", + " try:\n", + " response = requests.get(url, params=params)\n", + "\n", + " if response.status_code == 200:\n", + " data = response.json()\n", + " return data\n", + " else:\n", + " raise Exception(f\"Failed to retrieve data: {response.status_code}\")\n", + " except Exception as e:\n", + " return {\"error\": str(e)}\n", + "\n", + "\n", + "get_data_versions(\"hsapiens\")" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [], + "source": [ + "ncbi_tf_gprofiler_df_human = pd.merge(\n", + " ncbi_tf_df_human,\n", + " gprofiler_human_final,\n", + " left_on=\"identifier\",\n", + " right_on=\"intersections\",\n", + " how=\"outer\",\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "0 ENSG00000000003 Ensembl 7105 NCBI Gene TSPAN6 \n", + "1 ENSG00000000419 Ensembl 8813 NCBI Gene DPM1 \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea ... \\\n", + "0 106.899174 -0.401659 0.143909 -2.791057 0.005254 ... \n", + "1 601.924666 -0.104654 0.161936 -0.646270 0.518105 ... \n", + "\n", + " g:Profiler_go:bp g:Profiler_go:cc g:Profiler_go:mf g:Profiler_hp \\\n", + "0 NaN NaN NaN NaN \n", + "1 NaN NaN NaN NaN \n", + "\n", + " g:Profiler_hpa g:Profiler_kegg g:Profiler_mirna g:Profiler_reac \\\n", + "0 NaN NaN NaN NaN \n", + "1 NaN NaN NaN NaN \n", + "\n", + " g:Profiler_tf g:Profiler_wp \n", + "0 NaN NaN \n", + "1 NaN NaN \n", + "\n", + "[2 rows x 28 columns]" + ] + }, + "execution_count": 29, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_gprofiler_df_human.head(2)" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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6ENSG00000001084Ensembl2729NCBI GeneGCLC412.4493450.4540350.13023.4872220.000488...[{'id': 'GO:0044281', 'name': 'small molecule ...[{'id': 'GO:0005739', 'name': 'mitochondrion',...[{'id': 'GO:0003824', 'name': 'catalytic activ...[{'id': 'HP:0012337', 'name': 'Abnormal homeos...[{'id': 'HPA:0440341', 'name': 'skeletal muscl...[{'id': 'KEGG:01100', 'name': 'Metabolic pathw...[{'id': 'MIRNA:hsa-miR-30c-5p', 'name': 'hsa-m...[{'id': 'REAC:R-HSA-1430728', 'name': 'Metabol...[{'id': 'TF:M07428', 'name': 'Factor: Six-3; m...[{'id': 'WP:WP2882', 'name': 'Nuclear receptor...
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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "6 ENSG00000001084 Ensembl 2729 NCBI Gene GCLC \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea ... \\\n", + "6 412.449345 0.454035 0.1302 3.487222 0.000488 ... \n", + "\n", + " g:Profiler_go:bp \\\n", + "6 [{'id': 'GO:0044281', 'name': 'small molecule ... \n", + "\n", + " g:Profiler_go:cc \\\n", + "6 [{'id': 'GO:0005739', 'name': 'mitochondrion',... \n", + "\n", + " g:Profiler_go:mf \\\n", + "6 [{'id': 'GO:0003824', 'name': 'catalytic activ... \n", + "\n", + " g:Profiler_hp \\\n", + "6 [{'id': 'HP:0012337', 'name': 'Abnormal homeos... \n", + "\n", + " g:Profiler_hpa \\\n", + "6 [{'id': 'HPA:0440341', 'name': 'skeletal muscl... \n", + "\n", + " g:Profiler_kegg \\\n", + "6 [{'id': 'KEGG:01100', 'name': 'Metabolic pathw... \n", + "\n", + " g:Profiler_mirna \\\n", + "6 [{'id': 'MIRNA:hsa-miR-30c-5p', 'name': 'hsa-m... \n", + "\n", + " g:Profiler_reac \\\n", + "6 [{'id': 'REAC:R-HSA-1430728', 'name': 'Metabol... \n", + "\n", + " g:Profiler_tf \\\n", + "6 [{'id': 'TF:M07428', 'name': 'Factor: Six-3; m... \n", + "\n", + " g:Profiler_wp \n", + "6 [{'id': 'WP:WP2882', 'name': 'Nuclear receptor... \n", + "\n", + "[1 rows x 28 columns]" + ] + }, + "execution_count": 30, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_gprofiler_df_human[ncbi_tf_gprofiler_df_human[\"g:Profiler_reac\"].notna()].head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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6ENSG00000001084Ensembl2729NCBI GeneGCLC412.4493450.4540350.13023.4872220.000488...[{'id': 'GO:0044281', 'name': 'small molecule ...[{'id': 'GO:0005739', 'name': 'mitochondrion',...[{'id': 'GO:0003824', 'name': 'catalytic activ...[{'id': 'HP:0012337', 'name': 'Abnormal homeos...[{'id': 'HPA:0440341', 'name': 'skeletal muscl...[{'id': 'KEGG:01100', 'name': 'Metabolic pathw...[{'id': 'MIRNA:hsa-miR-30c-5p', 'name': 'hsa-m...[{'id': 'REAC:R-HSA-1430728', 'name': 'Metabol...[{'id': 'TF:M07428', 'name': 'Factor: Six-3; m...[{'id': 'WP:WP2882', 'name': 'Nuclear receptor...
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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "6 ENSG00000001084 Ensembl 2729 NCBI Gene GCLC \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea ... \\\n", + "6 412.449345 0.454035 0.1302 3.487222 0.000488 ... \n", + "\n", + " g:Profiler_go:bp \\\n", + "6 [{'id': 'GO:0044281', 'name': 'small molecule ... \n", + "\n", + " g:Profiler_go:cc \\\n", + "6 [{'id': 'GO:0005739', 'name': 'mitochondrion',... \n", + "\n", + " g:Profiler_go:mf \\\n", + "6 [{'id': 'GO:0003824', 'name': 'catalytic activ... \n", + "\n", + " g:Profiler_hp \\\n", + "6 [{'id': 'HP:0012337', 'name': 'Abnormal homeos... \n", + "\n", + " g:Profiler_hpa \\\n", + "6 [{'id': 'HPA:0440341', 'name': 'skeletal muscl... \n", + "\n", + " g:Profiler_kegg \\\n", + "6 [{'id': 'KEGG:01100', 'name': 'Metabolic pathw... \n", + "\n", + " g:Profiler_mirna \\\n", + "6 [{'id': 'MIRNA:hsa-miR-30c-5p', 'name': 'hsa-m... \n", + "\n", + " g:Profiler_reac \\\n", + "6 [{'id': 'REAC:R-HSA-1430728', 'name': 'Metabol... \n", + "\n", + " g:Profiler_tf \\\n", + "6 [{'id': 'TF:M07428', 'name': 'Factor: Six-3; m... \n", + "\n", + " g:Profiler_wp \n", + "6 [{'id': 'WP:WP2882', 'name': 'Nuclear receptor... \n", + "\n", + "[1 rows x 28 columns]" + ] + }, + "execution_count": 31, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_gprofiler_df_human[ncbi_tf_gprofiler_df_human[\"g:Profiler_reac\"].notna()].head(1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Add MitoCarta data" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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HumanGeneIDMouseOrthologGeneIDSymbolSynonymsDescriptionMitoCarta3.0_ListMitoCarta3.0_EvidenceMitoCarta3.0_SubMitoLocalizationMitoCarta3.0_MitoPathwaysTrainingDataset...liver_total_peak_intensity_log10heart_total_peak_intensity_log10skeletalmuscle_total_peak_intensity_log10adipose_total_peak_intensity_log10smallintestine_total_peak_intensity_log10largeintestine_total_peak_intensity_log10stomach_total_peak_intensity_log10placenta_total_peak_intensity_log10testis_total_peak_intensity_log10HPA_Main_Location_2020 (Reliability)
0153766445.0CYC1MC3DN6|UQCR4cytochrome c1MitoCarta3.0literature, APEX_IMS, APEX_matrix, targetP sig...MIMOXPHOS > Complex III > CIII subunits | Metabol...Tmito...10.010.49.810.110.210.210.010.09.8Mitochondria (Supported)
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1 rows × 48 columns

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" + ], + "text/plain": [ + " HumanGeneID MouseOrthologGeneID Symbol Synonyms Description \\\n", + "0 1537 66445.0 CYC1 MC3DN6|UQCR4 cytochrome c1 \n", + "\n", + " MitoCarta3.0_List MitoCarta3.0_Evidence \\\n", + "0 MitoCarta3.0 literature, APEX_IMS, APEX_matrix, targetP sig... \n", + "\n", + " MitoCarta3.0_SubMitoLocalization \\\n", + "0 MIM \n", + "\n", + " MitoCarta3.0_MitoPathways TrainingDataset ... \\\n", + "0 OXPHOS > Complex III > CIII subunits | Metabol... Tmito ... \n", + "\n", + " liver_total_peak_intensity_log10 heart_total_peak_intensity_log10 \\\n", + "0 10.0 10.4 \n", + "\n", + " skeletalmuscle_total_peak_intensity_log10 \\\n", + "0 9.8 \n", + "\n", + " adipose_total_peak_intensity_log10 \\\n", + "0 10.1 \n", + "\n", + " smallintestine_total_peak_intensity_log10 \\\n", + "0 10.2 \n", + "\n", + " largeintestine_total_peak_intensity_log10 \\\n", + "0 10.2 \n", + "\n", + " stomach_total_peak_intensity_log10 placenta_total_peak_intensity_log10 \\\n", + "0 10.0 10.0 \n", + "\n", + " testis_total_peak_intensity_log10 HPA_Main_Location_2020 (Reliability) \n", + "0 9.8 Mitochondria (Supported) \n", + "\n", + "[1 rows x 48 columns]" + ] + }, + "execution_count": 32, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# URLs for the Human MitoCarta Dataset\n", + "mitocarta_url_human = (\n", + " \"https://personal.broadinstitute.org/scalvo/MitoCarta3.0/Human.MitoCarta3.0.xls\"\n", + ")\n", + "\n", + "\n", + "# Function to download and read a gzipped file into a dataframe\n", + "def download_save_and_read(url, filename):\n", + " if not os.path.exists(filename):\n", + " response = requests.get(url)\n", + " with open(filename, \"wb\") as file:\n", + " file.write(response.content)\n", + " else:\n", + " print(f\"{filename} already exists, skipping download.\")\n", + "\n", + " # Load the second sheet (\"A Human MitoCarta3.0\") into a DataFrame\n", + " df = pd.read_excel(url, sheet_name=\"A Human MitoCarta3.0\")\n", + " return df\n", + "\n", + "\n", + "# Download and read the Human MitoCarta dataset\n", + "mitocarta_human_df = download_save_and_read(mitocarta_url_human, \"data/human/human_mitocarta3.0.xls\")\n", + "\n", + "mitocarta_human_df.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "metadata": {}, + "outputs": [], + "source": [ + "# Select relevant columns for inclusion in the graph\n", + "selected_columns_human = [\n", + " \"EnsemblGeneID_mapping_version_20200130\",\n", + " \"Description\",\n", + " \"MitoCarta3.0_Evidence\",\n", + " \"MitoCarta3.0_SubMitoLocalization\",\n", + " \"MitoCarta3.0_MitoPathways\",\n", + " \"HPA_Main_Location_2020 (Reliability)\",\n", + " \"Tissues\",\n", + "]\n", + "\n", + "mitocarta_human_selected = mitocarta_human_df[selected_columns_human]\n", + "\n", + "# Rename columns for clarity\n", + "mitocarta_human_selected.rename(\n", + " columns={\n", + " \"EnsemblGeneID_mapping_version_20200130\": \"ensembl_id\",\n", + " \"Description\": \"gene_description\",\n", + " \"MitoCarta3.0_Evidence\": \"evidence\",\n", + " \"MitoCarta3.0_SubMitoLocalization\": \"sub_mito_localization\",\n", + " \"MitoCarta3.0_MitoPathways\": \"mito_pathways\",\n", + " \"HPA_Main_Location_2020 (Reliability)\": \"hpa_location\",\n", + " \"Tissues\": \"tissue_expression\",\n", + " },\n", + " inplace=True,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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ensembl_idgene_descriptionevidencesub_mito_localizationmito_pathwayshpa_locationtissue_expression
0ENSG00000179091cytochrome c1literature, APEX_IMS, APEX_matrix, targetP sig...MIMOXPHOS subunitsMitochondria (Supported)all 14
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" + ], + "text/plain": [ + " ensembl_id gene_description \\\n", + "0 ENSG00000179091 cytochrome c1 \n", + "\n", + " evidence sub_mito_localization \\\n", + "0 literature, APEX_IMS, APEX_matrix, targetP sig... MIM \n", + "\n", + " mito_pathways hpa_location tissue_expression \n", + "0 OXPHOS subunits Mitochondria (Supported) all 14 " + ] + }, + "execution_count": 34, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "mitocarta_human_selected[\"mito_pathways\"] = (\n", + " mitocarta_human_selected[\"mito_pathways\"]\n", + " .str.split(\">\")\n", + " .str[-1]\n", + " .str.split(\"|\")\n", + " .str[0]\n", + " .str.strip()\n", + ")\n", + "mitocarta_human_selected.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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ensembl_idMitoCarta
0ENSG00000179091[{'gene_description': 'cytochrome c1', 'eviden...
1ENSG00000117118[{'gene_description': 'succinate dehydrogenase...
2ENSG00000167186[{'gene_description': 'coenzyme Q7, hydroxylas...
3ENSG00000073578[{'gene_description': 'succinate dehydrogenase...
4ENSG00000010256[{'gene_description': 'ubiquinol-cytochrome c ...
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" + ], + "text/plain": [ + " ensembl_id MitoCarta\n", + "0 ENSG00000179091 [{'gene_description': 'cytochrome c1', 'eviden...\n", + "1 ENSG00000117118 [{'gene_description': 'succinate dehydrogenase...\n", + "2 ENSG00000167186 [{'gene_description': 'coenzyme Q7, hydroxylas...\n", + "3 ENSG00000073578 [{'gene_description': 'succinate dehydrogenase...\n", + "4 ENSG00000010256 [{'gene_description': 'ubiquinol-cytochrome c ..." + ] + }, + "execution_count": 35, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from pyBiodatafuse.constants import MITOCARTA\n", + "\n", + "df_melted = mitocarta_human_selected.apply(\n", + " lambda row: [row[\"ensembl_id\"], [row.drop(\"ensembl_id\").to_dict()]], axis=1\n", + ")\n", + "df_transformed = pd.DataFrame(df_melted.tolist(), columns=[\"ensembl_id\", MITOCARTA])\n", + "df_transformed.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_dea...g:Profiler_go:ccg:Profiler_go:mfg:Profiler_hpg:Profiler_hpag:Profiler_keggg:Profiler_mirnag:Profiler_reacg:Profiler_tfg:Profiler_wpMitoCarta
0ENSG00000000003Ensembl7105NCBI GeneTSPAN6106.899174-0.4016590.143909-2.7910570.005254...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
1ENSG00000000419Ensembl8813NCBI GeneDPM1601.924666-0.1046540.161936-0.6462700.518105...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
2ENSG00000000457Ensembl57147NCBI GeneSCYL3244.623536-0.2854180.118343-2.4117840.015875...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
3ENSG00000000938Ensembl2268NCBI GeneFGR91.9587670.5993040.3421101.7517860.079811...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
4ENSG00000000971Ensembl3075NCBI GeneCFH499.5831250.0794480.2553760.3111010.755724...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
..................................................................
62ENSG00000005073Ensembl3207NCBI GeneHOXA11143.7048570.3015590.2001881.5063790.131970...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
63ENSG00000005075Ensembl5439NCBI GenePOLR2J1204.040045-0.1335000.107618-1.2405030.214789...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
64ENSG00000005100Ensembl56919NCBI GeneDHX33256.1379170.1666540.1469941.1337460.256901...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
65ENSG00000005102Ensembl4222NCBI GeneMEOX1329.566304-0.3959620.258980-1.5289290.126282...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
66ENSG00000005156Ensembl3980NCBI GeneLIG3407.8708770.1868000.1196281.5615040.118405...NaNNaNNaNNaNNaNNaNNaNNaNNaN[{'gene_description': 'DNA ligase 3', 'evidenc...
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67 rows × 29 columns

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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "0 ENSG00000000003 Ensembl 7105 NCBI Gene TSPAN6 \n", + "1 ENSG00000000419 Ensembl 8813 NCBI Gene DPM1 \n", + "2 ENSG00000000457 Ensembl 57147 NCBI Gene SCYL3 \n", + "3 ENSG00000000938 Ensembl 2268 NCBI Gene FGR \n", + "4 ENSG00000000971 Ensembl 3075 NCBI Gene CFH \n", + ".. ... ... ... ... ... \n", + "62 ENSG00000005073 Ensembl 3207 NCBI Gene HOXA11 \n", + "63 ENSG00000005075 Ensembl 5439 NCBI Gene POLR2J \n", + "64 ENSG00000005100 Ensembl 56919 NCBI Gene DHX33 \n", + "65 ENSG00000005102 Ensembl 4222 NCBI Gene MEOX1 \n", + "66 ENSG00000005156 Ensembl 3980 NCBI Gene LIG3 \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea ... \\\n", + "0 106.899174 -0.401659 0.143909 -2.791057 0.005254 ... \n", + "1 601.924666 -0.104654 0.161936 -0.646270 0.518105 ... \n", + "2 244.623536 -0.285418 0.118343 -2.411784 0.015875 ... \n", + "3 91.958767 0.599304 0.342110 1.751786 0.079811 ... \n", + "4 499.583125 0.079448 0.255376 0.311101 0.755724 ... \n", + ".. ... ... ... ... ... ... \n", + "62 143.704857 0.301559 0.200188 1.506379 0.131970 ... \n", + "63 1204.040045 -0.133500 0.107618 -1.240503 0.214789 ... \n", + "64 256.137917 0.166654 0.146994 1.133746 0.256901 ... \n", + "65 329.566304 -0.395962 0.258980 -1.528929 0.126282 ... \n", + "66 407.870877 0.186800 0.119628 1.561504 0.118405 ... \n", + "\n", + " g:Profiler_go:cc g:Profiler_go:mf g:Profiler_hp g:Profiler_hpa \\\n", + "0 NaN NaN NaN NaN \n", + "1 NaN NaN NaN NaN \n", + "2 NaN NaN NaN NaN \n", + "3 NaN NaN NaN NaN \n", + "4 NaN NaN NaN NaN \n", + ".. ... ... ... ... \n", + "62 NaN NaN NaN NaN \n", + "63 NaN NaN NaN NaN \n", + "64 NaN NaN NaN NaN \n", + "65 NaN NaN NaN NaN \n", + "66 NaN NaN NaN NaN \n", + "\n", + " g:Profiler_kegg g:Profiler_mirna g:Profiler_reac g:Profiler_tf \\\n", + "0 NaN NaN NaN NaN \n", + "1 NaN NaN NaN NaN \n", + "2 NaN NaN NaN NaN \n", + "3 NaN NaN NaN NaN \n", + "4 NaN NaN NaN NaN \n", + ".. ... ... ... ... \n", + "62 NaN NaN NaN NaN \n", + "63 NaN NaN NaN NaN \n", + "64 NaN NaN NaN NaN \n", + "65 NaN NaN NaN NaN \n", + "66 NaN NaN NaN NaN \n", + "\n", + " g:Profiler_wp MitoCarta \n", + "0 NaN NaN \n", + "1 NaN NaN \n", + "2 NaN NaN \n", + "3 NaN NaN \n", + "4 NaN NaN \n", + ".. ... ... \n", + "62 NaN NaN \n", + "63 NaN NaN \n", + "64 NaN NaN \n", + "65 NaN NaN \n", + "66 NaN [{'gene_description': 'DNA ligase 3', 'evidenc... \n", + "\n", + "[67 rows x 29 columns]" + ] + }, + "execution_count": 36, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Merge Human MitoCarta with the graph dataset\n", + "ncbi_tf_gprofiler_mitocarta_df_human = pd.merge(\n", + " ncbi_tf_gprofiler_df_human,\n", + " df_transformed,\n", + " left_on=\"identifier\",\n", + " right_on=\"ensembl_id\",\n", + " how=\"left\",\n", + ").drop(columns=[\"ensembl_id\"])\n", + "\n", + "ncbi_tf_gprofiler_mitocarta_df_human.head(67)" + ] + }, + { + "cell_type": "code", + "execution_count": 37, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[{'gene_description': 'DNA ligase 3',\n", + " 'evidence': 'literature, targetP signal, mito protein domain, coexpression',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'mtDNA repair',\n", + " 'hpa_location': 'Nucleoplasm (Supported)',\n", + " 'tissue_expression': nan}]" + ] + }, + "execution_count": 37, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_gprofiler_mitocarta_df_human[MITOCARTA][66]" + ] + }, + { + "cell_type": "code", + "execution_count": 38, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_dea...g:Profiler_go:ccg:Profiler_go:mfg:Profiler_hpg:Profiler_hpag:Profiler_keggg:Profiler_mirnag:Profiler_reacg:Profiler_tfg:Profiler_wpMitoCarta
0ENSG00000000003Ensembl7105ncbi_gene_idTSPAN6106.899174-0.4016590.143909-2.7910570.005254...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
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1 rows × 29 columns

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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "0 ENSG00000000003 Ensembl 7105 ncbi_gene_id TSPAN6 \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea ... \\\n", + "0 106.899174 -0.401659 0.143909 -2.791057 0.005254 ... \n", + "\n", + " g:Profiler_go:cc g:Profiler_go:mf g:Profiler_hp g:Profiler_hpa \\\n", + "0 NaN NaN NaN NaN \n", + "\n", + " g:Profiler_kegg g:Profiler_mirna g:Profiler_reac g:Profiler_tf \\\n", + "0 NaN NaN NaN NaN \n", + "\n", + " g:Profiler_wp MitoCarta \n", + "0 NaN NaN \n", + "\n", + "[1 rows x 29 columns]" + ] + }, + "execution_count": 38, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_gprofiler_mitocarta_df_human[\"target.source\"] = ncbi_tf_gprofiler_mitocarta_df_human[\n", + " \"target.source\"\n", + "].str.replace(\"NCBI Gene\", \"ncbi_gene_id\", regex=False)\n", + "\n", + "ncbi_tf_gprofiler_mitocarta_df_human.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 39, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{0: nan,\n", + " 1: nan,\n", + " 2: nan,\n", + " 3: nan,\n", + " 4: nan,\n", + " 5: nan,\n", + " 6: nan,\n", + " 7: nan,\n", + " 8: nan,\n", + " 9: nan,\n", + " 10: nan,\n", + " 11: nan,\n", + " 12: nan,\n", + " 13: nan,\n", + " 14: nan,\n", + " 15: nan,\n", + " 16: [{'gene_description': 'BCL2 associated agonist of cell death',\n", + " 'evidence': 'literature, mito protein domain',\n", + " 'sub_mito_localization': 'MOM',\n", + " 'mito_pathways': 'Apoptosis',\n", + " 'hpa_location': 'Mitochondria (Enhanced)',\n", + " 'tissue_expression': nan}],\n", + " 17: [{'gene_description': 'leucine aminopeptidase 3',\n", + " 'evidence': 'APEX_matrix, targetP signal+, Rickettsial homolog, coexpression, MS/MS++',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Proteases',\n", + " 'hpa_location': 'Cytosol (Supported)',\n", + " 'tissue_expression': 'all 14'}],\n", + " 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nan,\n", + " 819: nan,\n", + " 820: [{'gene_description': 'haloacid dehalogenase like hydrolase domain containing 5',\n", + " 'evidence': 'APEX_matrix, targetP signal, yeast mito homolog, mito protein domain, MS/MS++',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': nan,\n", + " 'hpa_location': 'Mitochondria (Approved)',\n", + " 'tissue_expression': 'cerebellum, kidney, liver, skeletalmuscle, adipose, largeintestine, stomach, placenta, testis'}],\n", + " 821: nan,\n", + " 822: nan,\n", + " 823: nan,\n", + " 824: nan,\n", + " 825: nan,\n", + " 826: nan,\n", + " 827: nan,\n", + " 828: nan,\n", + " 829: nan,\n", + " 830: nan,\n", + " 831: nan,\n", + " 832: nan,\n", + " 833: nan,\n", + " 834: nan,\n", + " 835: nan,\n", + " 836: nan,\n", + " 837: nan,\n", + " 838: nan,\n", + " 839: nan,\n", + " 840: [{'gene_description': 'DNA polymerase beta',\n", + " 'evidence': 'literature',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'mtDNA repair',\n", + " 'hpa_location': 'Vesicles (Uncertain)',\n", + " 'tissue_expression': nan}],\n", + " 841: nan,\n", + " 842: nan,\n", + " 843: nan,\n", + " 844: nan,\n", + " 845: nan,\n", + " 846: nan,\n", + " 847: nan,\n", + " 848: nan,\n", + " 849: nan,\n", + " 850: nan,\n", + " 851: nan,\n", + " 852: nan,\n", + " 853: nan,\n", + " 854: nan,\n", + " 855: nan,\n", + " 856: nan,\n", + " 857: nan,\n", + " 858: nan,\n", + " 859: nan,\n", + " 860: nan,\n", + " 861: nan,\n", + " 862: nan,\n", + " 863: nan,\n", + " 864: nan,\n", + " 865: nan,\n", + " 866: nan,\n", + " 867: nan,\n", + " 868: nan,\n", + " 869: nan,\n", + " 870: nan,\n", + " 871: nan,\n", + " 872: nan,\n", + " 873: nan,\n", + " 874: nan,\n", + " 875: nan,\n", + " 876: nan,\n", + " 877: nan,\n", + " 878: nan,\n", + " 879: nan,\n", + " 880: nan,\n", + " 881: nan,\n", + " 882: nan,\n", + " 883: nan,\n", + " 884: nan,\n", + " 885: nan,\n", + " 886: nan,\n", + " 887: nan,\n", + " 888: nan,\n", + " 889: nan,\n", + " 890: nan,\n", + " 891: nan,\n", + " 892: nan,\n", + " 893: nan,\n", + " 894: [{'gene_description': 'aldehyde dehydrogenase 3 family member A2',\n", + " 'evidence': 'targetP signal+, mito protein domain, coexpression',\n", + " 'sub_mito_localization': 'Membrane',\n", + " 'mito_pathways': 'ROS and glutathione metabolism',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'spinalcord, kidney, liver, smallintestine, largeintestine, stomach, placenta, testis'}],\n", + " 895: nan,\n", + " 896: nan,\n", + " 897: nan,\n", + " 898: nan,\n", + " 899: nan,\n", + " 900: nan,\n", + " 901: nan,\n", + " 902: [{'gene_description': 'hydroxysteroid 17-beta dehydrogenase 10',\n", + " 'evidence': 'literature, APEX_matrix, Rickettsial homolog, mito protein domain, induction, coexpression, MS/MS++',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Branched-chain amino acid metabolism',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'all 14'}],\n", + " 903: nan,\n", + " 904: nan,\n", + " 905: nan,\n", + " 906: nan,\n", + " 907: nan,\n", + " 908: [{'gene_description': 'tRNA nucleotidyl transferase 1',\n", + " 'evidence': 'literature, targetP signal, yeast mito homolog, Rickettsial homolog, mito protein domain, induction, MS/MS',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'mt-tRNA modifications',\n", + " 'hpa_location': 'Mitochondria (Supported)',\n", + " 'tissue_expression': 'spinalcord, adipose, placenta, testis'}],\n", + " 909: [{'gene_description': 'acyl-CoA dehydrogenase very long chain',\n", + " 'evidence': 'literature, APEX_matrix, targetP signal+, mito protein domain+, coexpression+, MS/MS++',\n", + " 'sub_mito_localization': 'MIM',\n", + " 'mito_pathways': 'Fatty acid oxidation',\n", + " 'hpa_location': 'Mitochondria;Nucleoli (Supported)',\n", + " 'tissue_expression': 'all 14'}],\n", + " 910: nan,\n", + " 911: nan,\n", + " 912: nan,\n", + " 913: nan,\n", + " 914: nan,\n", + " 915: nan,\n", + " 916: nan,\n", + " 917: nan,\n", + " 918: nan,\n", + " 919: nan,\n", + " 920: nan,\n", + " 921: nan,\n", + " 922: [{'gene_description': 'selenoprotein O',\n", + " 'evidence': 'targetP signal+, yeast mito homolog, mito protein domain+, coexpression',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Selenoproteins',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'spinalcord, liver, skeletalmuscle, adipose, smallintestine, largeintestine, stomach, placenta, testis'}],\n", + " 923: nan,\n", + " 924: nan,\n", + " 925: nan,\n", + " 926: nan,\n", + " 927: nan,\n", + " 928: [{'gene_description': 'succinate dehydrogenase complex flavoprotein subunit A',\n", + " 'evidence': 'literature, APEX_matrix, targetP signal+, yeast mito homolog++, Rickettsial homolog, mito protein domain, induction, coexpression++, MS/MS++',\n", + " 'sub_mito_localization': 'MIM',\n", + " 'mito_pathways': 'OXPHOS subunits',\n", + " 'hpa_location': 'Mitochondria (Supported)',\n", + " 'tissue_expression': 'all 14'}],\n", + " 929: nan,\n", + " 930: 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'MIM',\n", + " 'mito_pathways': 'OXPHOS assembly factors',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'cerebrum, cerebellum, brainstem, spinalcord, liver, heart, skeletalmuscle, adipose, smallintestine, largeintestine, stomach, placenta, testis'}],\n", + " 953: nan,\n", + " 954: nan,\n", + " 955: nan,\n", + " 956: nan,\n", + " 957: nan,\n", + " 958: nan,\n", + " 959: nan,\n", + " 960: nan,\n", + " 961: nan,\n", + " 962: nan,\n", + " 963: nan,\n", + " 964: nan,\n", + " 965: nan,\n", + " 966: nan,\n", + " 967: nan,\n", + " 968: nan,\n", + " 969: nan,\n", + " 970: nan,\n", + " 971: nan,\n", + " 972: [{'gene_description': 'acetyl-CoA acetyltransferase 1',\n", + " 'evidence': 'literature, APEX_matrix, targetP signal+, Rickettsial homolog, mito protein domain, induction, coexpression+, MS/MS++',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Lysine metabolism',\n", + " 'hpa_location': 'Mitochondria (Enhanced)',\n", + " 'tissue_expression': 'all 14'}],\n", + " 973: nan,\n", + " 974: nan,\n", + " 975: [{'gene_description': 'solute carrier family 25 member 40',\n", + " 'evidence': 'literature, yeast mito homolog+, mito protein domain+, MS/MS',\n", + " 'sub_mito_localization': 'MIM',\n", + " 'mito_pathways': 'SLC25A family',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'cerebrum, cerebellum, brainstem, spinalcord, adipose, largeintestine, stomach, placenta, testis'}],\n", + " 976: [{'gene_description': 'translocase of inner mitochondrial membrane 21',\n", + " 'evidence': 'APEX_IMS, GFP, yeast mito homolog++, mito protein domain+, coexpression, MS/MS',\n", + " 'sub_mito_localization': 'MIM',\n", + " 'mito_pathways': 'OXPHOS assembly factors',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'cerebrum, cerebellum, brainstem, spinalcord, liver, heart, skeletalmuscle, adipose, largeintestine, stomach, placenta, testis'}],\n", + " 977: nan,\n", + " 978: nan,\n", + " 979: nan,\n", + " 980: nan,\n", + " 981: [{'gene_description': 'solute carrier family 25 member 3',\n", + " 'evidence': 'literature, yeast mito homolog++, mito protein domain+, induction, coexpression++, MS/MS++',\n", + " 'sub_mito_localization': 'MIM',\n", + " 'mito_pathways': 'SLC25A family',\n", + " 'hpa_location': 'Mitochondria (Supported)',\n", + " 'tissue_expression': 'all 14'}],\n", + " 982: nan,\n", + " 983: nan,\n", + " 984: nan,\n", + " 985: nan,\n", + " 986: nan,\n", + " 987: nan,\n", + " 988: nan,\n", + " 989: nan,\n", + " 990: nan,\n", + " 991: nan,\n", + " 992: nan,\n", + " 993: nan,\n", + " 994: nan,\n", + " 995: nan,\n", + " 996: nan,\n", + " 997: nan,\n", + " 998: nan,\n", + " 999: [{'gene_description': 'RNA exonuclease 2',\n", + " 'evidence': 'APEX_matrix, targetP signal, yeast mito homolog++, mito protein domain, MS/MS+',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'mtRNA stability and decay',\n", + " 'hpa_location': 'Mitochondria (Supported)',\n", + " 'tissue_expression': 'all 14'}],\n", + " ...}" + ] + }, + "execution_count": 39, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_gprofiler_mitocarta_df_human[MITOCARTA].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[{'NCBI.GeneID.Target': '1647',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000116717',\n", + " 'Name.Target': 'GADD45A',\n", + " 'UniprotID.Target': 'P24522',\n", + " 'Target.TFLink.ortho': 'Dr:Q6GMM1;Mm:P48316;Rn:Q66HL6',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay;inferred by curator',\n", + " 'PubmedID': '29126285;11525640;11420680;27924024;29087512',\n", + " 'Source.database': 'GTRD;ReMap;TRRUST',\n", + " 'Small-scale.evidence': 'Yes'},\n", + " {'NCBI.GeneID.Target': '84271',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000100227',\n", + " 'Name.Target': 'POLDIP3',\n", + " 'UniprotID.Target': 'Q9BY77',\n", + " 'Target.TFLink.ortho': 'Mm:Q8BG81;Rn:D4A2B0',\n", + " 'Target.nonTFLink.ortho': 'Dr:A0A0R4ILC0',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '54842',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000151690',\n", + " 'Name.Target': 'MFSD6',\n", + " 'UniprotID.Target': 'Q6ZSS7',\n", + " 'Target.TFLink.ortho': 'Ce:Q95Y88;Dm:A1Z9U2;Rn:D3ZCJ3',\n", + " 'Target.nonTFLink.ortho': 'Mm:D3Z183',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '389203',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000250317',\n", + " 'Name.Target': 'SMIM20',\n", + " 'UniprotID.Target': 'Q8N5G0',\n", + " 'Target.TFLink.ortho': '-',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '4043',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000163956',\n", + " 'Name.Target': 'LRPAP1',\n", + " 'UniprotID.Target': 'P30533',\n", + " 'Target.TFLink.ortho': 'Ce:G5EF26;Dm:Q9VH64;Dr:A2BGU5;Mm:P55302;Rn:Q99068',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '5188',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000059691',\n", + " 'Name.Target': 'GATB',\n", + " 'UniprotID.Target': 'O75879',\n", + " 'Target.TFLink.ortho': 'Dm:Q9VCD0;Mm:Q99JT1;Rn:M0R4L6;Sc:P33893',\n", + " 'Target.nonTFLink.ortho': 'Dr:Q7T010',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': 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'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '1052',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000221869',\n", + " 'Name.Target': 'CEBPD',\n", + " 'UniprotID.Target': 'P49716',\n", + " 'Target.TFLink.ortho': 'Dr:Q6P612;Mm:Q00322;Rn:Q03484',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '3155',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000117305',\n", + " 'Name.Target': 'HMGCL',\n", + " 'UniprotID.Target': 'P35914',\n", + " 'Target.TFLink.ortho': 'Dr:F1QTF0;Mm:P38060;Rn:P97519',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '90423',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000250565',\n", 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'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '4705',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000130414',\n", + " 'Name.Target': 'NDUFA10',\n", + " 'UniprotID.Target': 'O95299',\n", + " 'Target.TFLink.ortho': 'Dm:P91929;Dr:F1RDV2;Mm:Q99LC3;Rn:Q561S0',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '38',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000075239',\n", + " 'Name.Target': 'ACAT1',\n", + " 'UniprotID.Target': 'P24752',\n", + " 'Target.TFLink.ortho': 'Ce:Q22100;Dm:Q9W3N9;Mm:Q8QZT1;Rn:P17764;Sc:P41338',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '4720',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000158864',\n", + " 'Name.Target': 'NDUFS2',\n", + " 'UniprotID.Target': 'O75306',\n", + " 'Target.TFLink.ortho': 'Ce:Q22800;Ce:Q93873;Dm:Q9V4E0;Dr:F1Q4N4;Mm:Q91WD5;Rn:Q641Y2',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '2668',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000168621',\n", + " 'Name.Target': 'GDNF',\n", + " 'UniprotID.Target': 'P39905',\n", + " 'Target.TFLink.ortho': '-',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '89796',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000134369',\n", + " 'Name.Target': 'NAV1',\n", + " 'UniprotID.Target': 'Q8NEY1',\n", + " 'Target.TFLink.ortho': 'Rn:D4A5I4',\n", + " 'Target.nonTFLink.ortho': 'Dr:F1QQI8;Mm:A0A589P973',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '64061',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000184205',\n", + " 'Name.Target': 'TSPYL2',\n", + " 'UniprotID.Target': 'Q9H2G4',\n", + " 'Target.TFLink.ortho': 'Mm:Q7TQI8;Rn:A0A096MJ32',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '5947',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000114115',\n", + " 'Name.Target': 'RBP1',\n", + " 'UniprotID.Target': 'P09455',\n", + " 'Target.TFLink.ortho': '-',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '2926',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000132463',\n", + " 'Name.Target': 'GRSF1',\n", + " 'UniprotID.Target': 'Q12849',\n", + " 'Target.TFLink.ortho': 'Dr:F8W4V6;Mm:Q8C5Q4',\n", + " 'Target.nonTFLink.ortho': 'Rn:F1LRK4',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '5979',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000165731',\n", + " 'Name.Target': 'RET',\n", + " 'UniprotID.Target': 'P07949',\n", + " 'Target.TFLink.ortho': 'Dr:A8E7C6;Mm:P35546',\n", + " 'Target.nonTFLink.ortho': 'Rn:G3V9H8',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '201562',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000206527',\n", + " 'Name.Target': 'HACD2',\n", + " 'UniprotID.Target': 'Q6Y1H2',\n", + " 'Target.TFLink.ortho': 'Ce:O17040;Dr:B0V199;Mm:Q9D3B1;Rn:D3ZHG0',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '23632',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000118298',\n", + " 'Name.Target': 'CA14',\n", + " 'UniprotID.Target': 'Q9ULX7',\n", + " 'Target.TFLink.ortho': 'Mm:Q9WVT6;Rn:A2IBE0',\n", + " 'Target.nonTFLink.ortho': 'Dr:F8W4I7',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285',\n", + " 'Source.database': 'ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '114882',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000091039',\n", + " 'Name.Target': 'OSBPL8',\n", + " 'UniprotID.Target': 'Q9BZF1',\n", + " 'Target.TFLink.ortho': 'Rn:A0A0G2JXN8',\n", + " 'Target.nonTFLink.ortho': 'Mm:A0A0R4J150',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '1160',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000131730',\n", + " 'Name.Target': 'CKMT2',\n", + " 'UniprotID.Target': 'P17540',\n", + " 'Target.TFLink.ortho': 'Mm:Q6P8J7',\n", + " 'Target.nonTFLink.ortho': 'Dm:Q9VF23;Rn:A0A0G2JVQ1',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '54948',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000166902',\n", + " 'Name.Target': 'MRPL16',\n", + " 'UniprotID.Target': 'Q9NX20',\n", + " 'Target.TFLink.ortho': 'Ce:Q22140;Dm:Q9W547;Mm:Q99N93;Rn:Q5M818',\n", + " 'Target.nonTFLink.ortho': 'Dr:F1R2K1',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '8604',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000115840',\n", + " 'Name.Target': 'SLC25A12',\n", + " 'UniprotID.Target': 'O75746',\n", + " 'Target.TFLink.ortho': 'Mm:Q8BH59;Rn:F1LX07',\n", + " 'Target.nonTFLink.ortho': 'Dr:A0A0R4II73',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '2037',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000079819',\n", + " 'Name.Target': 'EPB41L2',\n", + " 'UniprotID.Target': 'O43491',\n", + " 'Target.TFLink.ortho': 'Mm:O70318',\n", + " 'Target.nonTFLink.ortho': 'Rn:D3ZM69',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '51279',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000139178',\n", + " 'Name.Target': 'C1RL',\n", + " 'UniprotID.Target': 'Q9NZP8',\n", + " 'Target.TFLink.ortho': 'Mm:Q3UZ09;Rn:F1LP96',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '6391',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000143252',\n", + " 'Name.Target': 'SDHC',\n", + " 'UniprotID.Target': 'Q99643',\n", + " 'Target.TFLink.ortho': 'Ce:P41956;Dm:Q9VGS3;Mm:Q9CZB0;Rn:Q641Z9',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '57787',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000007047',\n", + " 'Name.Target': 'MARK4',\n", + " 'UniprotID.Target': 'Q96L34',\n", + " 'Target.TFLink.ortho': 'Dr:R4GEN1;Mm:Q8CIP4;Rn:D4A6T9',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '55245',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000101019',\n", + " 'Name.Target': 'UQCC1',\n", + " 'UniprotID.Target': 'Q9NVA1',\n", + " 'Target.TFLink.ortho': 'Dm:Q9VRZ7;Dr:F1QK92;Mm:Q9CWU6;Rn:Q32Q54',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '64222',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000186283',\n", + " 'Name.Target': 'TOR3A',\n", + " 'UniprotID.Target': 'Q9H497',\n", + " 'Target.TFLink.ortho': 'Dr:A9C3S4;Mm:Q9ER38;Rn:Q5M936',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '141',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000144843',\n", + " 'Name.Target': 'ADPRH',\n", + " 'UniprotID.Target': 'P54922',\n", + " 'Target.TFLink.ortho': 'Mm:P54923;Rn:Q02589',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '5396',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000116132',\n", + " 'Name.Target': 'PRRX1',\n", + " 'UniprotID.Target': 'P54821',\n", + " 'Target.TFLink.ortho': 'Dr:Q6P295;Dr:Q7T373;Mm:P63013;Rn:P63014',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '400451',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000185442',\n", + " 'Name.Target': 'FAM174B',\n", + " 'UniprotID.Target': 'Q3ZCQ3',\n", + " 'Target.TFLink.ortho': 'Mm:Q8K064',\n", + " 'Target.nonTFLink.ortho': 'Rn:D4A4W1',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '7494',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000100219',\n", + " 'Name.Target': 'XBP1',\n", + " 'UniprotID.Target': 'P17861',\n", + " 'Target.TFLink.ortho': 'Rn:A0A140TAA7',\n", + " 'Target.nonTFLink.ortho': 'Dr:F1R5F9;Mm:A0A5F8MPD3',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '2119',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000244405',\n", + " 'Name.Target': 'ETV5',\n", + " 'UniprotID.Target': 'P41161',\n", + " 'Target.TFLink.ortho': 'Dr:B0S6S7;Mm:Q9CXC9;Rn:D4AC56',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '23596',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000203668',\n", + " 'Name.Target': 'OPN3',\n", + " 'UniprotID.Target': 'Q9H1Y3',\n", + " 'Target.TFLink.ortho': 'Dr:A9NJI7;Mm:Q9WUK7;Rn:D3ZFS1',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '60314',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000139637',\n", + " 'Name.Target': 'MYG1',\n", + " 'UniprotID.Target': 'Q9HB07',\n", + " 'Target.TFLink.ortho': '-',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '5116',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000160299',\n", + " 'Name.Target': 'PCNT',\n", + " 'UniprotID.Target': 'O95613',\n", + " 'Target.TFLink.ortho': 'Dr:I3ISP1;Mm:F8VPV0;Rn:D3ZMY8',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '54715',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000078328',\n", + " 'Name.Target': 'RBFOX1',\n", + " 'UniprotID.Target': 'Q9NWB1',\n", + " 'Target.TFLink.ortho': 'Dr:Q642J5;Mm:Q9JJ43;Rn:D3ZSL1',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '10657',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000121774',\n", + " 'Name.Target': 'KHDRBS1',\n", + " 'UniprotID.Target': 'Q07666',\n", + " 'Target.TFLink.ortho': 'Dr:Q6NW62;Mm:Q60749;Rn:Q91V33',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '10105',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000108179',\n", + " 'Name.Target': 'PPIF',\n", + " 'UniprotID.Target': 'P30405',\n", + " 'Target.TFLink.ortho': 'Dm:Q7K2I4;Dm:P25007;Mm:Q99KR7;Rn:P29117',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '79758',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000102796',\n", + " 'Name.Target': 'DHRS12',\n", + " 'UniprotID.Target': 'A0PJE2',\n", + " 'Target.TFLink.ortho': 'Dr:B0UYL5',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '29889',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000134697',\n", + " 'Name.Target': 'GNL2',\n", + " 'UniprotID.Target': 'Q13823',\n", + " 'Target.TFLink.ortho': 'Ce:Q9XXN4;Dm:Q7JXU4;Dr:A0A0R4IXF1;Mm:Q99LH1;Rn:Q4KLJ3',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '23408',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000124523',\n", + " 'Name.Target': 'SIRT5',\n", + " 'UniprotID.Target': 'Q9NXA8',\n", + " 'Target.TFLink.ortho': 'Mm:Q8K2C6;Rn:Q68FX9',\n", + " 'Target.nonTFLink.ortho': 'Dr:Q6DHI5',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '51027',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000178096',\n", + " 'Name.Target': 'BOLA1',\n", + " 'UniprotID.Target': 'Q9Y3E2',\n", + " 'Target.TFLink.ortho': 'Ce:P91375;Dm:Q9VC53;Mm:Q9D8S9;Rn:Q06C60',\n", + " 'Target.nonTFLink.ortho': 'Dr:F1R2T4',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '8925',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000103657',\n", + " 'Name.Target': 'HERC1',\n", + " 'UniprotID.Target': 'Q15751',\n", + " 'Target.TFLink.ortho': 'Mm:E9PZP8;Rn:A0A0G2JTT6',\n", + " 'Target.nonTFLink.ortho': 'Dr:E7FBA7',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '81796',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000137571',\n", + " 'Name.Target': 'SLCO5A1',\n", + " 'UniprotID.Target': 'Q9H2Y9',\n", + " 'Target.TFLink.ortho': 'Dr:E7F2I7;Mm:E9PVD9;Rn:D3ZZM7',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '7264',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000104522',\n", + " 'Name.Target': 'TSTA3',\n", + " 'UniprotID.Target': 'Q13630',\n", + " 'Target.TFLink.ortho': 'Ce:G5EER4;Dm:Q9W1X8;Dr:Q6DC41;Mm:P23591;Rn:G3V762',\n", + " 'Target.nonTFLink.ortho': 'Dr:B0S7C9;Dr:Q5SPD5',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '145957',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000169752',\n", + " 'Name.Target': 'NRG4',\n", + " 'UniprotID.Target': 'Q8WWG1',\n", + " 'Target.TFLink.ortho': 'Mm:Q9WTX4;Rn:A0A0G2JYC9',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '23180',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000131378',\n", + " 'Name.Target': 'RFTN1',\n", + " 'UniprotID.Target': 'Q14699',\n", + " 'Target.TFLink.ortho': 'Dr:A0A0G2L3G6;Mm:Q6A0D4',\n", + " 'Target.nonTFLink.ortho': 'Dr:E9QG04;Rn:G3V7I2',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'}]" + ] + }, + "execution_count": 40, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# ncbi_tf_gprofiler_mitocarta_df_human[\"its_target\"][ncbi_tf_gprofiler_mitocarta_df_human[\"its_target\"].notna()]\n", + "ncbi_tf_gprofiler_mitocarta_df_human[\"its_target\"][7]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Protein-Protein Interactions from STRING" + ] + }, + { + "cell_type": "code", + "execution_count": 45, + "metadata": {}, + "outputs": [], + "source": [ + "# # Create a mapping dictionary for identifiers\n", + "# mapping = bridgedb_df_human[\n", + "# (bridgedb_df_human['target.source'] == \"HGNC\") & (pd.notna(bridgedb_df_human['target']))\n", + "# ].set_index('identifier')['target'].to_dict()\n", + "\n", + "# # Apply mapping and replace values in identifier and identifier.source\n", + "# bridgedb_df_human['identifier'] = bridgedb_df_human['identifier'].map(mapping).combine_first(bridgedb_df_human['identifier'])\n", + "# bridgedb_df_human['identifier.source'] = bridgedb_df_human.apply(\n", + "# lambda row: \"HGNC\" if row['identifier'] in mapping.values() else row['identifier.source'], axis=1\n", + "# )" + ] + }, + { + "cell_type": "code", + "execution_count": 46, + "metadata": {}, + "outputs": [], + "source": [ + "# bridgedb_df_human[[\"identifier\", \"GENE_SYMBOL_dea\"]][~(bridgedb_df_human[\"identifier\"] == bridgedb_df_human[\"GENE_SYMBOL_dea\"])].drop_duplicates()" + ] + }, + { + "cell_type": "code", + "execution_count": 41, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_deapadj_deaminus_log10_pvalue_deaStringDB_ppi
0ENSG00000001084EnsemblENSG00000001084EnsemblGCLC412.4493450.4540350.1302003.4872220.0004880.0186593.311521[{'stringdb_link_to': 'ENSG00000100906', 'Ense...
1ENSG00000004468EnsemblENSG00000004468EnsemblCD38975.036348-0.5888040.173952-3.3848690.0007120.0239093.147446[{'stringdb_link_to': 'ENSG00000089163', 'Ense...
2ENSG00000004779EnsemblENSG00000004779EnsemblNDUFAB12346.167702-0.4329840.135670-3.1914460.0014160.0364922.849052[{'stringdb_link_to': 'ENSG00000010256', 'Ense...
3ENSG00000005700EnsemblENSG00000005700EnsemblIBTK1511.600789-0.4363260.103624-4.2106610.0000250.0030244.594099[{'stringdb_link_to': 'ENSG00000198886', 'Ense...
4ENSG00000006327EnsemblENSG00000006327EnsemblTNFRSF12A445.7373331.6557810.5192913.1885390.0014300.0365872.844684[{'stringdb_link_to': nan, 'Ensembl': nan, 'sc...
\n", + "
" + ], + "text/plain": [ + " identifier identifier.source target target.source \\\n", + "0 ENSG00000001084 Ensembl ENSG00000001084 Ensembl \n", + "1 ENSG00000004468 Ensembl ENSG00000004468 Ensembl \n", + "2 ENSG00000004779 Ensembl ENSG00000004779 Ensembl \n", + "3 ENSG00000005700 Ensembl ENSG00000005700 Ensembl \n", + "4 ENSG00000006327 Ensembl ENSG00000006327 Ensembl \n", + "\n", + " GENE_SYMBOL_dea baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea \\\n", + "0 GCLC 412.449345 0.454035 0.130200 3.487222 \n", + "1 CD38 975.036348 -0.588804 0.173952 -3.384869 \n", + "2 NDUFAB1 2346.167702 -0.432984 0.135670 -3.191446 \n", + "3 IBTK 1511.600789 -0.436326 0.103624 -4.210661 \n", + "4 TNFRSF12A 445.737333 1.655781 0.519291 3.188539 \n", + "\n", + " pvalue_dea padj_dea minus_log10_pvalue_dea \\\n", + "0 0.000488 0.018659 3.311521 \n", + "1 0.000712 0.023909 3.147446 \n", + "2 0.001416 0.036492 2.849052 \n", + "3 0.000025 0.003024 4.594099 \n", + "4 0.001430 0.036587 2.844684 \n", + "\n", + " StringDB_ppi \n", + "0 [{'stringdb_link_to': 'ENSG00000100906', 'Ense... \n", + "1 [{'stringdb_link_to': 'ENSG00000089163', 'Ense... \n", + "2 [{'stringdb_link_to': 'ENSG00000010256', 'Ense... \n", + "3 [{'stringdb_link_to': 'ENSG00000198886', 'Ense... \n", + "4 [{'stringdb_link_to': nan, 'Ensembl': nan, 'sc... " + ] + }, + "execution_count": 41, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "string_path = os.path.join(base_dir, \"data/human/string.pkl\")\n", + "string_metadata_path = os.path.join(base_dir, \"data/human/string_metadata.pkl\")\n", + "\n", + "if not os.path.exists(string_path):\n", + " ppi_df, ppi_metadata = stringdb.get_ppi(\n", + " bridgedb_df=bridgedb_df_human[bridgedb_df_human[\"padj_dea\"] <= 0.05]\n", + " )\n", + " ppi_df.to_pickle(string_path)\n", + " with open(string_metadata_path, \"wb\") as file:\n", + " pickle.dump(ppi_metadata, file)\n", + "else:\n", + " ppi_df = pd.read_pickle(string_path)\n", + " with open(string_metadata_path, \"rb\") as file:\n", + " ppi_metadata = pickle.load(file)\n", + "\n", + "ppi_df.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 42, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{0: [{'stringdb_link_to': 'ENSG00000100906',\n", + " 'Ensembl': 'ENSP00000216797',\n", + " 'score': 0.556,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000125166',\n", + " 'Ensembl': 'ENSP00000245206',\n", + " 'score': 0.838,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000126432',\n", + " 'Ensembl': 'ENSP00000265462',\n", + " 'score': 0.518,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000167996',\n", + " 'Ensembl': 'ENSP00000273550',\n", + " 'score': 0.508,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000148672',\n", + " 'Ensembl': 'ENSP00000277865',\n", + " 'score': 0.847,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000165672',\n", + " 'Ensembl': 'ENSP00000298510',\n", + " 'score': 0.457,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000167815',\n", + " 'Ensembl': 'ENSP00000301522',\n", + " 'score': 0.4,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000169715',\n", + " 'Ensembl': 'ENSP00000328137',\n", + " 'score': 0.455,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000167468',\n", + " 'Ensembl': 'ENSP00000346103',\n", + " 'score': 0.809,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000177606',\n", + " 'Ensembl': 'ENSP00000360266',\n", + " 'score': 0.419,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000117448',\n", + " 'Ensembl': 'ENSP00000361140',\n", + " 'score': 0.409,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000271303',\n", + " 'Ensembl': 'ENSP00000371388',\n", + " 'score': 0.756,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000211445',\n", + " 'Ensembl': 'ENSP00000373477',\n", + " 'score': 0.705,\n", + " 'Uniprot-TrEMBL': 'P22352',\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000111640',\n", + " 'Ensembl': 'ENSP00000380070',\n", + " 'score': 0.598,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000116044',\n", + " 'Ensembl': 'ENSP00000380252',\n", + " 'score': 0.966,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000066926',\n", + " 'Ensembl': 'ENSP00000498358',\n", + " 'score': 0.457,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 1: [{'stringdb_link_to': 'ENSG00000089163',\n", + " 'Ensembl': 'ENSP00000202967',\n", + " 'score': 0.921,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000100219',\n", + " 'Ensembl': 'ENSP00000216037',\n", + " 'score': 0.527,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000128016',\n", + " 'Ensembl': 'ENSP00000471239',\n", + " 'score': 0.41,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000143799',\n", + " 'Ensembl': 'ENSP00000355759',\n", + " 'score': 0.429,\n", + " 'Uniprot-TrEMBL': 'P09874',\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000163864',\n", + " 'Ensembl': 'ENSP00000495112',\n", + " 'score': 0.446,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000111640',\n", + " 'Ensembl': 'ENSP00000380070',\n", + " 'score': 0.459,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000113916',\n", + " 'Ensembl': 'ENSP00000384371',\n", + " 'score': 0.695,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000136997',\n", + " 'Ensembl': 'ENSP00000478887',\n", + " 'score': 0.7,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000154096',\n", + " 'Ensembl': 'ENSP00000284240',\n", + " 'score': 0.708,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000072274',\n", + " 'Ensembl': 'ENSP00000376197',\n", + " 'score': 0.788,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000112992',\n", + " 'Ensembl': 'ENSP00000264663',\n", + " 'score': 0.909,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000152620',\n", + " 'Ensembl': 'ENSP00000371362',\n", + " 'score': 0.91,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000124523',\n", + " 'Ensembl': 'ENSP00000476228',\n", + " 'score': 0.923,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000166741',\n", + " 'Ensembl': 'ENSP00000441434',\n", + " 'score': 0.925,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000142082',\n", + " 'Ensembl': 'ENSP00000372191',\n", + " 'score': 0.939,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 2: [{'stringdb_link_to': 'ENSG00000010256',\n", + " 'Ensembl': 'ENSP00000203407',\n", + " 'score': 0.983,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000091140',\n", + " 'Ensembl': 'ENSP00000205402',\n", + " 'score': 0.669,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000100412',\n", + " 'Ensembl': 'ENSP00000216254',\n", + " 'score': 0.658,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000104325',\n", + " 'Ensembl': 'ENSP00000220764',\n", + " 'score': 0.455,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000108179',\n", + " 'Ensembl': 'ENSP00000225174',\n", + " 'score': 0.445,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000110435',\n", + " 'Ensembl': 'ENSP00000227868',\n", + " 'score': 0.47,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000111669',\n", + " 'Ensembl': 'ENSP00000229270',\n", + " 'score': 0.546,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000130414',\n", + " 'Ensembl': 'ENSP00000252711',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000135900',\n", + " 'Ensembl': 'ENSP00000258383',\n", + " 'score': 0.945,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000110955',\n", + " 'Ensembl': 'ENSP00000262030',\n", + " 'score': 0.677,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000213619',\n", + " 'Ensembl': 'ENSP00000263774',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000106049',\n", + " 'Ensembl': 'ENSP00000265395',\n", + " 'score': 0.521,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000139180',\n", + " 'Ensembl': 'ENSP00000266544',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000147592',\n", + " 'Ensembl': 'ENSP00000276590',\n", + " 'score': 0.48,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000151093',\n", + " 'Ensembl': 'ENSP00000280701',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000154518',\n", + " 'Ensembl': 'ENSP00000284727',\n", + " 'score': 0.752,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000166902',\n", + " 'Ensembl': 'ENSP00000300151',\n", + " 'score': 0.957,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000171861',\n", + " 'Ensembl': 'ENSP00000306080',\n", + " 'score': 0.965,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000168291',\n", + " 'Ensembl': 'ENSP00000307241',\n", + " 'score': 0.741,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000140905',\n", + " 'Ensembl': 'ENSP00000319531',\n", + " 'score': 0.858,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000067225',\n", + " 'Ensembl': 'ENSP00000320171',\n", + " 'score': 0.421,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000139131',\n", + " 'Ensembl': 'ENSP00000320658',\n", + " 'score': 0.415,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000176340',\n", + " 'Ensembl': 'ENSP00000321260',\n", + " 'score': 0.661,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000187630',\n", + " 'Ensembl': 'ENSP00000334801',\n", + " 'score': 0.405,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000119689',\n", + " 'Ensembl': 'ENSP00000335304',\n", + " 'score': 0.538,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198804',\n", + " 'Ensembl': 'ENSP00000354499',\n", + " 'score': 0.891,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198727',\n", + " 'Ensembl': 'ENSP00000354554',\n", + " 'score': 0.925,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198888',\n", + " 'Ensembl': 'ENSP00000354687',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198786',\n", + " 'Ensembl': 'ENSP00000354813',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198712',\n", + " 'Ensembl': 'ENSP00000354876',\n", + " 'score': 0.793,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " 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'ENSP00000498803',\n", + " 'score': 0.732,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000124228',\n", + " 'Ensembl': 'ENSP00000483495',\n", + " 'score': 0.873,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 583: [{'stringdb_link_to': nan,\n", + " 'Ensembl': nan,\n", + " 'score': nan,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 584: [{'stringdb_link_to': 'ENSG00000132463',\n", + " 'Ensembl': 'ENSP00000254799',\n", + " 'score': 0.552,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000135900',\n", + " 'Ensembl': 'ENSP00000258383',\n", + " 'score': 0.941,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000136463',\n", + " 'Ensembl': 'ENSP00000258975',\n", + " 'score': 0.444,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000139180',\n", + " 'Ensembl': 'ENSP00000266544',\n", + " 'score': 0.54,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000166902',\n", + " 'Ensembl': 'ENSP00000300151',\n", + " 'score': 0.89,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000171861',\n", + " 'Ensembl': 'ENSP00000306080',\n", + " 'score': 0.816,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000062582',\n", + " 'Ensembl': 'ENSP00000318158',\n", + " 'score': 0.861,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198712',\n", + " 'Ensembl': 'ENSP00000354876',\n", + " 'score': 0.477,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000101019',\n", + " 'Ensembl': 'ENSP00000363506',\n", + " 'score': 0.403,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000117118',\n", + " 'Ensembl': 'ENSP00000364649',\n", + " 'score': 0.546,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000004779',\n", + " 'Ensembl': 'ENSP00000458770',\n", + " 'score': 0.939,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 585: [{'stringdb_link_to': nan,\n", + " 'Ensembl': nan,\n", + " 'score': nan,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 586: [{'stringdb_link_to': nan,\n", + " 'Ensembl': nan,\n", + " 'score': nan,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 587: [{'stringdb_link_to': nan,\n", + " 'Ensembl': nan,\n", + " 'score': nan,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 588: [{'stringdb_link_to': nan,\n", + " 'Ensembl': nan,\n", + " 'score': nan,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 589: [{'stringdb_link_to': nan,\n", + " 'Ensembl': nan,\n", + " 'score': nan,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 590: [{'stringdb_link_to': 'ENSG00000111641',\n", + " 'Ensembl': 'ENSP00000371858',\n", + " 'score': 0.432,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000106263',\n", + " 'Ensembl': 'ENSP00000354125',\n", + " 'score': 0.482,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000134697',\n", + " 'Ensembl': 'ENSP00000362153',\n", + " 'score': 0.495,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000120725',\n", + " 'Ensembl': 'ENSP00000265195',\n", + " 'score': 0.497,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000166902',\n", + " 'Ensembl': 'ENSP00000300151',\n", + " 'score': 0.5,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000101361',\n", + " 'Ensembl': 'ENSP00000370589',\n", + " 'score': 0.534,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000115657',\n", + " 'Ensembl': 'ENSP00000265316',\n", + " 'score': 0.643,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}]}" + ] + }, + "execution_count": 42, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from pyBiodatafuse.constants import STRING_PPI_COL\n", + "\n", + "ppi_df[STRING_PPI_COL].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 43, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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targetStringDB_ppi
0ENSG00000001084[{'stringdb_link_to': 'ENSG00000100906', 'Ense...
1ENSG00000004468[{'stringdb_link_to': 'ENSG00000089163', 'Ense...
2ENSG00000004779[{'stringdb_link_to': 'ENSG00000010256', 'Ense...
3ENSG00000005700[{'stringdb_link_to': 'ENSG00000198886', 'Ense...
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0.536,\n", + " 'Uniprot-TrEMBL': 'P78537',\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000070371',\n", + " 'Ensembl': 'ENSP00000441158',\n", + " 'score': 0.54,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000139998',\n", + " 'Ensembl': 'ENSP00000434103',\n", + " 'score': 0.548,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000066926',\n", + " 'Ensembl': 'ENSP00000498358',\n", + " 'score': 0.567,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000136997',\n", + " 'Ensembl': 'ENSP00000478887',\n", + " 'score': 0.596,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000128016',\n", + " 'Ensembl': 'ENSP00000471239',\n", + " 'score': 0.618,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000111640',\n", + " 'Ensembl': 'ENSP00000380070',\n", + " 'score': 0.753,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 896: nan,\n", + " 897: nan,\n", + " 898: nan,\n", + " 899: nan,\n", + " 900: nan,\n", + " 901: nan,\n", + " 902: nan,\n", + " 903: nan,\n", + " 904: nan,\n", + " 905: nan,\n", + " 906: nan,\n", + " 907: nan,\n", + " 908: nan,\n", + " 909: nan,\n", + " 910: nan,\n", + " 911: nan,\n", + " 912: nan,\n", + " 913: nan,\n", + " 914: nan,\n", + " 915: nan,\n", + " 916: nan,\n", + " 917: nan,\n", + " 918: nan,\n", + " 919: nan,\n", + " 920: nan,\n", + " 921: nan,\n", + " 922: nan,\n", + " 923: [{'stringdb_link_to': 'ENSG00000186951',\n", + " 'Ensembl': 'ENSP00000385523',\n", + " 'score': 0.4,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000197451',\n", + " 'Ensembl': 'ENSP00000425031',\n", + " 'score': 0.51,\n", + " 'Uniprot-TrEMBL': None,\n", + " 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'ENSP00000307305',\n", + " 'score': 0.842,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 924: nan,\n", + " 925: nan,\n", + " 926: nan,\n", + " 927: nan,\n", + " 928: nan,\n", + " 929: nan,\n", + " 930: nan,\n", + " 931: nan,\n", + " 932: nan,\n", + " 933: [{'stringdb_link_to': 'ENSG00000168542',\n", + " 'Ensembl': 'ENSP00000304408',\n", + " 'score': 0.43,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000022267',\n", + " 'Ensembl': 'ENSP00000498684',\n", + " 'score': 0.445,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000070371',\n", + " 'Ensembl': 'ENSP00000441158',\n", + " 'score': 0.452,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000136997',\n", + " 'Ensembl': 'ENSP00000478887',\n", + " 'score': 0.484,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 934: nan,\n", + " 935: nan,\n", + " 936: nan,\n", + " 937: nan,\n", + " 938: nan,\n", + " 939: [{'stringdb_link_to': 'ENSG00000123570',\n", + " 'Ensembl': 'ENSP00000243298',\n", + " 'score': 0.677,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000029534',\n", + " 'Ensembl': 'ENSP00000265709',\n", + " 'score': 0.568,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000197081',\n", + " 'Ensembl': 'ENSP00000349437',\n", + " 'score': 0.514,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000145362',\n", + " 'Ensembl': 'ENSP00000349588',\n", + " 'score': 0.567,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000215305',\n", + " 'Ensembl': 'ENSP00000369810',\n", + " 'score': 0.533,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000070182',\n", + " 'Ensembl': 'ENSP00000495909',\n", + " 'score': 0.524,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000070371',\n", + " 'Ensembl': 'ENSP00000441158',\n", + " 'score': 0.544,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000141252',\n", + " 'Ensembl': 'ENSP00000401435',\n", + " 'score': 0.63,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000203879',\n", + " 'Ensembl': 'ENSP00000394071',\n", + " 'score': 0.655,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 940: nan,\n", + " 941: nan,\n", + " 942: nan,\n", + " 943: nan,\n", + " 944: nan,\n", + " 945: nan,\n", + " 946: nan,\n", + " 947: nan,\n", + " 948: nan,\n", + " 949: nan,\n", + " 950: nan,\n", + " 951: nan,\n", + " 952: nan,\n", + " 953: nan,\n", + " 954: nan,\n", + " 955: nan,\n", + " 956: nan,\n", + " 957: nan,\n", + " 958: nan,\n", + " 959: nan,\n", + " 960: nan,\n", + " 961: nan,\n", + " 962: nan,\n", + " 963: nan,\n", + " 964: nan,\n", + " 965: nan,\n", + " 966: nan,\n", + " 967: nan,\n", + " 968: nan,\n", + " 969: nan,\n", + " 970: nan,\n", + " 971: nan,\n", + " 972: [{'stringdb_link_to': 'ENSG00000091140',\n", + " 'Ensembl': 'ENSP00000205402',\n", + " 'score': 0.632,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000100412',\n", + " 'Ensembl': 'ENSP00000216254',\n", + " 'score': 0.652,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000110435',\n", + " 'Ensembl': 'ENSP00000227868',\n", + " 'score': 0.513,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000111669',\n", + " 'Ensembl': 'ENSP00000229270',\n", + " 'score': 0.405,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000109929',\n", + " 'Ensembl': 'ENSP00000264027',\n", + " 'score': 0.559,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000165672',\n", + " 'Ensembl': 'ENSP00000298510',\n", + " 'score': 0.416,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000067225',\n", + " 'Ensembl': 'ENSP00000320171',\n", + " 'score': 0.419,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000083123',\n", + " 'Ensembl': 'ENSP00000318351',\n", + " 'score': 0.42,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000148672',\n", + " 'Ensembl': 'ENSP00000277865',\n", + " 'score': 0.423,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000204356',\n", + " 'Ensembl': 'ENSP00000364578',\n", + " 'score': 0.451,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000107897',\n", + " 'Ensembl': 'ENSP00000365049',\n", + " 'score': 0.475,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000175198',\n", + " 'Ensembl': 'ENSP00000365462',\n", + " 'score': 0.487,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000168291',\n", + " 'Ensembl': 'ENSP00000307241',\n", + " 'score': 0.491,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000151093',\n", + " 'Ensembl': 'ENSP00000280701',\n", + " 'score': 0.492,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000157184',\n", + " 'Ensembl': 'ENSP00000360541',\n", + " 'score': 0.493,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000182054',\n", + " 'Ensembl': 'ENSP00000331897',\n", + " 'score': 0.517,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000117118',\n", + " 'Ensembl': 'ENSP00000364649',\n", + " 'score': 0.565,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000171503',\n", + " 'Ensembl': 'ENSP00000426638',\n", + " 'score': 0.575,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000112357',\n", + " 'Ensembl': 'ENSP00000315680',\n", + " 'score': 0.682,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000093144',\n", + " 'Ensembl': 'ENSP00000436585',\n", + " 'score': 0.712,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000148090',\n", + " 'Ensembl': 'ENSP00000364883',\n", + " 'score': 0.719,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000116171',\n", + " 'Ensembl': 'ENSP00000360569',\n", + " 'score': 0.724,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000152904',\n", + " 'Ensembl': 'ENSP00000282841',\n", + " 'score': 0.735,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198130',\n", + " 'Ensembl': 'ENSP00000352706',\n", + " 'score': 0.751,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000163344',\n", + " 'Ensembl': 'ENSP00000357452',\n", + " 'score': 0.758,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000140374',\n", + " 'Ensembl': 'ENSP00000452762',\n", + " 'score': 0.821,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000119689',\n", + " 'Ensembl': 'ENSP00000335304',\n", + " 'score': 0.847,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000127884',\n", + " 'Ensembl': 'ENSP00000357535',\n", + " 'score': 0.85,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000172340',\n", + " 'Ensembl': 'ENSP00000419325',\n", + " 'score': 0.867,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000136143',\n", + " 'Ensembl': 'ENSP00000494360',\n", + " 'score': 0.883,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000163541',\n", + " 'Ensembl': 'ENSP00000377446',\n", + " 'score': 0.907,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000081760',\n", + " 'Ensembl': 'ENSP00000324842',\n", + " 'score': 0.962,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000196177',\n", + " 'Ensembl': 'ENSP00000357873',\n", + " 'score': 0.968,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000117305',\n", + " 'Ensembl': 'ENSP00000363614',\n", + " 'score': 0.972,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 973: nan,\n", + " 974: nan,\n", + " 975: nan,\n", + " 976: nan,\n", + " 977: nan,\n", + " 978: nan,\n", + " 979: nan,\n", + " 980: nan,\n", + " 981: nan,\n", + " 982: nan,\n", + " 983: nan,\n", + " 984: nan,\n", + " 985: nan,\n", + " 986: nan,\n", + " 987: nan,\n", + " 988: nan,\n", + " 989: nan,\n", + " 990: nan,\n", + " 991: nan,\n", + " 992: nan,\n", + " 993: nan,\n", + " 994: nan,\n", + " 995: nan,\n", + " 996: nan,\n", + " 997: nan,\n", + " 998: nan,\n", + " 999: nan,\n", + " ...}" + ] + }, + "execution_count": 49, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df[\"StringDB_ppi\"].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 50, + "metadata": {}, + "outputs": [], + "source": [ + "filename_human = \"data/human/combined_df.pkl\"\n", + "\n", + "combined_df.to_pickle(filename_human)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### graph" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [], + "source": [ + "filename_human = \"data/human/combined_df.pkl\"\n", + "with open(filename_human, \"rb\") as f:\n", + " combined_df = pickle.load(f)" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "997" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Extract all 'NCBI.GeneID.TF' values into a single list\n", + "ncbi_gene_ids = (\n", + " combined_df[\"its_tf\"]\n", + " .apply(lambda x: [d[\"NCBI.GeneID.TF\"] for d in x] if isinstance(x, list) else [])\n", + " .explode()\n", + " .dropna()\n", + " .unique()\n", + " .tolist()\n", + ")\n", + "\n", + "len(ncbi_gene_ids)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(537, 30)" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df_tf = combined_df[combined_df[\"target\"].isin(ncbi_gene_ids)]\n", + "combined_df_sig = combined_df[combined_df[\"padj_dea\"] <= 0.05]\n", + "combined_df_sig = combined_df_sig[~combined_df_sig[\"target\"].isin(ncbi_gene_ids)]\n", + "combined_df_sig.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(1535, 30)" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df_tf_sig = pd.concat([combined_df_sig, combined_df_tf], axis=0, ignore_index=True)\n", + "combined_df_tf_sig.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "207 True\n", + "Name: its_tf, dtype: bool" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df_tf_sig[combined_df_tf_sig[\"GENE_SYMBOL_dea\"] == \"COQ10A\"][\"its_tf\"].apply(\n", + " lambda x: isinstance(x, list)\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{207: [{'NCBI.GeneID.TF': '112398',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000269858',\n", + " 'Name.TF': 'EGLN2',\n", + " 'UniprotID.TF': 'Q96KS0',\n", + " 'TF.TFLink.ortho': 'Mm:Q91YE2;Rn:Q6AYU4',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285',\n", + " 'Source.database': 'ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '11091',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000196363',\n", + " 'Name.TF': 'WDR5',\n", + " 'UniprotID.TF': 'P61964',\n", + " 'TF.TFLink.ortho': 'Dm:Q9V3J8;Dr:Q7ZTX2;Mm:P61965',\n", + " 'TF.nonTFLink.ortho': 'Rn:Q498M4',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '1024',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000132964',\n", + " 'Name.TF': 'CDK8',\n", + " 'UniprotID.TF': 'P49336',\n", + " 'TF.TFLink.ortho': 'Dm:Q9VT57;Dr:A8E4S2;Mm:Q8R3L8',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '4149',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000125952',\n", + " 'Name.TF': 'MAX',\n", + " 'UniprotID.TF': 'P61244',\n", + " 'TF.TFLink.ortho': 'Ce:G5EEH5;Dm:P91664;Mm:P28574;Rn:P52164',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '94039',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000181896',\n", + " 'Name.TF': 'ZNF101',\n", + " 'UniprotID.TF': 'Q8IZC7',\n", + " 'TF.TFLink.ortho': '-',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '64763',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000105732',\n", + " 'Name.TF': 'ZNF574',\n", + " 'UniprotID.TF': 'Q6ZN55',\n", + " 'TF.TFLink.ortho': 'Mm:Q8BY46;Rn:Q504L7',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '6613',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000188612',\n", + " 'Name.TF': 'SUMO2',\n", + " 'UniprotID.TF': 'P61956',\n", + " 'TF.TFLink.ortho': '-',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '23361',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000102870',\n", + " 'Name.TF': 'ZNF629',\n", + " 'UniprotID.TF': 'Q9UEG4',\n", + " 'TF.TFLink.ortho': 'Mm:Q6A085',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '55145',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000131931',\n", + " 'Name.TF': 'THAP1',\n", + " 'UniprotID.TF': 'Q9NVV9',\n", + " 'TF.TFLink.ortho': 'Dr:Q1JPT7;Mm:Q8CHW1;Rn:Q5U208',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285',\n", + " 'Source.database': 'ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '657',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000107779',\n", + " 'Name.TF': 'BMPR1A',\n", + " 'UniprotID.TF': 'P36894',\n", + " 'TF.TFLink.ortho': 'Mm:P36895;Rn:Q78EA7',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285',\n", + " 'Source.database': 'ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '4841',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000147140',\n", + " 'Name.TF': 'NONO',\n", + " 'UniprotID.TF': 'Q15233',\n", + " 'TF.TFLink.ortho': 'Dr:Q802Z5;Mm:Q99K48;Rn:Q5FVM4',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '27107',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000066422',\n", + " 'Name.TF': 'ZBTB11',\n", + " 'UniprotID.TF': 'O95625',\n", + " 'TF.TFLink.ortho': 'Dr:F1RAC1;Mm:G5E8B9;Rn:D3ZDP9',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '57504',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000057935',\n", + " 'Name.TF': 'MTA3',\n", + " 'UniprotID.TF': 'Q9BTC8',\n", + " 'TF.TFLink.ortho': 'Mm:Q924K8;Rn:A0A0G2JTK6',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '4790',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000109320',\n", + " 'Name.TF': 'NFKB1',\n", + " 'UniprotID.TF': 'P19838',\n", + " 'TF.TFLink.ortho': 'Dm:Q94527;Mm:P25799;Rn:F1LQH2',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '3611',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000166333',\n", + " 'Name.TF': 'ILK',\n", + " 'UniprotID.TF': 'Q13418',\n", + " 'TF.TFLink.ortho': 'Ce:Q9TZC4;Dm:Q9V400;Dr:Q6PHD6;Mm:O55222;Rn:Q99J82',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285',\n", + " 'Source.database': 'ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '7936',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000204356',\n", + " 'Name.TF': 'NELFE',\n", + " 'UniprotID.TF': 'P18615',\n", + " 'TF.TFLink.ortho': '-',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '10614',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000186834',\n", + " 'Name.TF': 'HEXIM1',\n", + " 'UniprotID.TF': 'O94992',\n", + " 'TF.TFLink.ortho': 'Mm:Q8R409;Rn:Q5M9G1',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '4928',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000110713',\n", + " 'Name.TF': 'NUP98',\n", + " 'UniprotID.TF': 'P52948',\n", + " 'TF.TFLink.ortho': 'Ce:G5EEH9;Rn:P49793;Sc:P49687',\n", + " 'TF.nonTFLink.ortho': 'Mm:A0A1B0GSX7',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '23133',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000172943',\n", + " 'Name.TF': 'PHF8',\n", + " 'UniprotID.TF': 'Q9UPP1',\n", + " 'TF.TFLink.ortho': 'Dr:P0CH95;Mm:Q80TJ7;Rn:D4AD31',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '6659',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000124766',\n", + " 'Name.TF': 'SOX4',\n", + " 'UniprotID.TF': 'Q06945',\n", + " 'TF.TFLink.ortho': 'Dr:A0A0R4IQD2;Mm:Q06831',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': 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'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '23064',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000107290',\n", + " 'Name.TF': 'SETX',\n", + " 'UniprotID.TF': 'Q7Z333',\n", + " 'TF.TFLink.ortho': 'Dr:E7FBJ2;Mm:A2AKX3',\n", + " 'TF.nonTFLink.ortho': 'Rn:D4AEB3',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '3054',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000172534',\n", + " 'Name.TF': 'HCFC1',\n", + " 'UniprotID.TF': 'P51610',\n", + " 'TF.TFLink.ortho': 'Dr:F1Q750;Dr:A8WIP5;Mm:Q61191;Rn:D3ZN95',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '7756',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000010244',\n", + " 'Name.TF': 'ZNF207',\n", + " 'UniprotID.TF': 'O43670',\n", + " 'TF.TFLink.ortho': 'Mm:Q9JMD0;Rn:Q498C9',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285',\n", + " 'Source.database': 'ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '10781',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000174652',\n", + " 'Name.TF': 'ZNF266',\n", + " 'UniprotID.TF': 'Q14584',\n", + " 'TF.TFLink.ortho': '-',\n", + " 'TF.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '6046',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000204256',\n", + " 'Name.TF': 'BRD2',\n", + " 'UniprotID.TF': 'P25440',\n", + " 'TF.TFLink.ortho': 'Mm:Q7JJ13',\n", + " 'TF.nonTFLink.ortho': 'Dr:Q1LWX7;Rn:Q6MGA9',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': 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" {'NCBI.GeneID.TF': '2313',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000151702',\n", + " 'Name.TF': 'FLI1',\n", + " 'UniprotID.TF': 'Q01543',\n", + " 'TF.TFLink.ortho': 'Mm:P26323;Rn:Q4Z8P1',\n", + " 'TF.nonTFLink.ortho': 'Dr:Q9PU61',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '167465',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000178175',\n", + " 'Name.TF': 'ZNF366',\n", + " 'UniprotID.TF': 'Q8N895',\n", + " 'TF.TFLink.ortho': 'Mm:Q6NS86',\n", + " 'TF.nonTFLink.ortho': 'Rn:D4A715',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.TF': '23435',\n", + " 'Ensembl.GeneID.TF': 'ENSG00000120948',\n", + " 'Name.TF': 'TARDBP',\n", + " 'UniprotID.TF': 'Q13148',\n", + " 'TF.TFLink.ortho': 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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_dea...g:Profiler_go:mfg:Profiler_hpg:Profiler_hpag:Profiler_keggg:Profiler_mirnag:Profiler_reacg:Profiler_tfg:Profiler_wpMitoCartaStringDB_ppi
7ENSG00000001167Ensembl4800ncbi_gene_idNFYA198.9635150.3390270.1330752.5476270.010846...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
43ENSG00000004487Ensembl23028ncbi_gene_idKDM1A1310.6154840.0458210.0674000.6798300.496612...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
74ENSG00000005339Ensembl1387ncbi_gene_idCREBBP1852.2423300.1165100.1626120.7164890.473690...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
88ENSG00000005889Ensembl7543ncbi_gene_idZFX732.044736-0.1640810.159735-1.0272050.304324...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
99ENSG00000006194Ensembl10127ncbi_gene_idZNF263337.6185030.1414910.1322311.0700340.284604...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
..................................................................
11743ENSG00000275700Ensembl26574ncbi_gene_idAATF405.2506190.4222120.1346133.1364840.001710...[{'id': 'GO:0019901', 'name': 'protein kinase ...NaNNaNNaN[{'id': 'MIRNA:hsa-miR-634', 'name': 'hsa-miR-...[{'id': 'REAC:R-HSA-162582', 'name': 'Signal T...[{'id': 'TF:M10696', 'name': 'Factor: HOXA6; m...[{'id': 'WP:WP5287', 'name': '17q12 copy numbe...NaN[{'stringdb_link_to': 'ENSG00000112578', 'Ense...
11756ENSG00000276644Ensembl1602ncbi_gene_idDACH187.387806-0.0016580.179004-0.0092620.992610...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
11758ENSG00000277258Ensembl7703ncbi_gene_idPCGF2160.0484070.0029320.2038060.0143860.988522...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
11760ENSG00000277494Ensembl338328ncbi_gene_idGPIHBP1585.805576-0.1909330.355165-0.5375910.590860...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
11764ENSG00000278129Ensembl7554ncbi_gene_idZNF854.639929-0.3627940.239010-1.5179040.129039...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
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{'NCBI.GeneID.Target': '3491',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000142871',\n", + " 'Name.Target': 'CCN1',\n", + " 'UniprotID.Target': 'O00622',\n", + " 'Target.TFLink.ortho': 'Dr:F1QL10;Mm:P18406;Rn:Q66HT5',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '1349',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000131174',\n", + " 'Name.Target': 'COX7B',\n", + " 'UniprotID.Target': 'P24311',\n", + " 'Target.TFLink.ortho': 'Mm:P56393;Rn:P80431',\n", + " 'Target.nonTFLink.ortho': 'Dr:B3DJA6',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '1376',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000157184',\n", + " 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" 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '80144',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000138759',\n", + " 'Name.Target': 'FRAS1',\n", + " 'UniprotID.Target': 'Q86XX4',\n", + " 'Target.TFLink.ortho': 'Mm:Q80T14',\n", + " 'Target.nonTFLink.ortho': 'Dr:F1Q633;Rn:F1M3H3',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '79738',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000179941',\n", + " 'Name.Target': 'BBS10',\n", + " 'UniprotID.Target': 'Q8TAM1',\n", + " 'Target.TFLink.ortho': 'Mm:Q9DBI2;Rn:B1H296',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 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" {'NCBI.GeneID.Target': '50',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000100412',\n", + " 'Name.Target': 'ACO2',\n", + " 'UniprotID.Target': 'Q99798',\n", + " 'Target.TFLink.ortho': '-',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '51133',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000136636',\n", + " 'Name.Target': 'KCTD3',\n", + " 'UniprotID.Target': 'Q9Y597',\n", + " 'Target.TFLink.ortho': 'Mm:Q8BFX3;Rn:D3ZNX0',\n", + " 'Target.nonTFLink.ortho': 'Dr:F1Q6W0',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '138199',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000156017',\n", + " 'Name.Target': 'CARNMT1',\n", + " 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'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '81796',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000137571',\n", + " 'Name.Target': 'SLCO5A1',\n", + " 'UniprotID.Target': 'Q9H2Y9',\n", + " 'Target.TFLink.ortho': 'Dr:E7F2I7;Mm:E9PVD9;Rn:D3ZZM7',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '7264',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000104522',\n", + " 'Name.Target': 'TSTA3',\n", + " 'UniprotID.Target': 'Q13630',\n", + " 'Target.TFLink.ortho': 'Ce:G5EER4;Dm:Q9W1X8;Dr:Q6DC41;Mm:P23591;Rn:G3V762',\n", + " 'Target.nonTFLink.ortho': 'Dr:B0S7C9;Dr:Q5SPD5',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '145957',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000169752',\n", + " 'Name.Target': 'NRG4',\n", + " 'UniprotID.Target': 'Q8WWG1',\n", + " 'Target.TFLink.ortho': 'Mm:Q9WTX4;Rn:A0A0G2JYC9',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '23180',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000131378',\n", + " 'Name.Target': 'RFTN1',\n", + " 'UniprotID.Target': 'Q14699',\n", + " 'Target.TFLink.ortho': 'Dr:A0A0G2L3G6;Mm:Q6A0D4',\n", + " 'Target.nonTFLink.ortho': 'Dr:E9QG04;Rn:G3V7I2',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'}]}" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df_tf_sig[combined_df_tf_sig[\"identifier\"] == \"ENSG00000001167\"][\"its_target\"].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [], + "source": [ + "combined_df_tf_sig[\"its_target\"][10]" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "502" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Extract all targets for NFYA ('NCBI.GeneID.TF')\n", + "ncbi_gene_ids_NFYA_targets = (\n", + " combined_df_tf_sig[combined_df_tf_sig[\"identifier\"] == \"ENSG00000001167\"][\"its_target\"]\n", + " .apply(lambda x: [d[\"NCBI.GeneID.Target\"] for d in x] if isinstance(x, list) else [])\n", + " .explode()\n", + " .dropna()\n", + " .unique()\n", + " .tolist()\n", + ")\n", + "\n", + "len(ncbi_gene_ids_NFYA_targets)" + ] + }, + { + "cell_type": "code", + "execution_count": 70, + "metadata": {}, + "outputs": [], + "source": [ + "# combined_df = combine_sources(\n", + "# merged_df_human,\n", + "# [\n", + "# ppi_df,\n", + "# ],\n", + "# )" + ] + }, + { + "cell_type": "code", + "execution_count": 71, + "metadata": {}, + "outputs": [], + "source": [ + "# combined_metadata = create_or_append_to_metadata(\n", + "# bridgedb_metadata_human,\n", + "# [\n", + "# ppi_metadata,\n", + "# get_data_versions(\"hsapiens\")\n", + "# ],\n", + "# )" + ] + }, + { + "cell_type": "code", + "execution_count": 72, + "metadata": {}, + "outputs": [], + "source": [ + "# combined_metadata" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{}" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df[combined_df[\"identifier\"] == \"CDKN1A\"][\"StringDB_ppi\"].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_dea...g:Profiler_go:mfg:Profiler_hpg:Profiler_hpag:Profiler_keggg:Profiler_mirnag:Profiler_reacg:Profiler_tfg:Profiler_wpMitoCartaStringDB_ppi
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_dea...g:Profiler_go:mfg:Profiler_hpg:Profiler_hpag:Profiler_keggg:Profiler_mirnag:Profiler_reacg:Profiler_tfg:Profiler_wpMitoCartaStringDB_ppi
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m... \n", + "\n", + " g:Profiler_wp \\\n", + "10722 [{'id': 'WP:WP111', 'name': 'Electron transpor... \n", + "\n", + " MitoCarta \\\n", + "10722 [{'gene_description': 'NADH dehydrogenase, sub... \n", + "\n", + " StringDB_ppi \n", + "10722 [{'stringdb_link_to': 'ENSG00000010256', 'Ense... \n", + "\n", + "[1 rows x 30 columns]" + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df[combined_df[\"GENE_SYMBOL_dea\"] == \"MT-ND4\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{10722: [{'stringdb_link_to': 'ENSG00000010256',\n", + " 'Ensembl': 'ENSP00000203407',\n", + " 'score': 0.971,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000108179',\n", + " 'Ensembl': 'ENSP00000225174',\n", + " 'score': 0.404,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000130414',\n", + " 'Ensembl': 'ENSP00000252711',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000110955',\n", + " 'Ensembl': 'ENSP00000262030',\n", + " 'score': 0.553,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000213619',\n", + " 'Ensembl': 'ENSP00000263774',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000139180',\n", + " 'Ensembl': 'ENSP00000266544',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000139631',\n", + " 'Ensembl': 'ENSP00000267085',\n", + " 'score': 0.428,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000154518',\n", + " 'Ensembl': 'ENSP00000284727',\n", + " 'score': 0.513,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000005700',\n", + " 'Ensembl': 'ENSP00000305721',\n", + " 'score': 0.457,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198804',\n", + " 'Ensembl': 'ENSP00000354499',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198727',\n", + " 'Ensembl': 'ENSP00000354554',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198899',\n", + " 'Ensembl': 'ENSP00000354632',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': 'P00846',\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198888',\n", + " 'Ensembl': 'ENSP00000354687',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198786',\n", + " 'Ensembl': 'ENSP00000354813',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198712',\n", + " 'Ensembl': 'ENSP00000354876',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000105341',\n", + " 'Ensembl': 'ENSP00000403910',\n", + " 'score': 0.445,\n", + " 'Uniprot-TrEMBL': 'Q9NW81',\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000163541',\n", + " 'Ensembl': 'ENSP00000377446',\n", + " 'score': 0.458,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000103657',\n", + " 'Ensembl': 'ENSP00000390158',\n", + " 'score': 0.464,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000111640',\n", + " 'Ensembl': 'ENSP00000380070',\n", + " 'score': 0.507,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000101247',\n", + " 'Ensembl': 'ENSP00000367346',\n", + " 'score': 0.587,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000152234',\n", + " 'Ensembl': 'ENSP00000381736',\n", + " 'score': 0.654,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000142875',\n", + " 'Ensembl': 'ENSP00000359719',\n", + " 'score': 0.666,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000143252',\n", + " 'Ensembl': 'ENSP00000356953',\n", + " 'score': 0.696,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000131174',\n", + " 'Ensembl': 'ENSP00000497474',\n", + " 'score': 0.873,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000117118',\n", + " 'Ensembl': 'ENSP00000364649',\n", + " 'score': 0.958,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000023228',\n", + " 'Ensembl': 'ENSP00000392709',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000004779',\n", + " 'Ensembl': 'ENSP00000458770',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198840',\n", + " 'Ensembl': 'ENSP00000355206',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000167792',\n", + " 'Ensembl': 'ENSP00000497587',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSG00000198763',\n", + " 'Ensembl': 'ENSP00000355046',\n", + " 'score': 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"metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df[combined_df[\"identifier\"] == \"ENSG00000005700\"][\"StringDB_ppi\"].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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" + ], + "text/plain": [ + " identifier identifier.source target target.source \\\n", + "2558 ENSG00000108387 Ensembl 5414 ncbi_gene_id \n", + "\n", + " GENE_SYMBOL_dea baseMean_dea log2FoldChange_dea lfcSE_dea \\\n", + "2558 2004-09-01 00:00:00 193.471021 0.073477 0.13493 \n", + "\n", + " stat_dea pvalue_dea ... g:Profiler_go:mf g:Profiler_hp \\\n", + "2558 0.544556 0.586059 ... NaN NaN \n", + "\n", + " g:Profiler_hpa g:Profiler_kegg g:Profiler_mirna g:Profiler_reac \\\n", + "2558 NaN NaN NaN NaN \n", + "\n", + " g:Profiler_tf g:Profiler_wp \\\n", + "2558 NaN NaN \n", + "\n", + " MitoCarta StringDB_ppi \n", + "2558 [{'gene_description': 'septin 4', 'evidence': ... NaN \n", + "\n", + "[1 rows x 30 columns]" + ] + }, + "execution_count": 23, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df[combined_df[\"identifier\"] == \"ENSG00000108387\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Combined DataFrame saved in ./data/human/graph_human/graph_human_df.pkl\n", + "Metadata saved in ./data/human/graph_human/graph_human_metadata.pkl\n", + "Building graph: 100%|██████████| 1535/1535 [00:04<00:00, 310.14it/s]\n", + "Graph is built successfully\n", + "Graph saved in ./data/human/graph_human/graph_human_graph.pkl and ./data/human/graph_human/graph_human_graph.gml\n" + ] + } + ], + "source": [ + "pygraph = generator.save_graph(\n", + " combined_df=combined_df_tf_sig,\n", + " combined_metadata=bridgedb_metadata_human,\n", + " graph_name=\"graph_human\",\n", + " graph_dir=\"./data/human\",\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "MultiDiGraph with 17603 nodes and 316748 edges\n" + ] + } + ], + "source": [ + "print(pygraph)" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "ename": "", + "evalue": "", + "output_type": "error", + "traceback": [ + "\u001b[1;31mThe Kernel crashed while executing code in the current cell or a previous cell. \n", + "\u001b[1;31mPlease review the code in the cell(s) to identify a possible cause of the failure. \n", + "\u001b[1;31mClick here for more info. \n", + "\u001b[1;31mView Jupyter log for further details." + ] + } + ], + "source": [ + "from pyBiodatafuse.graph import neo4j\n", + "\n", + "neo4j.save_graph_to_graphml(pygraph, \"data/human/graph_human/networkx_graph_human.graphml\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.13" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/examples/usecases/mito/graph_generation_mice_final.ipynb b/examples/usecases/mito/graph_generation_mice_final.ipynb new file mode 100644 index 0000000..249edb6 --- /dev/null +++ b/examples/usecases/mito/graph_generation_mice_final.ipynb @@ -0,0 +1,48221 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Explore mitochondrial impairment in tumars " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "**Aim**: in this notebook, you will see all the steps for collecting data and constructing a KG to explore mitochondrial impairment in tumer (both in mice and mice)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Import required libraries" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "# Import modules\n", + "import gzip\n", + "import os\n", + "import pickle\n", + "from io import BytesIO\n", + "\n", + "import numpy as np\n", + "import pandas as pd\n", + "import requests\n", + "from gprofiler.gprofiler import GProfiler\n", + "\n", + "from pyBiodatafuse import id_mapper\n", + "from pyBiodatafuse.annotators import (\n", + " bgee,\n", + " disgenet,\n", + " minerva,\n", + " molmedb,\n", + " opentargets,\n", + " pubchem,\n", + " stringdb,\n", + " wikipathways,\n", + ")\n", + "from pyBiodatafuse.constants import BGEE_GENE_EXPRESSION_LEVELS_COL, DISGENET_DISEASE_COL, GPROFILER\n", + "from pyBiodatafuse.graph import generator\n", + "from pyBiodatafuse.utils import (\n", + " combine_sources,\n", + " create_harmonized_input_file,\n", + " create_or_append_to_metadata,\n", + " get_identifier_of_interest,\n", + ")\n", + "\n", + "os.makedirs(\"data\", exist_ok=True)\n", + "base_dir = os.path.abspath(os.getcwd())" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Load the input files" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifierGENE_SYMBOLbaseMeanlog2FoldChangelfcSEstatpvaluepadjminus_log10_pvalue
0ENSMUSG00000021903Galnt152770.4375082.5211820.09994125.2266012.046157e-1402.373133e-136139.689061
1ENSMUSG00000059824Dbp2816.783019-2.9852390.191760-15.5676141.208303e-547.006949e-5153.917824
2ENSMUSG00000041417Pik3r12934.3272642.0474830.13677614.9696291.159658e-504.483238e-4749.935670
3ENSMUSG00000004939Nmrk2675.068734-3.9814740.274358-14.5119781.017437e-472.950057e-4446.992493
4ENSMUSG00000028834Trim6344995.1044133.7382750.26128914.3070481.977304e-464.586555e-4345.703926
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" + ], + "text/plain": [ + " identifier GENE_SYMBOL baseMean log2FoldChange lfcSE \\\n", + "0 ENSMUSG00000021903 Galnt15 2770.437508 2.521182 0.099941 \n", + "1 ENSMUSG00000059824 Dbp 2816.783019 -2.985239 0.191760 \n", + "2 ENSMUSG00000041417 Pik3r1 2934.327264 2.047483 0.136776 \n", + "3 ENSMUSG00000004939 Nmrk2 675.068734 -3.981474 0.274358 \n", + "4 ENSMUSG00000028834 Trim63 44995.104413 3.738275 0.261289 \n", + "\n", + " stat pvalue padj minus_log10_pvalue \n", + "0 25.226601 2.046157e-140 2.373133e-136 139.689061 \n", + "1 -15.567614 1.208303e-54 7.006949e-51 53.917824 \n", + "2 14.969629 1.159658e-50 4.483238e-47 49.935670 \n", + "3 -14.511978 1.017437e-47 2.950057e-44 46.992493 \n", + "4 14.307048 1.977304e-46 4.586555e-43 45.703926 " + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "all_genes_mice = pd.read_excel(\"datasets/Copy of 344P_cachexia_vs_sham_FDR_0.01_all_genes.xlsx\" , usecols=\"B:J\")\n", + "all_genes_mice.rename(\n", + " columns={\"Unnamed: 1\": \"identifier\", \"Unnamed: 2\": \"GENE_SYMBOL\"}, inplace=True\n", + ")\n", + "all_genes_mice.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Number of genes: 11599\n", + "Number of DEGs: 846\n" + ] + }, + { + "data": { + "text/html": [ + "
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identifierGENE_SYMBOLbaseMeanlog2FoldChangelfcSEstatpvaluepadjminus_log10_pvalue
0ENSMUSG00000021903Galnt152770.4375082.5211820.09994125.2266012.046157e-1402.373133e-136139.689061
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" + ], + "text/plain": [ + " identifier GENE_SYMBOL baseMean log2FoldChange lfcSE \\\n", + "0 ENSMUSG00000021903 Galnt15 2770.437508 2.521182 0.099941 \n", + "\n", + " stat pvalue padj minus_log10_pvalue \n", + "0 25.226601 2.046157e-140 2.373133e-136 139.689061 " + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Read only specific columns and skip the first row\n", + "all_genes_mice = pd.read_excel(\"datasets/Copy of 344P_cachexia_vs_sham_FDR_0.01_all_genes.xlsx\" , usecols=\"B:J\")\n", + "all_genes_mice.rename(\n", + " columns={\"Unnamed: 1\": \"identifier\", \"Unnamed: 2\": \"GENE_SYMBOL\"}, inplace=True\n", + ")\n", + "deg_mice = all_genes_mice[\n", + " (all_genes_mice['padj'] < 0.01) &\n", + " (\n", + " (all_genes_mice['log2FoldChange'] > 1) |\n", + " (all_genes_mice['log2FoldChange'] < -1)\n", + " )\n", + "]\n", + "print(\"Number of genes:\", len(all_genes_mice[\"identifier\"].unique()))\n", + "print(\"Number of DEGs:\", len(deg_mice[\"identifier\"].unique()))\n", + "deg_mice.head(1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Entity resolution with BridgeDB" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [], + "source": [ + "pickle_path_mice = os.path.join(base_dir, \"data/mice/bridgedb_df_mice.pkl\")\n", + "metadata_path_mice = os.path.join(base_dir, \"data/mice/bridgedb_metadata_mice.pkl\")\n", + "\n", + "if not os.path.exists(pickle_path_mice):\n", + " bridgedb_df_mice, bridgedb_metadata_mice = id_mapper.bridgedb_xref(\n", + " identifiers=all_genes_mice,\n", + " input_species=\"Mouse\",\n", + " input_datasource=\"Ensembl\",\n", + " output_datasource=\"All\",\n", + " )\n", + " bridgedb_df_mice.to_pickle(pickle_path_mice)\n", + " with open(metadata_path_mice, \"wb\") as file:\n", + " pickle.dump(bridgedb_metadata_mice, file)\n", + "else:\n", + " bridgedb_df_mice = pd.read_pickle(pickle_path_mice)\n", + " with open(metadata_path_mice, \"rb\") as file:\n", + " bridgedb_metadata_mice = pickle.load(file)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Number of genes with mapping in BridgeDb: 11588\n" + ] + }, + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_deapadj_deaminus_log10_pvalue_dea
0ENSMUSG00000021903EnsemblQ9D2N8Uniprot-TrEMBLGalnt152770.4375082.5211820.09994125.2266012.046157e-1402.373133e-136139.689061
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" + ], + "text/plain": [ + " identifier identifier.source target target.source \\\n", + "0 ENSMUSG00000021903 Ensembl Q9D2N8 Uniprot-TrEMBL \n", + "\n", + " GENE_SYMBOL_dea baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea \\\n", + "0 Galnt15 2770.437508 2.521182 0.099941 25.226601 \n", + "\n", + " pvalue_dea padj_dea minus_log10_pvalue_dea \n", + "0 2.046157e-140 2.373133e-136 139.689061 " + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "print(\"Number of genes with mapping in BridgeDb:\", len(bridgedb_df_mice[\"identifier\"].unique()))\n", + "bridgedb_df_mice.head(1)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Extract \"NCBI Gene\" ids for adding transcription factor (TF) and target interaction " + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_deapadj_deaminus_log10_pvalue_dea
0ENSMUSG00000021903Ensembl78754NCBI GeneGalnt152770.4375082.5211820.09994125.2266012.046157e-1402.373133e-136139.689061
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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "0 ENSMUSG00000021903 Ensembl 78754 NCBI Gene Galnt15 \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea \\\n", + "0 2770.437508 2.521182 0.099941 25.226601 2.046157e-140 \n", + "\n", + " padj_dea minus_log10_pvalue_dea \n", + "0 2.373133e-136 139.689061 " + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_df_mice = get_identifier_of_interest(bridgedb_df_mice, \"NCBI Gene\")\n", + "ncbi_to_ensembl = dict(zip(ncbi_df_mice['target'], ncbi_df_mice['identifier']))\n", + "ncbi_df_mice.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_deapadj_deaminus_log10_pvalue_dea
1ENSMUSG00000021903Ensembl78754NCBI GeneGalnt152770.4375082.5211820.09994125.2266012.046157e-1402.373133e-136139.689061
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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "1 ENSMUSG00000021903 Ensembl 78754 NCBI Gene Galnt15 \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea \\\n", + "1 2770.437508 2.521182 0.099941 25.226601 2.046157e-140 \n", + "\n", + " padj_dea minus_log10_pvalue_dea \n", + "1 2.373133e-136 139.689061 " + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "bridgedb_df_mice[bridgedb_df_mice[\"target\"] == \"78754\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Number of humman genes with mapping for NCBI Gene: 11219\n" + ] + } + ], + "source": [ + "print(\"Number of humman genes with mapping for NCBI Gene:\", len(ncbi_df_mice[\"target\"].unique()))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Download TF-target interactions\n", + "\n", + "You can download the Gene-TF interactions dataset from **TFLink**. Please visit the following page for the download:\n", + "\n", + "[TFLink Download Page](https://tflink.net/download/)\n", + "\n", + "The datasets you need can be downloaded from the following links:\n", + "\n", + "**For Human (Homo sapiens):**\n", + "- [TFLink_Homo_sapiens_interactions_All_simpleFormat_v1.0.tsv.gz](https://cdn.netbiol.org/tflink/download_files/TFLink_Homo_sapiens_interactions_All_simpleFormat_v1.0.tsv.gz)\n", + "\n", + "**For Mice (Mus musculus):**\n", + "- [TFLink_Mus_musculus_interactions_All_simpleFormat_v1.0.tsv.gz](https://cdn.netbiol.org/tflink/download_files/TFLink_Mus_musculus_interactions_All_simpleFormat_v1.0.tsv.gz)\n", + "\n", + "These files contain the TF-target interaction data in a simple format for each species.\n" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "data/mice/tflink_mice.tsv.gz already exists, skipping download.\n" + ] + }, + { + "data": { + "text/html": [ + "
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UniprotID.TFUniprotID.TargetNCBI.GeneID.TFNCBI.GeneID.TargetName.TFName.TargetDetection.methodPubmedIDOrganismSource.databaseSmall-scale.evidenceTF.TFLink.orthoTF.nonTFLink.orthoTarget.TFLink.orthoTarget.nonTFLink.ortho
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" + ], + "text/plain": [ + " UniprotID.TF UniprotID.Target NCBI.GeneID.TF NCBI.GeneID.Target Name.TF \\\n", + "0 Q9JL61 P14483 53970 14961 Rfx5 \n", + "\n", + " Name.Target Detection.method PubmedID Organism \\\n", + "0 H2-Ab1 inferred by curator 29087512;11258423 Mus musculus \n", + "\n", + " Source.database Small-scale.evidence TF.TFLink.ortho \\\n", + "0 TRRUST Yes Hs:P48382;Rn:D3ZHD7 \n", + "\n", + " TF.nonTFLink.ortho Target.TFLink.ortho Target.nonTFLink.ortho \n", + "0 - Rn:Q6AYB1 Hs:Q5SU54 " + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# URLs for the TF datasets\n", + "url_mice = \"https://cdn.netbiol.org/tflink/download_files/TFLink_Mus_musculus_interactions_All_simpleFormat_v1.0.tsv.gz\"\n", + "\n", + "# Function to download and read a gzipped file into a dataframe\n", + "def download_save_and_read(url, filename):\n", + " if not os.path.exists(filename):\n", + " response = requests.get(url)\n", + " with open(filename, \"wb\") as file:\n", + " file.write(response.content)\n", + " else:\n", + " print(f\"{filename} already exists, skipping download.\")\n", + "\n", + " with gzip.open(filename, \"rt\") as f:\n", + " df = pd.read_csv(f, sep=\"\\t\")\n", + " return df\n", + "\n", + "# Download and read the mouse and mice datasets\n", + "tf_df_mice = download_save_and_read(url_mice, \"data/mice/tflink_mice.tsv.gz\")\n", + "\n", + "# Keep rows where both TF and target exist in our dataset\n", + "tf_df_mice = tf_df_mice[tf_df_mice[\"NCBI.GeneID.TF\"].isin(ncbi_df_mice[\"target\"])]\n", + "tf_df_mice = tf_df_mice[tf_df_mice[\"NCBI.GeneID.Target\"].isin(ncbi_df_mice[\"target\"])]\n", + "\n", + "tf_df_mice.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(2014896, 15)" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tf_df_mice.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(is_target\n", + " True 10759\n", + " False 472\n", + " Name: count, dtype: int64,\n", + " is_tf\n", + " False 10557\n", + " True 674\n", + " Name: count, dtype: int64)" + ] + }, + "execution_count": 13, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Extract the TF and the TF targets\n", + "tf_list_mice = list(tf_df_mice[\"NCBI.GeneID.TF\"])\n", + "target_list_mice = list(tf_df_mice[\"NCBI.GeneID.Target\"])\n", + "\n", + "# Add 'is_tf' and 'is_target' columns\n", + "ncbi_df_mice[\"is_tf\"] = ncbi_df_mice[\"target\"].isin(tf_list_mice)\n", + "ncbi_df_mice[\"is_target\"] = ncbi_df_mice[\"target\"].isin(target_list_mice)\n", + "\n", + "ncbi_df_mice[\"is_target\"].value_counts(), ncbi_df_mice[\"is_tf\"].value_counts()" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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" + ], + "text/plain": [ + " UniprotID.TF UniprotID.Target NCBI.GeneID.TF NCBI.GeneID.Target Name.TF \\\n", + "0 Q9JL61 P14483 53970 14961 Rfx5 \n", + "\n", + " Name.Target Detection.method PubmedID Organism \\\n", + "0 H2-Ab1 inferred by curator 29087512;11258423 Mus musculus \n", + "\n", + " Source.database Small-scale.evidence TF.TFLink.ortho \\\n", + "0 TRRUST Yes Hs:P48382;Rn:D3ZHD7 \n", + "\n", + " TF.nonTFLink.ortho Target.TFLink.ortho Target.nonTFLink.ortho \\\n", + "0 - Rn:Q6AYB1 Hs:Q5SU54 \n", + "\n", + " Ensembl.GeneID.TF Ensembl.GeneID.Target \n", + "0 ENSMUSG00000005774 ENSMUSG00000073421 " + ] + }, + "execution_count": 14, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# kepp only rows where the target is a DEG\n", + "tf_sig_df_mice = tf_df_mice[tf_df_mice[\"NCBI.GeneID.Target\"].isin(ncbi_df_mice[\n", + " (ncbi_df_mice['padj_dea'] < 0.01) &\n", + " (\n", + " (ncbi_df_mice['log2FoldChange_dea'] > 1) |\n", + " (ncbi_df_mice['log2FoldChange_dea'] < -1)\n", + " )][\"target\"])]\n", + "# add ensembl gene id for the TF and target\n", + "tf_sig_df_mice['Ensembl.GeneID.TF'] = tf_sig_df_mice['NCBI.GeneID.TF'].map(ncbi_to_ensembl)\n", + "tf_sig_df_mice['Ensembl.GeneID.Target'] = tf_sig_df_mice['NCBI.GeneID.Target'].map(ncbi_to_ensembl)\n", + "tf_sig_df_mice.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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" + ], + "text/plain": [ + " UniprotID.TF UniprotID.Target NCBI.GeneID.TF NCBI.GeneID.Target \\\n", + "3614494 Q61221 Q9JJG5 15251 58172 \n", + "\n", + " Name.TF Name.Target Detection.method PubmedID \\\n", + "3614494 Hif1a Sertad2 chromatin immunoprecipitation assay 27924024 \n", + "\n", + " Organism Source.database Small-scale.evidence \\\n", + "3614494 Mus musculus GTRD No \n", + "\n", + " TF.TFLink.ortho TF.nonTFLink.ortho \\\n", + "3614494 Hs:Q16665;Dr:Q6EHI4;Rn:D4A8P8 - \n", + "\n", + " Target.TFLink.ortho Target.nonTFLink.ortho Ensembl.GeneID.TF \\\n", + "3614494 Hs:Q14140;Dr:Q7ZZ27 Rn:F7F8X3 ENSMUSG00000021109 \n", + "\n", + " Ensembl.GeneID.Target \n", + "3614494 ENSMUSG00000049800 " + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tf_sig_df_mice[(tf_sig_df_mice[\"Name.TF\"] == \"Hif1a\") & (tf_sig_df_mice[\"Name.Target\"] == \"Sertad2\")]" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "Series([], Name: Name.Target, dtype: object)" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tf_sig_df_mice[tf_sig_df_mice[\"Name.TF\"] == \"Pdhx\"][\"Name.Target\"].sort_values()" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(123350, 17)" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tf_sig_df_mice.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [], + "source": [ + "# Function to add targets and TFs to each row (gene)\n", + "def add_target_and_tf_interaction(ncbi_df, tf_df, filename):\n", + " if not os.path.exists(filename):\n", + " ncbi_df[\"its_target\"] = None\n", + " print(f\"Processing targets. {ncbi_df.shape}\")\n", + " for index, row in ncbi_df.iterrows():\n", + " if index % 2000 == 0 and index > 0:\n", + " print(f\"Processed {index} rows (targets).\")\n", + " if row[\"is_tf\"]:\n", + " targets = tf_df[tf_df[\"NCBI.GeneID.TF\"] == row[\"target\"]]\n", + " if not targets.empty:\n", + " target_info_list = targets[[\"NCBI.GeneID.Target\",\n", + " \"Ensembl.GeneID.Target\",\n", + " \"Name.Target\",\n", + " \"UniprotID.Target\",\n", + " \"Target.TFLink.ortho\",\n", + " \"Target.nonTFLink.ortho\",\n", + " \"Detection.method\",\n", + " \"PubmedID\",\n", + " \"Source.database\",\n", + " \"Small-scale.evidence\",\n", + " ]].to_dict(orient=\"records\")\n", + " ncbi_df.at[index, \"its_target\"] = target_info_list\n", + " else:\n", + " ncbi_df.at[index, \"its_target\"] = []\n", + "\n", + " ncbi_df[\"its_tf\"] = None\n", + " print(\"Processing TFs...\")\n", + " for index, row in ncbi_df.iterrows():\n", + " if index % 2000 == 0 and index > 0:\n", + " print(f\"Processed {index} rows (TFs).\")\n", + " if row[\"is_target\"] and row[\"padj_dea\"] <= 0.01 and (row[\"log2FoldChange_dea\"] > 1 or row[\"log2FoldChange_dea\"] < -1):\n", + " tf = tf_df[tf_df[\"NCBI.GeneID.Target\"] == row[\"target\"]]\n", + " if not tf.empty:\n", + " tf_info_list = tf[[\"NCBI.GeneID.TF\",\n", + " \"Ensembl.GeneID.TF\",\n", + " \"Name.TF\",\n", + " \"UniprotID.TF\",\n", + " \"TF.TFLink.ortho\",\n", + " \"TF.nonTFLink.ortho\",\n", + " \"Detection.method\",\n", + " \"PubmedID\",\n", + " \"Source.database\",\n", + " \"Small-scale.evidence\",\n", + " ]].to_dict(orient=\"records\")\n", + " ncbi_df.at[index, \"its_tf\"] = tf_info_list\n", + " else:\n", + " # if row[\"padj_dea\"] <= 0.01:\n", + " # ncbi_df.at[index, \"its_tf\"] = None\n", + " # else:\n", + " ncbi_df.at[index, \"its_tf\"] = []\n", + "\n", + " ncbi_df.to_pickle(filename)\n", + "\n", + " else:\n", + " with open(filename, 'rb') as f:\n", + " ncbi_df = pickle.load(f)\n", + "\n", + " return ncbi_df\n", + "\n", + "# Add target and TF\n", + "ncbi_tf_df_mice = add_target_and_tf_interaction(ncbi_df_mice, tf_sig_df_mice, filename=\"data/mice/ncbi_tf_df_mice.pkl\")" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_deapadj_deaminus_log10_pvalue_deais_tfis_targetits_targetits_tf
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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [identifier, identifier.source, target, target.source, GENE_SYMBOL_dea, baseMean_dea, log2FoldChange_dea, lfcSE_dea, stat_dea, pvalue_dea, padj_dea, minus_log10_pvalue_dea, is_tf, is_target, its_target, its_tf]\n", + "Index: []" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_df_mice[ncbi_tf_df_mice['target']==\"1647\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{}" + ] + }, + "execution_count": 22, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_df_mice[ncbi_tf_df_mice['target']==\"1647\"][\"its_tf\"].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{}" + ] + }, + "execution_count": 23, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_df_mice[ncbi_tf_df_mice['target']==\"1647\"][\"its_tf\"].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{}" + ] + }, + "execution_count": 24, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_df_mice[ncbi_tf_df_mice['target']==\"3725\"][\"its_target\"].to_dict()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Enrichment analysis using g:Profiler\n", + "all the pathways and annotations are being added despite being significance." + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "11588" + ] + }, + "execution_count": 25, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(bridgedb_df_mice[\"identifier\"].unique())" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "846" + ] + }, + "execution_count": 26, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(bridgedb_df_mice[\n", + " (bridgedb_df_mice['padj_dea'] < 0.01) &\n", + " (\n", + " (bridgedb_df_mice['log2FoldChange_dea'] > 1) |\n", + " (bridgedb_df_mice['log2FoldChange_dea'] < -1)\n", + " )][\"identifier\"]\n", + " .unique())" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "metadata": {}, + "outputs": [], + "source": [ + "gp = GProfiler(return_dataframe=True)\n", + "filename_mice = \"data/mice/gprofiler_mice.pkl\"\n", + "if not os.path.exists(filename_mice):\n", + " gprofiler_mice = gp.profile(\n", + " organism=\"mmusculus\",\n", + " all_results=True,\n", + " query=bridgedb_df_mice[\n", + " (bridgedb_df_mice['padj_dea'] < 0.01) &\n", + " (\n", + " (bridgedb_df_mice['log2FoldChange_dea'] > 1) |\n", + " (bridgedb_df_mice['log2FoldChange_dea'] < -1)\n", + " )][\"identifier\"]\n", + " .unique()\n", + " .tolist(),\n", + " background=bridgedb_df_mice[\"identifier\"].unique().tolist(),\n", + " no_evidences=False,\n", + " significance_threshold_method=\"fdr\",\n", + " user_threshold=0.05,\n", + " )\n", + " gprofiler_mice.rename(columns={\"native\": \"id\"}, inplace=True)\n", + " gprofiler_mice[\"datasource\"] = \"g:Profiler\"\n", + " gprofiler_mice.to_pickle(filename_mice)\n", + "else:\n", + " with open(filename_mice, \"rb\") as f:\n", + " gprofiler_mice = pickle.load(f)" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "(19692, 17)\n" + ] + }, + { + "data": { + "text/html": [ + "
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sourceidnamep_valuesignificantdescriptionterm_sizequery_sizeintersection_sizeeffective_domain_sizeprecisionrecallqueryparentsintersectionsevidencesdatasource
0GO:CCGO:0005615extracellular space6.349503e-12True\"That part of a multicellular organism outside...60684699115770.1170210.163366query_1[GO:0005576, GO:0110165][ENSMUSG00000027947, ENSMUSG00000070436, ENSMU...[[ISO], [IEA], [IDA, HDA, ISO, IBA, IEA], [ISO...g:Profiler
\n", + "
" + ], + "text/plain": [ + " source id name p_value significant \\\n", + "0 GO:CC GO:0005615 extracellular space 6.349503e-12 True \n", + "\n", + " description term_size query_size \\\n", + "0 \"That part of a multicellular organism outside... 606 846 \n", + "\n", + " intersection_size effective_domain_size precision recall query \\\n", + "0 99 11577 0.117021 0.163366 query_1 \n", + "\n", + " parents \\\n", + "0 [GO:0005576, GO:0110165] \n", + "\n", + " intersections \\\n", + "0 [ENSMUSG00000027947, ENSMUSG00000070436, ENSMU... \n", + "\n", + " evidences datasource \n", + "0 [[ISO], [IEA], [IDA, HDA, ISO, IBA, IEA], [ISO... g:Profiler " + ] + }, + "execution_count": 28, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "print(gprofiler_mice.shape)\n", + "gprofiler_mice.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([list(['ENSMUSG00000022270', 'ENSMUSG00000039242', 'ENSMUSG00000035606', 'ENSMUSG00000073418', 'ENSMUSG00000051627', 'ENSMUSG00000055435', 'ENSMUSG00000096054', 'ENSMUSG00000063275', 'ENSMUSG00000026012', 'ENSMUSG00000005360', 'ENSMUSG00000001627', 'ENSMUSG00000020593', 'ENSMUSG00000043639', 'ENSMUSG00000047407', 'ENSMUSG00000018076', 'ENSMUSG00000041235', 'ENSMUSG00000016559', 'ENSMUSG00000041798', 'ENSMUSG00000022094', 'ENSMUSG00000027274', 'ENSMUSG00000028766', 'ENSMUSG00000029009', 'ENSMUSG00000026179', 'ENSMUSG00000013539', 'ENSMUSG00000007613', 'ENSMUSG00000047635', 'ENSMUSG00000025509', 'ENSMUSG00000056537', 'ENSMUSG00000006307', 'ENSMUSG00000020744', 'ENSMUSG00000028414', 'ENSMUSG00000031381', 'ENSMUSG00000005686', 'ENSMUSG00000022510', 'ENSMUSG00000034083', 'ENSMUSG00000040363', 'ENSMUSG00000041695', 'ENSMUSG00000022617', 'ENSMUSG00000042548', 'ENSMUSG00000017491', 'ENSMUSG00000029683', 'ENSMUSG00000024589', 'ENSMUSG00000033107', 'ENSMUSG00000051456', 'ENSMUSG00000048126', 'ENSMUSG00000029163', 'ENSMUSG00000038594', 'ENSMUSG00000002831', 'ENSMUSG00000070348', 'ENSMUSG00000028736', 'ENSMUSG00000020241', 'ENSMUSG00000058454', 'ENSMUSG00000033323', 'ENSMUSG00000067825', 'ENSMUSG00000004951', 'ENSMUSG00000030278', 'ENSMUSG00000021994', 'ENSMUSG00000015243', 'ENSMUSG00000025352', 'ENSMUSG00000068699', 'ENSMUSG00000092035', 'ENSMUSG00000019842', 'ENSMUSG00000032788', 'ENSMUSG00000025608', 'ENSMUSG00000009471', 'ENSMUSG00000040136', 'ENSMUSG00000054978', 'ENSMUSG00000039410', 'ENSMUSG00000025777', 'ENSMUSG00000024803', 'ENSMUSG00000040724', 'ENSMUSG00000029610', 'ENSMUSG00000034799', 'ENSMUSG00000013584', 'ENSMUSG00000022500', 'ENSMUSG00000069919', 'ENSMUSG00000024330', 'ENSMUSG00000007122', 'ENSMUSG00000000567', 'ENSMUSG00000072235', 'ENSMUSG00000040841', 'ENSMUSG00000020475', 'ENSMUSG00000069917', 'ENSMUSG00000026043', 'ENSMUSG00000001119', 'ENSMUSG00000000489', 'ENSMUSG00000029304', 'ENSMUSG00000007888', 'ENSMUSG00000035969', 'ENSMUSG00000025007', 'ENSMUSG00000001506', 'ENSMUSG00000048279', 'ENSMUSG00000031425', 'ENSMUSG00000037251', 'ENSMUSG00000026971', 'ENSMUSG00000074622', 'ENSMUSG00000033579', 'ENSMUSG00000018217'])],\n", + " dtype=object)" + ] + }, + "execution_count": 29, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "gprofiler_mice[gprofiler_mice[\"id\"] == \"HP:0011805\"][\"intersections\"].values" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "metadata": {}, + "outputs": [], + "source": [ + "gprofiler_mice = gprofiler_mice[\n", + " ~gprofiler_mice[\"parents\"].apply(lambda x: x == [])\n", + "] # rm the root terms" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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intersectionsg:Profiler_corumg:Profiler_go:bpg:Profiler_go:ccg:Profiler_go:mfg:Profiler_hpg:Profiler_keggg:Profiler_mirnag:Profiler_reacg:Profiler_tfg:Profiler_wp
0ENSMUSG00000027947NaN[{'id': 'GO:0051239', 'name': 'regulation of m...[{'id': 'GO:0005615', 'name': 'extracellular s...[{'id': 'GO:0005102', 'name': 'signaling recep...[{'id': 'HP:0030386', 'name': 'Abnormal propor...[{'id': 'KEGG:04060', 'name': 'Cytokine-cytoki...[{'id': 'MIRNA:mmu-miR-155-5p', 'name': 'mmu-m...[{'id': 'REAC:R-MMU-162582', 'name': 'Signal T...[{'id': 'TF:M04454_1', 'name': 'Factor: AR; mo...[{'id': 'WP:WP2841', 'name': 'Focal adhesion P...
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" + ], + "text/plain": [ + " intersections g:Profiler_corum \\\n", + "0 ENSMUSG00000027947 NaN \n", + "\n", + " g:Profiler_go:bp \\\n", + "0 [{'id': 'GO:0051239', 'name': 'regulation of m... \n", + "\n", + " g:Profiler_go:cc \\\n", + "0 [{'id': 'GO:0005615', 'name': 'extracellular s... \n", + "\n", + " g:Profiler_go:mf \\\n", + "0 [{'id': 'GO:0005102', 'name': 'signaling recep... \n", + "\n", + " g:Profiler_hp \\\n", + "0 [{'id': 'HP:0030386', 'name': 'Abnormal propor... \n", + "\n", + " g:Profiler_kegg \\\n", + "0 [{'id': 'KEGG:04060', 'name': 'Cytokine-cytoki... \n", + "\n", + " g:Profiler_mirna \\\n", + "0 [{'id': 'MIRNA:mmu-miR-155-5p', 'name': 'mmu-m... \n", + "\n", + " g:Profiler_reac \\\n", + "0 [{'id': 'REAC:R-MMU-162582', 'name': 'Signal T... \n", + "\n", + " g:Profiler_tf \\\n", + "0 [{'id': 'TF:M04454_1', 'name': 'Factor: AR; mo... \n", + "\n", + " g:Profiler_wp \n", + "0 [{'id': 'WP:WP2841', 'name': 'Focal adhesion P... " + ] + }, + "execution_count": 31, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# from pyBiodatafuse.constants import GPROFILER\n", + "\n", + "\n", + "def create_path_info(row):\n", + " path_info = {\n", + " col: row[col] for col in gprofiler_mice.columns if col not in [\"intersections\", \"source\"]\n", + " }\n", + " return path_info\n", + "\n", + "\n", + "gprofiler_mice[\"gprofiler\"] = gprofiler_mice.apply(create_path_info, axis=1)\n", + "gprofiler_mice = gprofiler_mice.drop(\n", + " columns=[\n", + " col\n", + " for col in gprofiler_mice.columns\n", + " if col not in [\"source\", \"id\", \"intersections\", \"gprofiler\"]\n", + " ]\n", + ")\n", + "gprofiler_mice = gprofiler_mice.explode(\"intersections\").reset_index(drop=True)\n", + "unique_sources = sorted(gprofiler_mice[\"source\"].unique())\n", + "gprofiler_mice_final = pd.DataFrame()\n", + "gprofiler_mice_final[\"intersections\"] = gprofiler_mice[\"intersections\"].unique()\n", + "for source in unique_sources:\n", + " source_subset = gprofiler_mice[gprofiler_mice[\"source\"] == source]\n", + " source_dictionaries = source_subset.groupby(\"intersections\")[\"gprofiler\"].apply(list).to_dict()\n", + " gprofiler_mice_final[f\"{GPROFILER}_{str.lower(source)}\"] = gprofiler_mice_final[\n", + " \"intersections\"\n", + " ].map(source_dictionaries)\n", + "gprofiler_mice_final.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{'biomart': 'Ensembl',\n", + " 'biomart_version': '111',\n", + " 'display_name': 'Mouse',\n", + " 'genebuild': 'GRCm39',\n", + " 'gprofiler_version': 'e111_eg58_p18_f463989d',\n", + " 'organism': 'mmusculus',\n", + " 'sources': {'CORUM': {'name': 'CORUM protein complexes',\n", + " 'version': '28.11.2022 Corum 4.1'},\n", + " 'GO:BP': {'name': 'biological process',\n", + " 'version': 'annotations: BioMart\\nclasses: releases/2024-01-17'},\n", + " 'GO:CC': {'name': 'cellular component',\n", + " 'version': 'annotations: BioMart\\nclasses: releases/2024-01-17'},\n", + " 'GO:MF': {'name': 'molecular function',\n", + " 'version': 'annotations: BioMart\\nclasses: releases/2024-01-17'},\n", + " 'HP': {'name': 'Human Phenotype Ontology',\n", + " 'version': 'annotations: 01.2024\\nclasses: None'},\n", + " 'KEGG': {'name': 'Kyoto Encyclopedia of Genes and Genomes',\n", + " 'version': 'KEGG FTP Release 2024-01-22'},\n", + " 'MIRNA': {'name': 'miRTarBase', 'version': 'Release 9.0'},\n", + " 'REAC': {'name': 'Reactome',\n", + " 'version': 'annotations: BioMart\\nclasses: 2024-1-25'},\n", + " 'TF': {'name': 'Transfac',\n", + " 'version': 'annotations: TRANSFAC Release 2023.2\\nclasses: v2'},\n", + " 'WP': {'name': 'WikiPathways', 'version': '20240101'}},\n", + " 'taxonomy_id': '10090'}" + ] + }, + "execution_count": 32, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "## get version\n", + "\n", + "\n", + "def get_data_versions(organism):\n", + " url = \"https://biit.cs.ut.ee/gprofiler/api/util/data_versions\"\n", + " params = {\"organism\": organism}\n", + " try:\n", + " response = requests.get(url, params=params)\n", + "\n", + " if response.status_code == 200:\n", + " data = response.json()\n", + " return data\n", + " else:\n", + " raise Exception(f\"Failed to retrieve data: {response.status_code}\")\n", + " except Exception as e:\n", + " return {\"error\": str(e)}\n", + "\n", + "\n", + "get_data_versions(\"mmusculus\")" + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "metadata": {}, + "outputs": [], + "source": [ + "ncbi_tf_gprofiler_df_mice = pd.merge(\n", + " ncbi_tf_df_mice,\n", + " gprofiler_mice_final,\n", + " left_on=\"identifier\",\n", + " right_on=\"intersections\",\n", + " how=\"outer\",\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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0ENSMUSG00000021903Ensembl78754NCBI GeneGalnt152770.4375082.5211820.09994125.2266012.046157e-140...NaN[{'id': 'GO:0006493', 'name': 'protein O-linke...[{'id': 'GO:0030133', 'name': 'transport vesic...[{'id': 'GO:0030246', 'name': 'carbohydrate bi...NaN[{'id': 'KEGG:01100', 'name': 'Metabolic pathw...[{'id': 'MIRNA:mmu-miR-34b-5p', 'name': 'mmu-m...[{'id': 'REAC:R-MMU-5173105', 'name': 'O-linke...[{'id': 'TF:M04454_1', 'name': 'Factor: AR; mo...NaN
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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "0 ENSMUSG00000021903 Ensembl 78754 NCBI Gene Galnt15 \n", + "1 ENSMUSG00000059824 Ensembl 13170 NCBI Gene Dbp \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea ... \\\n", + "0 2770.437508 2.521182 0.099941 25.226601 2.046157e-140 ... \n", + "1 2816.783019 -2.985239 0.191760 -15.567614 1.208303e-54 ... \n", + "\n", + " g:Profiler_corum g:Profiler_go:bp \\\n", + "0 NaN [{'id': 'GO:0006493', 'name': 'protein O-linke... \n", + "1 NaN [{'id': 'GO:0048518', 'name': 'positive regula... \n", + "\n", + " g:Profiler_go:cc \\\n", + "0 [{'id': 'GO:0030133', 'name': 'transport vesic... \n", + "1 [{'id': 'GO:0005667', 'name': 'transcription r... \n", + "\n", + " g:Profiler_go:mf g:Profiler_hp \\\n", + "0 [{'id': 'GO:0030246', 'name': 'carbohydrate bi... NaN \n", + "1 [{'id': 'GO:0000981', 'name': 'DNA-binding tra... NaN \n", + "\n", + " g:Profiler_kegg \\\n", + "0 [{'id': 'KEGG:01100', 'name': 'Metabolic pathw... \n", + "1 [{'id': 'KEGG:04710', 'name': 'Circadian rhyth... \n", + "\n", + " g:Profiler_mirna \\\n", + "0 [{'id': 'MIRNA:mmu-miR-34b-5p', 'name': 'mmu-m... \n", + "1 [{'id': 'MIRNA:mmu-miR-122-5p', 'name': 'mmu-m... \n", + "\n", + " g:Profiler_reac \\\n", + "0 [{'id': 'REAC:R-MMU-5173105', 'name': 'O-linke... \n", + "1 NaN \n", + "\n", + " g:Profiler_tf g:Profiler_wp \n", + "0 [{'id': 'TF:M04454_1', 'name': 'Factor: AR; mo... NaN \n", + "1 [{'id': 'TF:M03882', 'name': 'Factor: RelB:p50... NaN \n", + "\n", + "[2 rows x 27 columns]" + ] + }, + "execution_count": 34, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_gprofiler_df_mice.head(2)" + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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MouseGeneIDHumanOrthologGeneIDSymbolSynonymsDescriptionMitoCarta3.0_ListMitoCarta3.0_EvidenceMitoCarta3.0_SubMitoLocalizationMitoCarta3.0_MitoPathwaysTrainingDataset...liver_total_peak_intensity_log10heart_total_peak_intensity_log10skeletalmuscle_total_peak_intensity_log10adipose_total_peak_intensity_log10smallintestine_total_peak_intensity_log10largeintestine_total_peak_intensity_log10stomach_total_peak_intensity_log10placenta_total_peak_intensity_log10testis_total_peak_intensity_log10HPA_Main_Location_2020 (Reliability)
0664451537.0Cyc12610002H19Rik|AA408921|Cyct1cytochrome c-1MitoCarta3.0literature, APEX_IMS, APEX_matrix, targetP sig...MIMOXPHOS > Complex III > CIII subunits | Metabol...Tmito...10.010.49.810.110.210.210.010.09.8Mitochondria (Supported)
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" + ], + "text/plain": [ + " MouseGeneID HumanOrthologGeneID Symbol Synonyms \\\n", + "0 66445 1537.0 Cyc1 2610002H19Rik|AA408921|Cyct1 \n", + "\n", + " Description MitoCarta3.0_List \\\n", + "0 cytochrome c-1 MitoCarta3.0 \n", + "\n", + " MitoCarta3.0_Evidence \\\n", + "0 literature, APEX_IMS, APEX_matrix, targetP sig... \n", + "\n", + " MitoCarta3.0_SubMitoLocalization \\\n", + "0 MIM \n", + "\n", + " MitoCarta3.0_MitoPathways TrainingDataset ... \\\n", + "0 OXPHOS > Complex III > CIII subunits | Metabol... Tmito ... \n", + "\n", + " liver_total_peak_intensity_log10 heart_total_peak_intensity_log10 \\\n", + "0 10.0 10.4 \n", + "\n", + " skeletalmuscle_total_peak_intensity_log10 \\\n", + "0 9.8 \n", + "\n", + " adipose_total_peak_intensity_log10 \\\n", + "0 10.1 \n", + "\n", + " smallintestine_total_peak_intensity_log10 \\\n", + "0 10.2 \n", + "\n", + " largeintestine_total_peak_intensity_log10 \\\n", + "0 10.2 \n", + "\n", + " stomach_total_peak_intensity_log10 placenta_total_peak_intensity_log10 \\\n", + "0 10.0 10.0 \n", + "\n", + " testis_total_peak_intensity_log10 HPA_Main_Location_2020 (Reliability) \n", + "0 9.8 Mitochondria (Supported) \n", + "\n", + "[1 rows x 48 columns]" + ] + }, + "execution_count": 37, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# URLs for the mice MitoCarta Dataset\n", + "mitocarta_url_mice = (\n", + " \"https://personal.broadinstitute.org/scalvo/MitoCarta3.0/Mouse.MitoCarta3.0.xls\"\n", + ")\n", + "\n", + "\n", + "# Function to download and read a gzipped file into a dataframe\n", + "def download_save_and_read(url, filename):\n", + " if not os.path.exists(filename):\n", + " response = requests.get(url)\n", + " with open(filename, \"wb\") as file:\n", + " file.write(response.content)\n", + " else:\n", + " print(f\"{filename} already exists, skipping download.\")\n", + "\n", + " # Load the second sheet (\"A Mouse MitoCarta3.0\") into a DataFrame\n", + " df = pd.read_excel(url, sheet_name=\"A Mouse MitoCarta3.0\")\n", + " return df\n", + "\n", + "\n", + "# Download and read the mice MitoCarta dataset\n", + "mitocarta_mice_df = download_save_and_read(mitocarta_url_mice, \"data/mice/mice_mitocarta3.0.xls\")\n", + "\n", + "mitocarta_mice_df.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 38, + "metadata": {}, + "outputs": [], + "source": [ + "# Select relevant columns for inclusion in the graph\n", + "selected_columns_mice = [\n", + " \"EnsemblGeneID\",\n", + " \"Description\",\n", + " \"MitoCarta3.0_Evidence\",\n", + " \"MitoCarta3.0_SubMitoLocalization\",\n", + " \"MitoCarta3.0_MitoPathways\",\n", + " \"HPA_Main_Location_2020 (Reliability)\",\n", + " \"Tissues\",\n", + "]\n", + "\n", + "mitocarta_mice_selected = mitocarta_mice_df[selected_columns_mice]\n", + "\n", + "# Rename columns for clarity\n", + "mitocarta_mice_selected.rename(\n", + " columns={\n", + " \"EnsemblGeneID\": \"ensembl_id\",\n", + " \"Description\": \"gene_description\",\n", + " \"MitoCarta3.0_Evidence\": \"evidence\",\n", + " \"MitoCarta3.0_SubMitoLocalization\": \"sub_mito_localization\",\n", + " \"MitoCarta3.0_MitoPathways\": \"mito_pathways\",\n", + " \"HPA_Main_Location_2020 (Reliability)\": \"hpa_location\",\n", + " \"Tissues\": \"tissue_expression\",\n", + " },\n", + " inplace=True,\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 39, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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ensembl_idgene_descriptionevidencesub_mito_localizationmito_pathwayshpa_locationtissue_expression
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ensembl_idMitoCarta
0ENSMUSG00000022551[{'gene_description': 'cytochrome c-1', 'evide...
1ENSMUSG00000031299[{'gene_description': 'pyruvate dehydrogenase ...
2ENSMUSG00000003072[{'gene_description': 'ATP synthase, H+ transp...
3ENSMUSG00000021241[{'gene_description': 'iron-sulfur cluster ass...
4ENSMUSG00000021748[{'gene_description': 'pyruvate dehydrogenase ...
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" + ], + "text/plain": [ + " ensembl_id MitoCarta\n", + "0 ENSMUSG00000022551 [{'gene_description': 'cytochrome c-1', 'evide...\n", + "1 ENSMUSG00000031299 [{'gene_description': 'pyruvate dehydrogenase ...\n", + "2 ENSMUSG00000003072 [{'gene_description': 'ATP synthase, H+ transp...\n", + "3 ENSMUSG00000021241 [{'gene_description': 'iron-sulfur cluster ass...\n", + "4 ENSMUSG00000021748 [{'gene_description': 'pyruvate dehydrogenase ..." + ] + }, + "execution_count": 40, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from pyBiodatafuse.constants import MITOCARTA\n", + "\n", + "df_melted = mitocarta_mice_selected.apply(\n", + " lambda row: [row[\"ensembl_id\"], [row.drop(\"ensembl_id\").to_dict()]], axis=1\n", + ")\n", + "df_transformed = pd.DataFrame(df_melted.tolist(), columns=[\"ensembl_id\", MITOCARTA])\n", + "df_transformed.head()" + ] + }, + { + "cell_type": "code", + "execution_count": 41, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_dea...g:Profiler_go:bpg:Profiler_go:ccg:Profiler_go:mfg:Profiler_hpg:Profiler_keggg:Profiler_mirnag:Profiler_reacg:Profiler_tfg:Profiler_wpMitoCarta
0ENSMUSG00000021903Ensembl78754NCBI GeneGalnt152770.4375082.5211820.09994125.2266012.046157e-140...[{'id': 'GO:0006493', 'name': 'protein O-linke...[{'id': 'GO:0030133', 'name': 'transport vesic...[{'id': 'GO:0030246', 'name': 'carbohydrate bi...NaN[{'id': 'KEGG:01100', 'name': 'Metabolic pathw...[{'id': 'MIRNA:mmu-miR-34b-5p', 'name': 'mmu-m...[{'id': 'REAC:R-MMU-5173105', 'name': 'O-linke...[{'id': 'TF:M04454_1', 'name': 'Factor: AR; mo...NaNNaN
1ENSMUSG00000059824Ensembl13170NCBI GeneDbp2816.783019-2.9852390.191760-15.5676141.208303e-54...[{'id': 'GO:0048518', 'name': 'positive regula...[{'id': 'GO:0005667', 'name': 'transcription r...[{'id': 'GO:0000981', 'name': 'DNA-binding tra...NaN[{'id': 'KEGG:04710', 'name': 'Circadian rhyth...[{'id': 'MIRNA:mmu-miR-122-5p', 'name': 'mmu-m...NaN[{'id': 'TF:M03882', 'name': 'Factor: RelB:p50...NaNNaN
2ENSMUSG00000041417Ensembl18708NCBI GenePik3r12934.3272642.0474830.13677614.9696291.159658e-50...[{'id': 'GO:0051239', 'name': 'regulation of m...[{'id': 'GO:0005942', 'name': 'phosphatidylino...[{'id': 'GO:0005102', 'name': 'signaling recep...[{'id': 'HP:0025539', 'name': 'Abnormal B cell...[{'id': 'KEGG:04933', 'name': 'AGE-RAGE signal...[{'id': 'MIRNA:mmu-miR-340-5p', 'name': 'mmu-m...[{'id': 'REAC:R-MMU-6806834', 'name': 'Signali...[{'id': 'TF:M00446_1', 'name': 'Factor: Spz1; ...[{'id': 'WP:WP2841', 'name': 'Focal adhesion P...NaN
3ENSMUSG00000004939Ensembl69564NCBI GeneNmrk2675.068734-3.9814740.274358-14.5119781.017437e-47...[{'id': 'GO:0048869', 'name': 'cellular develo...[{'id': 'GO:0071944', 'name': 'cell periphery'...[{'id': 'GO:0005515', 'name': 'protein binding...NaN[{'id': 'KEGG:00760', 'name': 'Nicotinate and ...[{'id': 'MIRNA:mmu-miR-709', 'name': 'mmu-miR-...[{'id': 'REAC:R-MMU-196854', 'name': 'Metaboli...[{'id': 'TF:M00446_1', 'name': 'Factor: Spz1; ...NaNNaN
4ENSMUSG00000028834Ensembl433766NCBI GeneTrim6344995.1044133.7382750.26128914.3070481.977304e-46...[{'id': 'GO:0051239', 'name': 'regulation of m...[{'id': 'GO:0043292', 'name': 'contractile fib...[{'id': 'GO:0005515', 'name': 'protein binding...NaNNaNNaNNaN[{'id': 'TF:M10174_1', 'name': 'Factor: AR; mo...[{'id': 'WP:WP5024', 'name': 'Hypoxia dependen...NaN
..................................................................
62ENSMUSG00000044938Ensembl244923NCBI GeneKlhl3114539.906824-1.1540390.120236-9.5981468.139554e-22...[{'id': 'GO:0050896', 'name': 'response to sti...[{'id': 'GO:0005737', 'name': 'cytoplasm', 'p_...[{'id': 'GO:0005515', 'name': 'protein binding...NaNNaN[{'id': 'MIRNA:mmu-miR-1897-5p', 'name': 'mmu-...NaN[{'id': 'TF:M00407', 'name': 'Factor: RSRFC4; ...NaNNaN
63ENSMUSG00000025612Ensembl12013NCBI GeneBach12266.8289851.6338570.1709249.5589771.189265e-21...[{'id': 'GO:0050896', 'name': 'response to sti...[{'id': 'GO:0005667', 'name': 'transcription r...[{'id': 'GO:0005515', 'name': 'protein binding...NaNNaN[{'id': 'MIRNA:mmu-miR-122-5p', 'name': 'mmu-m...[{'id': 'REAC:R-MMU-9707616', 'name': 'Heme si...[{'id': 'TF:M07094', 'name': 'Factor: FOXO1A; ...NaNNaN
64ENSMUSG00000027496Ensembl20878NCBI GeneAurka311.745006-1.8965450.198482-9.5552401.232977e-21...[{'id': 'GO:0050896', 'name': 'response to sti...[{'id': 'GO:0071944', 'name': 'cell periphery'...[{'id': 'GO:0140677', 'name': 'molecular funct...[{'id': 'HP:0001442', 'name': 'Typified by som...[{'id': 'KEGG:04114', 'name': 'Oocyte meiosis'...NaN[{'id': 'REAC:R-MMU-6804114', 'name': 'TP53 Re...[{'id': 'TF:M08998_1', 'name': 'Factor: GR; mo...NaNNaN
65ENSMUSG00000075327Ensembl381990NCBI GeneZbtb2454.4381411.7306600.1822929.4939142.225187e-21...[{'id': 'GO:0051239', 'name': 'regulation of m...[{'id': 'GO:0005622', 'name': 'intracellular a...[{'id': 'GO:0005515', 'name': 'protein binding...NaNNaN[{'id': 'MIRNA:mmu-miR-431-5p', 'name': 'mmu-m...NaN[{'id': 'TF:M10351', 'name': 'Factor: PTF1; mo...NaNNaN
66ENSMUSG00000046668Ensembl67393NCBI GeneCxxc5501.155326-1.6594950.174947-9.4857302.406926e-21...[{'id': 'GO:0048519', 'name': 'negative regula...[{'id': 'GO:0005737', 'name': 'cytoplasm', 'p_...[{'id': 'GO:0005515', 'name': 'protein binding...NaNNaN[{'id': 'MIRNA:mmu-miR-410-3p', 'name': 'mmu-m...NaN[{'id': 'TF:M00446_1', 'name': 'Factor: Spz1; ...NaNNaN
\n", + "

67 rows × 28 columns

\n", + "
" + ], + "text/plain": [ + " identifier identifier.source target target.source \\\n", + "0 ENSMUSG00000021903 Ensembl 78754 NCBI Gene \n", + "1 ENSMUSG00000059824 Ensembl 13170 NCBI Gene \n", + "2 ENSMUSG00000041417 Ensembl 18708 NCBI Gene \n", + "3 ENSMUSG00000004939 Ensembl 69564 NCBI Gene \n", + "4 ENSMUSG00000028834 Ensembl 433766 NCBI Gene \n", + ".. ... ... ... ... \n", + "62 ENSMUSG00000044938 Ensembl 244923 NCBI Gene \n", + "63 ENSMUSG00000025612 Ensembl 12013 NCBI Gene \n", + "64 ENSMUSG00000027496 Ensembl 20878 NCBI Gene \n", + "65 ENSMUSG00000075327 Ensembl 381990 NCBI Gene \n", + "66 ENSMUSG00000046668 Ensembl 67393 NCBI Gene \n", + "\n", + " GENE_SYMBOL_dea baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea \\\n", + "0 Galnt15 2770.437508 2.521182 0.099941 25.226601 \n", + "1 Dbp 2816.783019 -2.985239 0.191760 -15.567614 \n", + "2 Pik3r1 2934.327264 2.047483 0.136776 14.969629 \n", + "3 Nmrk2 675.068734 -3.981474 0.274358 -14.511978 \n", + "4 Trim63 44995.104413 3.738275 0.261289 14.307048 \n", + ".. ... ... ... ... ... \n", + "62 Klhl31 14539.906824 -1.154039 0.120236 -9.598146 \n", + "63 Bach1 2266.828985 1.633857 0.170924 9.558977 \n", + "64 Aurka 311.745006 -1.896545 0.198482 -9.555240 \n", + "65 Zbtb2 454.438141 1.730660 0.182292 9.493914 \n", + "66 Cxxc5 501.155326 -1.659495 0.174947 -9.485730 \n", + "\n", + " pvalue_dea ... g:Profiler_go:bp \\\n", + "0 2.046157e-140 ... [{'id': 'GO:0006493', 'name': 'protein O-linke... \n", + "1 1.208303e-54 ... [{'id': 'GO:0048518', 'name': 'positive regula... \n", + "2 1.159658e-50 ... [{'id': 'GO:0051239', 'name': 'regulation of m... \n", + "3 1.017437e-47 ... [{'id': 'GO:0048869', 'name': 'cellular develo... \n", + "4 1.977304e-46 ... [{'id': 'GO:0051239', 'name': 'regulation of m... \n", + ".. ... ... ... \n", + "62 8.139554e-22 ... [{'id': 'GO:0050896', 'name': 'response to sti... \n", + "63 1.189265e-21 ... [{'id': 'GO:0050896', 'name': 'response to sti... \n", + "64 1.232977e-21 ... [{'id': 'GO:0050896', 'name': 'response to sti... \n", + "65 2.225187e-21 ... [{'id': 'GO:0051239', 'name': 'regulation of m... \n", + "66 2.406926e-21 ... [{'id': 'GO:0048519', 'name': 'negative regula... \n", + "\n", + " g:Profiler_go:cc \\\n", + "0 [{'id': 'GO:0030133', 'name': 'transport vesic... \n", + "1 [{'id': 'GO:0005667', 'name': 'transcription r... \n", + "2 [{'id': 'GO:0005942', 'name': 'phosphatidylino... \n", + "3 [{'id': 'GO:0071944', 'name': 'cell periphery'... \n", + "4 [{'id': 'GO:0043292', 'name': 'contractile fib... \n", + ".. ... \n", + "62 [{'id': 'GO:0005737', 'name': 'cytoplasm', 'p_... \n", + "63 [{'id': 'GO:0005667', 'name': 'transcription r... \n", + "64 [{'id': 'GO:0071944', 'name': 'cell periphery'... \n", + "65 [{'id': 'GO:0005622', 'name': 'intracellular a... \n", + "66 [{'id': 'GO:0005737', 'name': 'cytoplasm', 'p_... \n", + "\n", + " g:Profiler_go:mf \\\n", + "0 [{'id': 'GO:0030246', 'name': 'carbohydrate bi... \n", + "1 [{'id': 'GO:0000981', 'name': 'DNA-binding tra... \n", + "2 [{'id': 'GO:0005102', 'name': 'signaling recep... \n", + "3 [{'id': 'GO:0005515', 'name': 'protein binding... \n", + "4 [{'id': 'GO:0005515', 'name': 'protein binding... \n", + ".. ... \n", + "62 [{'id': 'GO:0005515', 'name': 'protein binding... \n", + "63 [{'id': 'GO:0005515', 'name': 'protein binding... \n", + "64 [{'id': 'GO:0140677', 'name': 'molecular funct... \n", + "65 [{'id': 'GO:0005515', 'name': 'protein binding... \n", + "66 [{'id': 'GO:0005515', 'name': 'protein binding... \n", + "\n", + " g:Profiler_hp \\\n", + "0 NaN \n", + "1 NaN \n", + "2 [{'id': 'HP:0025539', 'name': 'Abnormal B cell... \n", + "3 NaN \n", + "4 NaN \n", + ".. ... \n", + "62 NaN \n", + "63 NaN \n", + "64 [{'id': 'HP:0001442', 'name': 'Typified by som... \n", + "65 NaN \n", + "66 NaN \n", + "\n", + " g:Profiler_kegg \\\n", + "0 [{'id': 'KEGG:01100', 'name': 'Metabolic pathw... \n", + "1 [{'id': 'KEGG:04710', 'name': 'Circadian rhyth... \n", + "2 [{'id': 'KEGG:04933', 'name': 'AGE-RAGE signal... \n", + "3 [{'id': 'KEGG:00760', 'name': 'Nicotinate and ... \n", + "4 NaN \n", + ".. ... \n", + "62 NaN \n", + "63 NaN \n", + "64 [{'id': 'KEGG:04114', 'name': 'Oocyte meiosis'... \n", + "65 NaN \n", + "66 NaN \n", + "\n", + " g:Profiler_mirna \\\n", + "0 [{'id': 'MIRNA:mmu-miR-34b-5p', 'name': 'mmu-m... \n", + "1 [{'id': 'MIRNA:mmu-miR-122-5p', 'name': 'mmu-m... \n", + "2 [{'id': 'MIRNA:mmu-miR-340-5p', 'name': 'mmu-m... \n", + "3 [{'id': 'MIRNA:mmu-miR-709', 'name': 'mmu-miR-... \n", + "4 NaN \n", + ".. ... \n", + "62 [{'id': 'MIRNA:mmu-miR-1897-5p', 'name': 'mmu-... \n", + "63 [{'id': 'MIRNA:mmu-miR-122-5p', 'name': 'mmu-m... \n", + "64 NaN \n", + "65 [{'id': 'MIRNA:mmu-miR-431-5p', 'name': 'mmu-m... \n", + "66 [{'id': 'MIRNA:mmu-miR-410-3p', 'name': 'mmu-m... \n", + "\n", + " g:Profiler_reac \\\n", + "0 [{'id': 'REAC:R-MMU-5173105', 'name': 'O-linke... \n", + "1 NaN \n", + "2 [{'id': 'REAC:R-MMU-6806834', 'name': 'Signali... \n", + "3 [{'id': 'REAC:R-MMU-196854', 'name': 'Metaboli... \n", + "4 NaN \n", + ".. ... \n", + "62 NaN \n", + "63 [{'id': 'REAC:R-MMU-9707616', 'name': 'Heme si... \n", + "64 [{'id': 'REAC:R-MMU-6804114', 'name': 'TP53 Re... \n", + "65 NaN \n", + "66 NaN \n", + "\n", + " g:Profiler_tf \\\n", + "0 [{'id': 'TF:M04454_1', 'name': 'Factor: AR; mo... \n", + "1 [{'id': 'TF:M03882', 'name': 'Factor: RelB:p50... \n", + "2 [{'id': 'TF:M00446_1', 'name': 'Factor: Spz1; ... \n", + "3 [{'id': 'TF:M00446_1', 'name': 'Factor: Spz1; ... \n", + "4 [{'id': 'TF:M10174_1', 'name': 'Factor: AR; mo... \n", + ".. ... \n", + "62 [{'id': 'TF:M00407', 'name': 'Factor: RSRFC4; ... \n", + "63 [{'id': 'TF:M07094', 'name': 'Factor: FOXO1A; ... \n", + "64 [{'id': 'TF:M08998_1', 'name': 'Factor: GR; mo... \n", + "65 [{'id': 'TF:M10351', 'name': 'Factor: PTF1; mo... \n", + "66 [{'id': 'TF:M00446_1', 'name': 'Factor: Spz1; ... \n", + "\n", + " g:Profiler_wp MitoCarta \n", + "0 NaN NaN \n", + "1 NaN NaN \n", + "2 [{'id': 'WP:WP2841', 'name': 'Focal adhesion P... NaN \n", + "3 NaN NaN \n", + "4 [{'id': 'WP:WP5024', 'name': 'Hypoxia dependen... NaN \n", + ".. ... ... \n", + "62 NaN NaN \n", + "63 NaN NaN \n", + "64 NaN NaN \n", + "65 NaN NaN \n", + "66 NaN NaN \n", + "\n", + "[67 rows x 28 columns]" + ] + }, + "execution_count": 41, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Merge mice MitoCarta with the graph dataset\n", + "ncbi_tf_gprofiler_mitocarta_df_mice = pd.merge(\n", + " ncbi_tf_gprofiler_df_mice,\n", + " df_transformed,\n", + " left_on=\"identifier\",\n", + " right_on=\"ensembl_id\",\n", + " how=\"left\",\n", + ").drop(columns=[\"ensembl_id\"])\n", + "\n", + "ncbi_tf_gprofiler_mitocarta_df_mice.head(67)" + ] + }, + { + "cell_type": "code", + "execution_count": 42, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[{'gene_description': 'lactate dehydrogenase A-like 6B',\n", + " 'evidence': 'targetP signal, Rickettsial homolog, mito protein domain, MS/MS',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Carbohydrate metabolism',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'cerebrum, cerebellum, brainstem, spinalcord, kidney, liver, adipose, smallintestine, largeintestine, stomach, placenta, testis'}]" + ] + }, + "execution_count": 42, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_gprofiler_mitocarta_df_mice[MITOCARTA][11242]" + ] + }, + { + "cell_type": "code", + "execution_count": 43, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_dea...g:Profiler_go:bpg:Profiler_go:ccg:Profiler_go:mfg:Profiler_hpg:Profiler_keggg:Profiler_mirnag:Profiler_reacg:Profiler_tfg:Profiler_wpMitoCarta
0ENSMUSG00000021903Ensembl78754ncbi_gene_idGalnt152770.4375082.5211820.09994125.2266012.046157e-140...[{'id': 'GO:0006493', 'name': 'protein O-linke...[{'id': 'GO:0030133', 'name': 'transport vesic...[{'id': 'GO:0030246', 'name': 'carbohydrate bi...NaN[{'id': 'KEGG:01100', 'name': 'Metabolic pathw...[{'id': 'MIRNA:mmu-miR-34b-5p', 'name': 'mmu-m...[{'id': 'REAC:R-MMU-5173105', 'name': 'O-linke...[{'id': 'TF:M04454_1', 'name': 'Factor: AR; mo...NaNNaN
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1 rows × 28 columns

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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "0 ENSMUSG00000021903 Ensembl 78754 ncbi_gene_id Galnt15 \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea ... \\\n", + "0 2770.437508 2.521182 0.099941 25.226601 2.046157e-140 ... \n", + "\n", + " g:Profiler_go:bp \\\n", + "0 [{'id': 'GO:0006493', 'name': 'protein O-linke... \n", + "\n", + " g:Profiler_go:cc \\\n", + "0 [{'id': 'GO:0030133', 'name': 'transport vesic... \n", + "\n", + " g:Profiler_go:mf g:Profiler_hp \\\n", + "0 [{'id': 'GO:0030246', 'name': 'carbohydrate bi... NaN \n", + "\n", + " g:Profiler_kegg \\\n", + "0 [{'id': 'KEGG:01100', 'name': 'Metabolic pathw... \n", + "\n", + " g:Profiler_mirna \\\n", + "0 [{'id': 'MIRNA:mmu-miR-34b-5p', 'name': 'mmu-m... \n", + "\n", + " g:Profiler_reac \\\n", + "0 [{'id': 'REAC:R-MMU-5173105', 'name': 'O-linke... \n", + "\n", + " g:Profiler_tf g:Profiler_wp MitoCarta \n", + "0 [{'id': 'TF:M04454_1', 'name': 'Factor: AR; mo... NaN NaN \n", + "\n", + "[1 rows x 28 columns]" + ] + }, + "execution_count": 43, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_gprofiler_mitocarta_df_mice[\"target.source\"] = ncbi_tf_gprofiler_mitocarta_df_mice[\n", + " \"target.source\"\n", + "].str.replace(\"NCBI Gene\", \"ncbi_gene_id\", regex=False)\n", + "\n", + "ncbi_tf_gprofiler_mitocarta_df_mice.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{0: nan,\n", + " 1: nan,\n", + " 2: nan,\n", + " 3: nan,\n", + " 4: nan,\n", + " 5: nan,\n", + " 6: nan,\n", + " 7: nan,\n", + " 8: nan,\n", + " 9: nan,\n", + " 10: nan,\n", + " 11: nan,\n", + " 12: nan,\n", + " 13: nan,\n", + " 14: nan,\n", + " 15: nan,\n", + " 16: nan,\n", + " 17: nan,\n", + " 18: nan,\n", + " 19: nan,\n", + " 20: nan,\n", + " 21: nan,\n", + " 22: nan,\n", + " 23: nan,\n", + " 24: nan,\n", + " 25: nan,\n", + " 26: nan,\n", + " 27: nan,\n", 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" 98: [{'gene_description': 'acyl-CoA synthetase long-chain family member 6',\n", + " 'evidence': 'yeast mito homolog, Rickettsial homolog, mito protein domain, MS/MS++',\n", + " 'sub_mito_localization': 'MOM',\n", + " 'mito_pathways': 'Fatty acid oxidation',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'cerebrum, cerebellum, brainstem, spinalcord, liver, heart, skeletalmuscle, adipose, largeintestine, stomach, testis'}],\n", + " 99: nan,\n", + " 100: nan,\n", + " 101: nan,\n", + " 102: nan,\n", + " 103: nan,\n", + " 104: nan,\n", + " 105: nan,\n", + " 106: nan,\n", + " 107: nan,\n", + " 108: nan,\n", + " 109: nan,\n", + " 110: nan,\n", + " 111: nan,\n", + " 112: nan,\n", + " 113: nan,\n", + " 114: nan,\n", + " 115: nan,\n", + " 116: nan,\n", + " 117: nan,\n", + " 118: nan,\n", + " 119: nan,\n", + " 120: nan,\n", + " 121: nan,\n", + " 122: nan,\n", + " 123: [{'gene_description': 'solute carrier family 25, member 39',\n", + " 'evidence': 'literature, yeast mito homolog+, 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376: nan,\n", + " 377: nan,\n", + " 378: nan,\n", + " 379: nan,\n", + " 380: [{'gene_description': 'optic atrophy 3',\n", + " 'evidence': 'literature, targetP signal, coexpression, MS/MS++',\n", + " 'sub_mito_localization': 'MOM',\n", + " 'mito_pathways': nan,\n", + " 'hpa_location': 'Cytosol (Approved)',\n", + " 'tissue_expression': 'all 14'}],\n", + " 381: nan,\n", + " 382: nan,\n", + " 383: [{'gene_description': 'acyl-CoA synthetase short-chain family member 1',\n", + " 'evidence': 'literature, APEX_matrix, targetP signal, mito protein domain, MS/MS++',\n", + " 'sub_mito_localization': 'MIM',\n", + " 'mito_pathways': 'Fatty acid oxidation',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'cerebrum, cerebellum, brainstem, spinalcord, kidney, heart, skeletalmuscle, adipose, smallintestine, largeintestine, stomach, placenta, testis'}],\n", + " 384: [{'gene_description': 'uncoupling protein 2 (mitochondrial, proton carrier)',\n", + " 'evidence': 'literature, yeast mito 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nan,\n", + " 556: nan,\n", + " 557: nan,\n", + " 558: nan,\n", + " 559: nan,\n", + " 560: nan,\n", + " 561: nan,\n", + " 562: [{'gene_description': 'cytochrome C oxidase assembly factor 3',\n", + " 'evidence': 'APEX_IMS, APEX_matrix, mito protein domain+, coexpression, MS/MS++',\n", + " 'sub_mito_localization': 'MIM',\n", + " 'mito_pathways': 'OXPHOS assembly factors',\n", + " 'hpa_location': 'Mitochondria (Supported)',\n", + " 'tissue_expression': 'all 14'}],\n", + " 563: nan,\n", + " 564: nan,\n", + " 565: [{'gene_description': 'mitochondrial ribosomal protein L34',\n", + " 'evidence': 'literature, APEX_matrix, targetP signal+, yeast mito homolog++, Rickettsial homolog, mito protein domain, induction, coexpression++, MS/MS',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Mitochondrial ribosome',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'cerebrum, cerebellum, brainstem, spinalcord, kidney, liver, heart, adipose, smallintestine, largeintestine, stomach, placenta, testis'}],\n", + " 566: nan,\n", + " 567: nan,\n", + " 568: nan,\n", + " 569: nan,\n", + " 570: nan,\n", + " 571: nan,\n", + " 572: nan,\n", + " 573: nan,\n", + " 574: nan,\n", + " 575: nan,\n", + " 576: nan,\n", + " 577: nan,\n", + " 578: nan,\n", + " 579: nan,\n", + " 580: nan,\n", + " 581: nan,\n", + " 582: [{'gene_description': 'armadillo repeat containing, X-linked 3',\n", + " 'evidence': 'literature',\n", + " 'sub_mito_localization': 'MOM',\n", + " 'mito_pathways': 'Trafficking',\n", + " 'hpa_location': 'Nucleoplasm (Approved)',\n", + " 'tissue_expression': nan}],\n", + " 583: nan,\n", + " 584: nan,\n", + " 585: nan,\n", + " 586: nan,\n", + " 587: nan,\n", + " 588: nan,\n", + " 589: nan,\n", + " 590: nan,\n", + " 591: nan,\n", + " 592: nan,\n", + " 593: nan,\n", + " 594: nan,\n", + " 595: nan,\n", + " 596: nan,\n", + " 597: nan,\n", + " 598: nan,\n", + " 599: nan,\n", + " 600: nan,\n", + " 601: nan,\n", + " 602: nan,\n", + " 603: nan,\n", + " 604: nan,\n", + " 605: nan,\n", + " 606: nan,\n", + " 607: nan,\n", + " 608: nan,\n", + " 609: nan,\n", + " 610: nan,\n", + " 611: nan,\n", + " 612: nan,\n", + " 613: nan,\n", + " 614: nan,\n", + " 615: nan,\n", + " 616: nan,\n", + " 617: nan,\n", + " 618: [{'gene_description': 'prenyl (solanesyl) diphosphate synthase, subunit 2',\n", + " 'evidence': 'literature, APEX_matrix, targetP signal, yeast mito homolog+, Rickettsial homolog, mito protein domain, coexpression+',\n", + " 'sub_mito_localization': 'MIM',\n", + " 'mito_pathways': 'Coenzyme Q metabolism',\n", + " 'hpa_location': 'Cytosol (Enhanced)',\n", + " 'tissue_expression': 'smallintestine, largeintestine'}],\n", + " 619: nan,\n", + " 620: nan,\n", + " 621: nan,\n", + " 622: nan,\n", + " 623: nan,\n", + " 624: nan,\n", + " 625: [{'gene_description': 'solute carrier family 25, member 33',\n", + " 'evidence': 'literature, yeast mito homolog+, mito protein domain+',\n", + " 'sub_mito_localization': 'MIM',\n", + " 'mito_pathways': 'SLC25A family',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'brainstem, spinalcord, placenta, testis'}],\n", + " 626: nan,\n", + " 627: nan,\n", + " 628: nan,\n", + " 629: nan,\n", + " 630: nan,\n", + " 631: nan,\n", + " 632: nan,\n", + " 633: nan,\n", + " 634: nan,\n", + " 635: nan,\n", + " 636: nan,\n", + " 637: nan,\n", + " 638: nan,\n", + " 639: nan,\n", + " 640: nan,\n", + " 641: [{'gene_description': 'thymidine kinase 2, mitochondrial',\n", + " 'evidence': 'literature, targetP signal+, mito protein domain, MS/MS',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Nucleotide synthesis and processing',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'cerebrum, cerebellum, brainstem, adipose'}],\n", + " 642: nan,\n", + " 643: nan,\n", + " 644: nan,\n", + " 645: nan,\n", + " 646: nan,\n", + " 647: nan,\n", + " 648: nan,\n", + " 649: nan,\n", + " 650: nan,\n", + " 651: nan,\n", + " 652: nan,\n", + " 653: nan,\n", + " 654: nan,\n", + " 655: nan,\n", + " 656: nan,\n", + " 657: nan,\n", + " 658: nan,\n", + " 659: nan,\n", + " 660: nan,\n", + " 661: nan,\n", + " 662: nan,\n", + " 663: nan,\n", + " 664: nan,\n", + " 665: nan,\n", + " 666: nan,\n", + " 667: nan,\n", + " 668: nan,\n", + " 669: nan,\n", + " 670: nan,\n", + " 671: [{'gene_description': 'translocase of outer mitochondrial membrane 40-like',\n", + " 'evidence': 'targetP signal, yeast mito homolog+, mito protein domain+, induction, coexpression+, MS/MS',\n", + " 'sub_mito_localization': 'MOM',\n", + " 'mito_pathways': 'TOM',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'cerebrum, cerebellum, brainstem, spinalcord, adipose, largeintestine, stomach, testis'}],\n", + " 672: nan,\n", + " 673: nan,\n", + " 674: nan,\n", + " 675: nan,\n", + " 676: nan,\n", + " 677: nan,\n", + " 678: nan,\n", + " 679: nan,\n", + " 680: nan,\n", + " 681: nan,\n", + " 682: nan,\n", + " 683: nan,\n", + " 684: nan,\n", + " 685: nan,\n", + " 686: nan,\n", + " 687: nan,\n", + " 688: nan,\n", + " 689: nan,\n", + " 690: nan,\n", + " 691: [{'gene_description': 'oxidoreductase NAD-binding domain containing 1',\n", + " 'evidence': 'APEX_matrix, GFP, targetP signal, yeast mito homolog, mito protein domain, coexpression++, MS/MS++',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': nan,\n", + " 'hpa_location': 'Nucleoplasm (Approved)',\n", + " 'tissue_expression': 'cerebrum, spinalcord, liver, heart, adipose, smallintestine, largeintestine, stomach, placenta, testis'}],\n", + " 692: nan,\n", + " 693: nan,\n", + " 694: [{'gene_description': 'family with sequence similarity 136, member A',\n", + " 'evidence': 'APEX_IMS, mito protein domain+, MS/MS++',\n", + " 'sub_mito_localization': 'IMS',\n", + " 'mito_pathways': nan,\n", + " 'hpa_location': 'Mitochondria (Approved)',\n", + " 'tissue_expression': 'all 14'}],\n", + " 695: [{'gene_description': 'family with sequence similarity 136, member A',\n", + " 'evidence': 'APEX_IMS, mito protein domain+, MS/MS++',\n", + " 'sub_mito_localization': 'IMS',\n", + " 'mito_pathways': nan,\n", + " 'hpa_location': 'Mitochondria (Approved)',\n", + " 'tissue_expression': 'all 14'}],\n", + " 696: [{'gene_description': 'COX assembly mitochondrial protein 2',\n", + " 'evidence': 'APEX_IMS, yeast mito homolog++, mito protein domain+, induction, coexpression, MS/MS+',\n", + " 'sub_mito_localization': 'IMS',\n", + " 'mito_pathways': 'OXPHOS assembly factors',\n", + " 'hpa_location': 'Mitochondria (Supported)',\n", + " 'tissue_expression': 'cerebrum, cerebellum, spinalcord, liver, heart, adipose, largeintestine, stomach, placenta, testis'}],\n", + " 697: nan,\n", + " 698: nan,\n", + " 699: nan,\n", + " 700: nan,\n", + " 701: [{'gene_description': 'flavin adenine dinucleotide synthetase 1',\n", + " 'evidence': 'APEX_matrix, mito protein domain, induction, coexpression',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Vitamin B2 metabolism',\n", + " 'hpa_location': 'Cytosol;Plasma membrane (Supported)',\n", + " 'tissue_expression': 'spinalcord, adipose, stomach'}],\n", + " 702: nan,\n", + " 703: nan,\n", + " 704: nan,\n", + " 705: nan,\n", + " 706: nan,\n", + " 707: nan,\n", + " 708: nan,\n", + " 709: nan,\n", + " 710: nan,\n", + " 711: nan,\n", + " 712: nan,\n", + " 713: nan,\n", + " 714: nan,\n", + " 715: nan,\n", + " 716: nan,\n", + " 717: nan,\n", + " 718: nan,\n", + " 719: nan,\n", + " 720: nan,\n", + " 721: nan,\n", + " 722: nan,\n", + " 723: nan,\n", + " 724: nan,\n", + " 725: nan,\n", + " 726: nan,\n", + " 727: nan,\n", + " 728: nan,\n", + " 729: nan,\n", + " 730: nan,\n", + " 731: nan,\n", + " 732: nan,\n", + " 733: nan,\n", + " 734: [{'gene_description': 'ATP-binding cassette, sub-family D (ALD), member 1',\n", + " 'evidence': 'targetP signal, Rickettsial homolog, mito protein domain, induction',\n", + " 'sub_mito_localization': 'Membrane',\n", + " 'mito_pathways': 'ABC transporters',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'adipose'}],\n", + " 735: nan,\n", + " 736: nan,\n", + " 737: nan,\n", + " 738: nan,\n", + " 739: nan,\n", + " 740: nan,\n", + " 741: nan,\n", + " 742: nan,\n", + " 743: nan,\n", + " 744: nan,\n", + " 745: nan,\n", + " 746: nan,\n", + " 747: nan,\n", + " 748: nan,\n", + " 749: nan,\n", + " 750: nan,\n", + " 751: nan,\n", + " 752: nan,\n", + " 753: nan,\n", + " 754: nan,\n", + " 755: nan,\n", + " 756: nan,\n", + " 757: nan,\n", + " 758: nan,\n", + " 759: nan,\n", + " 760: [{'gene_description': 'mitochondrial ribosomal protein L49',\n", + " 'evidence': 'literature, APEX_matrix, targetP signal, yeast mito homolog++, mito protein domain, coexpression, MS/MS++',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Mitochondrial ribosome',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'all 14'}],\n", + " 761: nan,\n", + " 762: nan,\n", + " 763: nan,\n", + " 764: nan,\n", + " 765: nan,\n", + " 766: nan,\n", + " 767: nan,\n", + " 768: nan,\n", + " 769: nan,\n", + " 770: nan,\n", + " 771: nan,\n", + " 772: nan,\n", + " 773: [{'gene_description': 'BCL2-like 11 (apoptosis facilitator)',\n", + " 'evidence': 'manual, targetP signal',\n", + " 'sub_mito_localization': 'MOM',\n", + " 'mito_pathways': 'Apoptosis',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': nan}],\n", + " 774: [{'gene_description': 'cytochrome c oxidase assembly factor 6',\n", + " 'evidence': 'APEX_IMS, yeast mito homolog++, mito protein domain+, induction, coexpression+, MS/MS',\n", + " 'sub_mito_localization': 'IMS',\n", + " 'mito_pathways': 'OXPHOS assembly factors',\n", + " 'hpa_location': 'Mitochondria (Supported)',\n", + " 'tissue_expression': 'cerebrum, cerebellum, spinalcord, liver, adipose, smallintestine, largeintestine, placenta, testis'}],\n", + " 775: nan,\n", + " 776: [{'gene_description': 'aldehyde dehydrogenase 1 family, member L1',\n", + " 'evidence': 'APEX_matrix, yeast mito homolog, Rickettsial homolog, mito protein domain, induction, coexpression, MS/MS',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Folate and 1-C metabolism',\n", + " 'hpa_location': 'Cytosol (Supported)',\n", + " 'tissue_expression': 'cerebrum, liver, smallintestine, largeintestine, stomach, placenta, testis'}],\n", + " 777: nan,\n", + " 778: nan,\n", + " 779: nan,\n", + " 780: nan,\n", + " 781: nan,\n", + " 782: nan,\n", + " 783: nan,\n", + " 784: nan,\n", + " 785: nan,\n", + " 786: nan,\n", + " 787: nan,\n", + " 788: nan,\n", + " 789: nan,\n", + " 790: nan,\n", + " 791: nan,\n", + " 792: nan,\n", + " 793: nan,\n", + " 794: nan,\n", + " 795: nan,\n", + " 796: nan,\n", + " 797: nan,\n", + " 798: nan,\n", + " 799: nan,\n", + " 800: nan,\n", + " 801: nan,\n", + " 802: nan,\n", + " 803: nan,\n", + " 804: nan,\n", + " 805: nan,\n", + " 806: nan,\n", + " 807: nan,\n", + " 808: nan,\n", + " 809: nan,\n", + " 810: nan,\n", + " 811: nan,\n", + " 812: nan,\n", + " 813: nan,\n", + " 814: nan,\n", + " 815: nan,\n", + " 816: nan,\n", + " 817: nan,\n", + " 818: nan,\n", + " 819: nan,\n", + " 820: nan,\n", + " 821: nan,\n", + " 822: nan,\n", + " 823: nan,\n", + " 824: nan,\n", + " 825: nan,\n", + " 826: nan,\n", + " 827: nan,\n", + " 828: nan,\n", + " 829: nan,\n", + " 830: nan,\n", + " 831: nan,\n", + " 832: nan,\n", + " 833: nan,\n", + " 834: nan,\n", + " 835: nan,\n", + " 836: nan,\n", + " 837: nan,\n", + " 838: nan,\n", + " 839: [{'gene_description': 'mitochondrial ribosomal protein L9',\n", + " 'evidence': 'literature, APEX_matrix, targetP signal, Rickettsial homolog, mito protein domain, induction, coexpression+, MS/MS',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Mitochondrial ribosome',\n", + " 'hpa_location': 'Mitochondria (Supported)',\n", + " 'tissue_expression': 'all 14'}],\n", + " 840: nan,\n", + " 841: nan,\n", + " 842: nan,\n", + " 843: nan,\n", + " 844: nan,\n", + " 845: nan,\n", + " 846: nan,\n", + " 847: nan,\n", + " 848: nan,\n", + " 849: nan,\n", + " 850: nan,\n", + " 851: nan,\n", + " 852: nan,\n", + " 853: nan,\n", + " 854: nan,\n", + " 855: nan,\n", + " 856: nan,\n", + " 857: nan,\n", + " 858: nan,\n", + " 859: nan,\n", + " 860: nan,\n", + " 861: nan,\n", + " 862: nan,\n", + " 863: nan,\n", + " 864: nan,\n", + " 865: nan,\n", + " 866: nan,\n", + " 867: nan,\n", + " 868: nan,\n", + " 869: nan,\n", + " 870: nan,\n", + " 871: nan,\n", + " 872: nan,\n", + " 873: nan,\n", + " 874: nan,\n", + " 875: nan,\n", + " 876: nan,\n", + " 877: nan,\n", + " 878: nan,\n", + " 879: nan,\n", + " 880: nan,\n", + " 881: nan,\n", + " 882: nan,\n", + " 883: nan,\n", + " 884: nan,\n", + " 885: nan,\n", + " 886: nan,\n", + " 887: nan,\n", + " 888: nan,\n", + " 889: nan,\n", + " 890: nan,\n", + " 891: nan,\n", + " 892: nan,\n", + " 893: nan,\n", + " 894: nan,\n", + " 895: nan,\n", + " 896: nan,\n", + " 897: nan,\n", + " 898: nan,\n", + " 899: nan,\n", + " 900: nan,\n", + " 901: nan,\n", + " 902: nan,\n", + " 903: [{'gene_description': 'DnaJ heat shock protein family (Hsp40) member C11',\n", + " 'evidence': 'GFP, yeast mito homolog+, Rickettsial homolog, mito protein domain, coexpression, MS/MS++',\n", + " 'sub_mito_localization': 'MOM',\n", + " 'mito_pathways': 'Intramitochondrial membrane interactions',\n", + " 'hpa_location': 'Cytosol (Approved)',\n", + " 'tissue_expression': 'all 14'}],\n", + " 904: nan,\n", + " 905: nan,\n", + " 906: nan,\n", + " 907: nan,\n", + " 908: nan,\n", + " 909: nan,\n", + " 910: nan,\n", + " 911: nan,\n", + " 912: [{'gene_description': 'mitochondrial ribosomal protein L36',\n", + " 'evidence': 'literature, targetP signal, yeast mito homolog++, mito protein domain, induction, coexpression+',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Mitochondrial ribosome',\n", + " 'hpa_location': 'Mitochondria;Nuclear bodies (Supported)',\n", + " 'tissue_expression': nan}],\n", + " 913: nan,\n", + " 914: nan,\n", + " 915: nan,\n", + " 916: nan,\n", + " 917: [{'gene_description': 'mitochondrial ribosomal protein L4',\n", + " 'evidence': 'literature, APEX_matrix, targetP signal, yeast mito homolog++, Rickettsial homolog, mito protein domain, induction, MS/MS++',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Mitochondrial ribosome',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'cerebrum, brainstem, spinalcord, kidney, liver, adipose, smallintestine, largeintestine, placenta, testis'}],\n", + " 918: nan,\n", + " 919: nan,\n", + " 920: nan,\n", + " 921: nan,\n", + " 922: nan,\n", + " 923: nan,\n", + " 924: nan,\n", + " 925: nan,\n", + " 926: nan,\n", + " 927: nan,\n", + " 928: nan,\n", + " 929: nan,\n", + " 930: nan,\n", + " 931: nan,\n", + " 932: nan,\n", + " 933: nan,\n", + " 934: nan,\n", + " 935: nan,\n", + " 936: nan,\n", + " 937: nan,\n", + " 938: nan,\n", + " 939: nan,\n", + " 940: nan,\n", + " 941: nan,\n", + " 942: nan,\n", + " 943: nan,\n", + " 944: [{'gene_description': 'acetyl-Coenzyme A carboxylase beta',\n", + " 'evidence': 'yeast mito homolog, Rickettsial homolog, mito protein domain, coexpression+',\n", + " 'sub_mito_localization': 'MOM',\n", + " 'mito_pathways': 'Biotin utilizing proteins',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'cerebrum, cerebellum, brainstem, spinalcord, kidney, liver, adipose, largeintestine, stomach, placenta, testis'}],\n", + " 945: nan,\n", + " 946: nan,\n", + " 947: nan,\n", + " 948: nan,\n", + " 949: nan,\n", + " 950: nan,\n", + " 951: [{'gene_description': 'aminolevulinic acid synthase 2, erythroid',\n", + " 'evidence': 'literature, targetP signal, yeast mito homolog+, Rickettsial homolog, mito protein domain+, coexpression',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Heme synthesis and processing',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': nan}],\n", + " 952: nan,\n", + " 953: nan,\n", + " 954: nan,\n", + " 955: [{'gene_description': 'caseinolytic mitochondrial matrix peptidase chaperone subunit',\n", + " 'evidence': 'literature, APEX_matrix, targetP signal, yeast mito homolog++, Rickettsial homolog, mito protein domain, induction, coexpression, MS/MS++',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'Proteases',\n", + " 'hpa_location': 'Mitochondria (Supported)',\n", + " 'tissue_expression': 'all 14'}],\n", + " 956: nan,\n", + " 957: nan,\n", + " 958: nan,\n", + " 959: nan,\n", + " 960: nan,\n", + " 961: nan,\n", + " 962: nan,\n", + " 963: nan,\n", + " 964: nan,\n", + " 965: nan,\n", + " 966: nan,\n", + " 967: nan,\n", + " 968: nan,\n", + " 969: nan,\n", + " 970: nan,\n", + " 971: [{'gene_description': 'acid phosphatase 6, lysophosphatidic',\n", + " 'evidence': 'literature, APEX_IMS, targetP signal, mito protein domain, MS/MS++',\n", + " 'sub_mito_localization': 'IMS',\n", + " 'mito_pathways': 'Phospholipid metabolism',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'cerebrum, spinalcord, kidney, liver, skeletalmuscle, adipose, smallintestine, largeintestine, stomach, placenta, testis'}],\n", + " 972: nan,\n", + " 973: nan,\n", + " 974: nan,\n", + " 975: [{'gene_description': 'alkB homolog 7',\n", + " 'evidence': 'APEX_matrix, targetP signal+, mito protein domain, induction, coexpression++, MS/MS',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': nan,\n", + " 'hpa_location': 'Mitochondria (Supported)',\n", + " 'tissue_expression': 'cerebellum, brainstem, largeintestine, testis'}],\n", + " 976: nan,\n", + " 977: nan,\n", + " 978: nan,\n", + " 979: nan,\n", + " 980: nan,\n", + " 981: nan,\n", + " 982: nan,\n", + " 983: nan,\n", + " 984: nan,\n", + " 985: nan,\n", + " 986: [{'gene_description': 'mitochondrial transcription termination factor 2',\n", + " 'evidence': 'literature, APEX_matrix, targetP signal, mito protein domain+, induction, coexpression, MS/MS',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': 'mtDNA nucleoid',\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'cerebrum, cerebellum, brainstem, spinalcord, liver, heart, skeletalmuscle, adipose, largeintestine, testis'}],\n", + " 987: nan,\n", + " 988: nan,\n", + " 989: nan,\n", + " 990: nan,\n", + " 991: nan,\n", + " 992: nan,\n", + " 993: nan,\n", + " 994: nan,\n", + " 995: nan,\n", + " 996: nan,\n", + " 997: [{'gene_description': 'reticulon 4 interacting protein 1',\n", + " 'evidence': 'literature, APEX_matrix, targetP signal+, yeast mito homolog, mito protein domain, induction, coexpression++, MS/MS++',\n", + " 'sub_mito_localization': 'Matrix',\n", + " 'mito_pathways': nan,\n", + " 'hpa_location': nan,\n", + " 'tissue_expression': 'all 14'}],\n", + " 998: nan,\n", + " 999: nan,\n", + " ...}" + ] + }, + "execution_count": 44, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_gprofiler_mitocarta_df_mice[MITOCARTA].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 45, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[{'NCBI.GeneID.Target': '18626',\n", + " 'Ensembl.GeneID.Target': 'ENSMUSG00000020893',\n", + " 'Name.Target': 'Per1',\n", + " 'UniprotID.Target': 'O35973',\n", + " 'Target.TFLink.ortho': 'Hs:O15534;Dr:B3DK47;Rn:A0A0H2UHZ7',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'inferred by curator',\n", + " 'PubmedID': '10848603;29087512',\n", + " 'Source.database': 'TRRUST',\n", + " 'Small-scale.evidence': 'Yes'}]" + ] + }, + "execution_count": 45, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_gprofiler_mitocarta_df_mice[\"its_target\"][ncbi_tf_gprofiler_mitocarta_df_mice[\"its_target\"].notna()]\n", + "ncbi_tf_gprofiler_mitocarta_df_mice[\"its_target\"][1]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### Protein-Protein Interactions from STRING" + ] + }, + { + "cell_type": "code", + "execution_count": 46, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_deapadj_deaminus_log10_pvalue_deaStringDB_ppi
0ENSMUSG00000021903EnsemblENSMUSG00000021903EnsemblGalnt152770.4375082.5211820.09994125.2266012.046157e-1402.373133e-136139.689061[{'stringdb_link_to': 'ENSMUSG00000021906', 'E...
1ENSMUSG00000059824EnsemblENSMUSG00000059824EnsemblDbp2816.783019-2.9852390.191760-15.5676141.208303e-547.006949e-5153.917824[{'stringdb_link_to': 'ENSMUSG00000020893', 'E...
2ENSMUSG00000041417EnsemblENSMUSG00000041417EnsemblPik3r12934.3272642.0474830.13677614.9696291.159658e-504.483238e-4749.935670[{'stringdb_link_to': 'ENSMUSG00000000290', 'E...
3ENSMUSG00000004939EnsemblENSMUSG00000004939EnsemblNmrk2675.068734-3.9814740.274358-14.5119781.017437e-472.950057e-4446.992493[{'stringdb_link_to': 'ENSMUSG00000079243', 'E...
4ENSMUSG00000028834EnsemblENSMUSG00000028834EnsemblTrim6344995.1044133.7382750.26128914.3070481.977304e-464.586555e-4345.703926[{'stringdb_link_to': 'ENSMUSG00000020475', 'E...
\n", + "
" + ], + "text/plain": [ + " identifier identifier.source target target.source \\\n", + "0 ENSMUSG00000021903 Ensembl ENSMUSG00000021903 Ensembl \n", + "1 ENSMUSG00000059824 Ensembl ENSMUSG00000059824 Ensembl \n", + "2 ENSMUSG00000041417 Ensembl ENSMUSG00000041417 Ensembl \n", + "3 ENSMUSG00000004939 Ensembl ENSMUSG00000004939 Ensembl \n", + "4 ENSMUSG00000028834 Ensembl ENSMUSG00000028834 Ensembl \n", + "\n", + " GENE_SYMBOL_dea baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea \\\n", + "0 Galnt15 2770.437508 2.521182 0.099941 25.226601 \n", + "1 Dbp 2816.783019 -2.985239 0.191760 -15.567614 \n", + "2 Pik3r1 2934.327264 2.047483 0.136776 14.969629 \n", + "3 Nmrk2 675.068734 -3.981474 0.274358 -14.511978 \n", + "4 Trim63 44995.104413 3.738275 0.261289 14.307048 \n", + "\n", + " pvalue_dea padj_dea minus_log10_pvalue_dea \\\n", + "0 2.046157e-140 2.373133e-136 139.689061 \n", + "1 1.208303e-54 7.006949e-51 53.917824 \n", + "2 1.159658e-50 4.483238e-47 49.935670 \n", + "3 1.017437e-47 2.950057e-44 46.992493 \n", + "4 1.977304e-46 4.586555e-43 45.703926 \n", + "\n", + " StringDB_ppi \n", + "0 [{'stringdb_link_to': 'ENSMUSG00000021906', 'E... \n", + "1 [{'stringdb_link_to': 'ENSMUSG00000020893', 'E... \n", + "2 [{'stringdb_link_to': 'ENSMUSG00000000290', 'E... \n", + "3 [{'stringdb_link_to': 'ENSMUSG00000079243', 'E... \n", + "4 [{'stringdb_link_to': 'ENSMUSG00000020475', 'E... " + ] + }, + "execution_count": 46, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "string_path = os.path.join(base_dir, \"data/mice/string.pkl\")\n", + "string_metadata_path = os.path.join(base_dir, \"data/mice/string_metadata.pkl\")\n", + "\n", + "if not os.path.exists(string_path):\n", + " ppi_df, ppi_metadata = stringdb.get_ppi(\n", + " bridgedb_df=bridgedb_df_mice[\n", + " (bridgedb_df_mice['padj_dea'] < 0.01) &\n", + " (\n", + " (bridgedb_df_mice['log2FoldChange_dea'] > 1) |\n", + " (bridgedb_df_mice['log2FoldChange_dea'] < -1)\n", + " )\n", + " ],\n", + " species= \"Mouse\"\n", + " )\n", + " ppi_df.to_pickle(string_path)\n", + " with open(string_metadata_path, \"wb\") as file:\n", + " pickle.dump(ppi_metadata, file)\n", + "else:\n", + " ppi_df = pd.read_pickle(string_path)\n", + " with open(string_metadata_path, \"rb\") as file:\n", + " ppi_metadata = pickle.load(file)\n", + "\n", + "ppi_df.head()\n" + ] + }, + { + "cell_type": "code", + "execution_count": 47, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(846, 13)" + ] + }, + "execution_count": 47, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ppi_df.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 48, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{0: [{'stringdb_link_to': 'ENSMUSG00000021906',\n", + " 'Ensembl': 'ENSMUSP00000022462',\n", + " 'score': 0.505,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 1: [{'stringdb_link_to': 'ENSMUSG00000020893',\n", + " 'Ensembl': 'ENSMUSP00000021271',\n", + " 'score': 0.7,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000023087',\n", + " 'Ensembl': 'ENSMUSP00000023849',\n", + " 'score': 0.425,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000030103',\n", + " 'Ensembl': 'ENSMUSP00000032194',\n", + " 'score': 0.47,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000032010',\n", + " 'Ensembl': 'ENSMUSP00000034508',\n", + " 'score': 0.415,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000068742',\n", + " 'Ensembl': 'ENSMUSP00000088047',\n", + " 'score': 0.704,\n", + " 'Uniprot-TrEMBL': 'Q9R194',\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000055116',\n", + " 'Ensembl': 'ENSMUSP00000147989',\n", + " 'score': 0.933,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 2: [{'stringdb_link_to': 'ENSMUSG00000000290',\n", + " 'Ensembl': 'ENSMUSP00000000299',\n", + " 'score': 0.916,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000000359',\n", + " 'Ensembl': 'ENSMUSP00000000369',\n", + " 'score': 0.682,\n", + " 'Uniprot-TrEMBL': 'O35929',\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000000489',\n", + " 'Ensembl': 'ENSMUSP00000000500',\n", + " 'score': 0.603,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000004508',\n", + " 'Ensembl': 'ENSMUSP00000004622',\n", + " 'score': 0.975,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000007613',\n", + " 'Ensembl': 'ENSMUSP00000007757',\n", + " 'score': 0.62,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000022346',\n", + " 'Ensembl': 'ENSMUSP00000022971',\n", + " 'score': 0.426,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000022797',\n", + " 'Ensembl': 'ENSMUSP00000023486',\n", + " 'score': 0.472,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000024697',\n", + " 'Ensembl': 'ENSMUSP00000025602',\n", + " 'score': 0.571,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000026012',\n", + " 'Ensembl': 'ENSMUSP00000027165',\n", + " 'score': 0.936,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000026072',\n", + " 'Ensembl': 'ENSMUSP00000027241',\n", + " 'score': 0.58,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000026173',\n", + " 'Ensembl': 'ENSMUSP00000027362',\n", + " 'score': 0.659,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000026656',\n", + " 'Ensembl': 'ENSMUSP00000027966',\n", + " 'score': 0.588,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000029186',\n", + " 'Ensembl': 'ENSMUSP00000031081',\n", + " 'score': 0.908,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000032766',\n", + " 'Ensembl': 'ENSMUSP00000031670',\n", + " 'score': 0.681,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000038894',\n", + " 'Ensembl': 'ENSMUSP00000038514',\n", + " 'score': 0.981,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000037104',\n", + " 'Ensembl': 'ENSMUSP00000038591',\n", + " 'score': 0.631,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000044641',\n", + " 'Ensembl': 'ENSMUSP00000052619',\n", + " 'score': 0.455,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000044167',\n", + " 'Ensembl': 'ENSMUSP00000055308',\n", + " 'score': 0.545,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000021782',\n", + " 'Ensembl': 'ENSMUSP00000087879',\n", + " 'score': 0.4,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000066571',\n", + " 'Ensembl': 'ENSMUSP00000103709',\n", + " 'score': 0.406,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000052684',\n", + " 'Ensembl': 'ENSMUSP00000102711',\n", + " 'score': 0.425,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000070348',\n", + " 'Ensembl': 'ENSMUSP00000091495',\n", + " 'score': 0.431,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000071713',\n", + " 'Ensembl': 'ENSMUSP00000154836',\n", + " 'score': 0.44,\n", + " 'Uniprot-TrEMBL': 'P26955',\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000021709',\n", + " 'Ensembl': 'ENSMUSP00000140536',\n", + " 'score': 0.445,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000040990',\n", + " 'Ensembl': 'ENSMUSP00000108075',\n", + " 'score': 0.474,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000074121',\n", + " 'Ensembl': 'ENSMUSP00000057916',\n", + " 'score': 0.499,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000048756',\n", + " 'Ensembl': 'ENSMUSP00000101141',\n", + " 'score': 0.511,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000110206',\n", + " 'Ensembl': 'ENSMUSP00000123506',\n", + " 'score': 0.528,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000048240',\n", + " 'Ensembl': 'ENSMUSP00000097061',\n", + " 'score': 0.65,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000053113',\n", + " 'Ensembl': 'ENSMUSP00000059129',\n", + " 'score': 0.673,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000023805',\n", + " 'Ensembl': 'ENSMUSP00000111457',\n", + " 'score': 0.684,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000032192',\n", + " 'Ensembl': 'ENSMUSP00000149938',\n", + " 'score': 0.684,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000075000',\n", + " 'Ensembl': 'ENSMUSP00000097254',\n", + " 'score': 0.72,\n", + " 'Uniprot-TrEMBL': 'Q8VCQ3',\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000029304',\n", + " 'Ensembl': 'ENSMUSP00000084043',\n", + " 'score': 0.753,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000025178',\n", + " 'Ensembl': 'ENSMUSP00000069284',\n", + " 'score': 0.91,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000021948',\n", + " 'Ensembl': 'ENSMUSP00000107830',\n", + " 'score': 0.925,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000026447',\n", + " 'Ensembl': 'ENSMUSP00000076911',\n", + " 'score': 0.945,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000022637',\n", + " 'Ensembl': 'ENSMUSP00000110115',\n", + " 'score': 0.947,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000031714',\n", + " 'Ensembl': 'ENSMUSP00000147784',\n", + " 'score': 0.99,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000039936',\n", + " 'Ensembl': 'ENSMUSP00000101315',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 3: [{'stringdb_link_to': 'ENSMUSG00000079243',\n", + " 'Ensembl': 'ENSMUSP00000107262',\n", + " 'score': 0.429,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000046345',\n", + " 'Ensembl': 'ENSMUSP00000090873',\n", + " 'score': 0.568,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 4: [{'stringdb_link_to': 'ENSMUSG00000020475',\n", + " 'Ensembl': 'ENSMUSP00000020768',\n", + " 'score': 0.418,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000022358',\n", + " 'Ensembl': 'ENSMUSP00000022986',\n", + " 'score': 0.925,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000028736',\n", + " 'Ensembl': 'ENSMUSP00000030508',\n", + " 'score': 0.478,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000030161',\n", + " 'Ensembl': 'ENSMUSP00000032264',\n", + " 'score': 0.478,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000031490',\n", + " 'Ensembl': 'ENSMUSP00000033880',\n", + " 'score': 0.468,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000044167',\n", + " 'Ensembl': 'ENSMUSP00000055308',\n", + " 'score': 0.905,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000053113',\n", + " 'Ensembl': 'ENSMUSP00000059129',\n", + " 'score': 0.408,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000068699',\n", + " 'Ensembl': 'ENSMUSP00000064163',\n", + " 'score': 0.444,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000009471',\n", + " 'Ensembl': 'ENSMUSP00000072330',\n", + " 'score': 0.665,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000048756',\n", + " 'Ensembl': 'ENSMUSP00000101141',\n", + " 'score': 0.664,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000030087',\n", + " 'Ensembl': 'ENSMUSP00000144962',\n", + " 'score': 0.414,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000021477',\n", + " 'Ensembl': 'ENSMUSP00000152169',\n", + " 'score': 0.471,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000078566',\n", + " 'Ensembl': 'ENSMUSP00000101718',\n", + " 'score': 0.472,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " 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'Uniprot-TrEMBL_link': None}],\n", + " 843: [{'stringdb_link_to': 'ENSMUSG00000000567',\n", + " 'Ensembl': 'ENSMUSP00000000579',\n", + " 'score': 0.502,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000031609',\n", + " 'Ensembl': 'ENSMUSP00000034022',\n", + " 'score': 0.609,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000040423',\n", + " 'Ensembl': 'ENSMUSP00000124871',\n", + " 'score': 0.552,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000035673',\n", + " 'Ensembl': 'ENSMUSP00000151590',\n", + " 'score': 0.574,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 844: [{'stringdb_link_to': 'ENSMUSG00000000290',\n", + " 'Ensembl': 'ENSMUSP00000000299',\n", + " 'score': 0.725,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000029163',\n", + " 'Ensembl': 'ENSMUSP00000031055',\n", + " 'score': 0.723,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000031425',\n", + " 'Ensembl': 'ENSMUSP00000033800',\n", + " 'score': 0.792,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000026971',\n", + " 'Ensembl': 'ENSMUSP00000054944',\n", + " 'score': 0.72,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000027009',\n", + " 'Ensembl': 'ENSMUSP00000099718',\n", + " 'score': 0.72,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 845: [{'stringdb_link_to': 'ENSMUSG00000000567',\n", + " 'Ensembl': 'ENSMUSP00000000579',\n", + " 'score': 0.545,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000022346',\n", + " 'Ensembl': 'ENSMUSP00000022971',\n", + " 'score': 0.5,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000022952',\n", + " 'Ensembl': 'ENSMUSP00000023673',\n", + " 'score': 0.526,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000027496',\n", + " 'Ensembl': 'ENSMUSP00000028997',\n", + " 'score': 0.513,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000055639',\n", + " 'Ensembl': 'ENSMUSP00000071464',\n", + " 'score': 0.502,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000029086',\n", + " 'Ensembl': 'ENSMUSP00000073751',\n", + " 'score': 0.44,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000070348',\n", + " 'Ensembl': 'ENSMUSP00000091495',\n", + " 'score': 0.468,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000055435',\n", + " 'Ensembl': 'ENSMUSP00000104732',\n", + " 'score': 0.572,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000052684',\n", + " 'Ensembl': 'ENSMUSP00000102711',\n", + " 'score': 0.597,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000055799',\n", + " 'Ensembl': 'ENSMUSP00000109687',\n", + " 'score': 0.761,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}]}" + ] + }, + "execution_count": 48, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "from pyBiodatafuse.constants import STRING_PPI_COL\n", + "\n", + "ppi_df[STRING_PPI_COL].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 49, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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targetStringDB_ppi
0ENSMUSG00000021903[{'stringdb_link_to': 'ENSMUSG00000021906', 'E...
1ENSMUSG00000059824[{'stringdb_link_to': 'ENSMUSG00000020893', 'E...
2ENSMUSG00000041417[{'stringdb_link_to': 'ENSMUSG00000000290', 'E...
3ENSMUSG00000004939[{'stringdb_link_to': 'ENSMUSG00000079243', 'E...
4ENSMUSG00000028834[{'stringdb_link_to': 'ENSMUSG00000020475', 'E...
\n", + "
" + ], + "text/plain": [ + " target StringDB_ppi\n", + "0 ENSMUSG00000021903 [{'stringdb_link_to': 'ENSMUSG00000021906', 'E...\n", + "1 ENSMUSG00000059824 [{'stringdb_link_to': 'ENSMUSG00000020893', 'E...\n", + "2 ENSMUSG00000041417 [{'stringdb_link_to': 'ENSMUSG00000000290', 'E...\n", + "3 ENSMUSG00000004939 [{'stringdb_link_to': 'ENSMUSG00000079243', 'E...\n", + "4 ENSMUSG00000028834 [{'stringdb_link_to': 'ENSMUSG00000020475', 'E..." + ] + }, + "execution_count": 49, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ppi_df[[\"target\", \"StringDB_ppi\"]].head()" + ] + }, + { + "cell_type": "code", + "execution_count": 50, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array([list([{'stringdb_link_to': 'ENSMUSG00000020893', 'Ensembl': 'ENSMUSP00000021271', 'score': 0.768, 'Uniprot-TrEMBL': None, 'Uniprot-TrEMBL_link': None}, {'stringdb_link_to': 'ENSMUSG00000051705', 'Ensembl': 'ENSMUSP00000149463', 'score': 0.401, 'Uniprot-TrEMBL': None, 'Uniprot-TrEMBL_link': None}, {'stringdb_link_to': 'ENSMUSG00000059824', 'Ensembl': 'ENSMUSP00000079693', 'score': 0.415, 'Uniprot-TrEMBL': None, 'Uniprot-TrEMBL_link': None}, {'stringdb_link_to': 'ENSMUSG00000068742', 'Ensembl': 'ENSMUSP00000088047', 'score': 0.503, 'Uniprot-TrEMBL': 'Q9R194', 'Uniprot-TrEMBL_link': None}, {'stringdb_link_to': 'ENSMUSG00000030967', 'Ensembl': 'ENSMUSP00000101763', 'score': 0.551, 'Uniprot-TrEMBL': None, 'Uniprot-TrEMBL_link': None}, {'stringdb_link_to': 'ENSMUSG00000055116', 'Ensembl': 'ENSMUSP00000147989', 'score': 0.688, 'Uniprot-TrEMBL': None, 'Uniprot-TrEMBL_link': None}, {'stringdb_link_to': 'ENSMUSG00000008348', 'Ensembl': 'ENSMUSP00000114180', 'score': 0.856, 'Uniprot-TrEMBL': None, 'Uniprot-TrEMBL_link': None}])],\n", + " dtype=object)" + ] + }, + "execution_count": 50, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ppi_df[ppi_df[\"target\"] == \"ENSMUSG00000032010\"][\"StringDB_ppi\"].values" + ] + }, + { + "cell_type": "code", + "execution_count": 51, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_dea...g:Profiler_go:bpg:Profiler_go:ccg:Profiler_go:mfg:Profiler_hpg:Profiler_keggg:Profiler_mirnag:Profiler_reacg:Profiler_tfg:Profiler_wpMitoCarta
0ENSMUSG00000021903Ensembl78754ncbi_gene_idGalnt152770.4375082.5211820.09994125.2266012.046157e-140...[{'id': 'GO:0006493', 'name': 'protein O-linke...[{'id': 'GO:0030133', 'name': 'transport vesic...[{'id': 'GO:0030246', 'name': 'carbohydrate bi...NaN[{'id': 'KEGG:01100', 'name': 'Metabolic pathw...[{'id': 'MIRNA:mmu-miR-34b-5p', 'name': 'mmu-m...[{'id': 'REAC:R-MMU-5173105', 'name': 'O-linke...[{'id': 'TF:M04454_1', 'name': 'Factor: AR; mo...NaNNaN
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1 rows × 28 columns

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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "0 ENSMUSG00000021903 Ensembl 78754 ncbi_gene_id Galnt15 \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea ... \\\n", + "0 2770.437508 2.521182 0.099941 25.226601 2.046157e-140 ... \n", + "\n", + " g:Profiler_go:bp \\\n", + "0 [{'id': 'GO:0006493', 'name': 'protein O-linke... \n", + "\n", + " g:Profiler_go:cc \\\n", + "0 [{'id': 'GO:0030133', 'name': 'transport vesic... \n", + "\n", + " g:Profiler_go:mf g:Profiler_hp \\\n", + "0 [{'id': 'GO:0030246', 'name': 'carbohydrate bi... NaN \n", + "\n", + " g:Profiler_kegg \\\n", + "0 [{'id': 'KEGG:01100', 'name': 'Metabolic pathw... \n", + "\n", + " g:Profiler_mirna \\\n", + "0 [{'id': 'MIRNA:mmu-miR-34b-5p', 'name': 'mmu-m... \n", + "\n", + " g:Profiler_reac \\\n", + "0 [{'id': 'REAC:R-MMU-5173105', 'name': 'O-linke... \n", + "\n", + " g:Profiler_tf g:Profiler_wp MitoCarta \n", + "0 [{'id': 'TF:M04454_1', 'name': 'Factor: AR; mo... NaN NaN \n", + "\n", + "[1 rows x 28 columns]" + ] + }, + "execution_count": 51, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ncbi_tf_gprofiler_mitocarta_df_mice.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 52, + "metadata": {}, + "outputs": [], + "source": [ + "combined_df = pd.merge(\n", + " ncbi_tf_gprofiler_mitocarta_df_mice,\n", + " ppi_df[[\"target\", \"StringDB_ppi\"]].rename(columns={\"target\": \"identifier\"}),\n", + " on=\"identifier\",\n", + " how=\"left\",\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 53, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "Index(['identifier', 'identifier.source', 'target', 'target.source',\n", + " 'GENE_SYMBOL_dea', 'baseMean_dea', 'log2FoldChange_dea', 'lfcSE_dea',\n", + " 'stat_dea', 'pvalue_dea', 'padj_dea', 'minus_log10_pvalue_dea', 'is_tf',\n", + " 'is_target', 'its_target', 'its_tf', 'intersections',\n", + " 'g:Profiler_corum', 'g:Profiler_go:bp', 'g:Profiler_go:cc',\n", + " 'g:Profiler_go:mf', 'g:Profiler_hp', 'g:Profiler_kegg',\n", + " 'g:Profiler_mirna', 'g:Profiler_reac', 'g:Profiler_tf', 'g:Profiler_wp',\n", + " 'MitoCarta', 'StringDB_ppi'],\n", + " dtype='object')" + ] + }, + "execution_count": 53, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df.columns" + ] + }, + { + "cell_type": "code", + "execution_count": 54, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_dea...g:Profiler_go:ccg:Profiler_go:mfg:Profiler_hpg:Profiler_keggg:Profiler_mirnag:Profiler_reacg:Profiler_tfg:Profiler_wpMitoCartaStringDB_ppi
0ENSMUSG00000021903Ensembl78754ncbi_gene_idGalnt152770.4375082.5211820.09994125.2266012.046157e-140...[{'id': 'GO:0030133', 'name': 'transport vesic...[{'id': 'GO:0030246', 'name': 'carbohydrate bi...NaN[{'id': 'KEGG:01100', 'name': 'Metabolic pathw...[{'id': 'MIRNA:mmu-miR-34b-5p', 'name': 'mmu-m...[{'id': 'REAC:R-MMU-5173105', 'name': 'O-linke...[{'id': 'TF:M04454_1', 'name': 'Factor: AR; mo...NaNNaN[{'stringdb_link_to': 'ENSMUSG00000021906', 'E...
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1 rows × 29 columns

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" + ], + "text/plain": [ + " identifier identifier.source target target.source GENE_SYMBOL_dea \\\n", + "0 ENSMUSG00000021903 Ensembl 78754 ncbi_gene_id Galnt15 \n", + "\n", + " baseMean_dea log2FoldChange_dea lfcSE_dea stat_dea pvalue_dea ... \\\n", + "0 2770.437508 2.521182 0.099941 25.226601 2.046157e-140 ... \n", + "\n", + " g:Profiler_go:cc \\\n", + "0 [{'id': 'GO:0030133', 'name': 'transport vesic... \n", + "\n", + " g:Profiler_go:mf g:Profiler_hp \\\n", + "0 [{'id': 'GO:0030246', 'name': 'carbohydrate bi... NaN \n", + "\n", + " g:Profiler_kegg \\\n", + "0 [{'id': 'KEGG:01100', 'name': 'Metabolic pathw... \n", + "\n", + " g:Profiler_mirna \\\n", + "0 [{'id': 'MIRNA:mmu-miR-34b-5p', 'name': 'mmu-m... \n", + "\n", + " g:Profiler_reac \\\n", + "0 [{'id': 'REAC:R-MMU-5173105', 'name': 'O-linke... \n", + "\n", + " g:Profiler_tf g:Profiler_wp MitoCarta \\\n", + "0 [{'id': 'TF:M04454_1', 'name': 'Factor: AR; mo... NaN NaN \n", + "\n", + " StringDB_ppi \n", + "0 [{'stringdb_link_to': 'ENSMUSG00000021906', 'E... \n", + "\n", + "[1 rows x 29 columns]" + ] + }, + "execution_count": 54, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df.head(1)" + ] + }, + { + "cell_type": "code", + "execution_count": 55, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{0: [{'stringdb_link_to': 'ENSMUSG00000021906',\n", + " 'Ensembl': 'ENSMUSP00000022462',\n", + " 'score': 0.505,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 1: [{'stringdb_link_to': 'ENSMUSG00000020893',\n", + " 'Ensembl': 'ENSMUSP00000021271',\n", + " 'score': 0.7,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000023087',\n", + " 'Ensembl': 'ENSMUSP00000023849',\n", + " 'score': 0.425,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000030103',\n", + " 'Ensembl': 'ENSMUSP00000032194',\n", + " 'score': 0.47,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000032010',\n", + " 'Ensembl': 'ENSMUSP00000034508',\n", + " 'score': 0.415,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000068742',\n", + " 'Ensembl': 'ENSMUSP00000088047',\n", + " 'score': 0.704,\n", + " 'Uniprot-TrEMBL': 'Q9R194',\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000055116',\n", + " 'Ensembl': 'ENSMUSP00000147989',\n", + " 'score': 0.933,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 2: [{'stringdb_link_to': 'ENSMUSG00000000290',\n", + " 'Ensembl': 'ENSMUSP00000000299',\n", + " 'score': 0.916,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000000359',\n", + " 'Ensembl': 'ENSMUSP00000000369',\n", + " 'score': 0.682,\n", + " 'Uniprot-TrEMBL': 'O35929',\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000000489',\n", + " 'Ensembl': 'ENSMUSP00000000500',\n", + " 'score': 0.603,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000004508',\n", + " 'Ensembl': 'ENSMUSP00000004622',\n", + " 'score': 0.975,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000007613',\n", + " 'Ensembl': 'ENSMUSP00000007757',\n", + " 'score': 0.62,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000022346',\n", + " 'Ensembl': 'ENSMUSP00000022971',\n", + " 'score': 0.426,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000022797',\n", + " 'Ensembl': 'ENSMUSP00000023486',\n", + " 'score': 0.472,\n", + " 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{'stringdb_link_to': 'ENSMUSG00000029186',\n", + " 'Ensembl': 'ENSMUSP00000031081',\n", + " 'score': 0.908,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000032766',\n", + " 'Ensembl': 'ENSMUSP00000031670',\n", + " 'score': 0.681,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000038894',\n", + " 'Ensembl': 'ENSMUSP00000038514',\n", + " 'score': 0.981,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000037104',\n", + " 'Ensembl': 'ENSMUSP00000038591',\n", + " 'score': 0.631,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000044641',\n", + " 'Ensembl': 'ENSMUSP00000052619',\n", + " 'score': 0.455,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000044167',\n", + " 'Ensembl': 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'ENSMUSG00000029135',\n", + " 'Ensembl': 'ENSMUSP00000031017',\n", + " 'score': 0.549,\n", + " 'Uniprot-TrEMBL': 'P47930',\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000033863',\n", + " 'Ensembl': 'ENSMUSP00000045639',\n", + " 'score': 0.457,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000053113',\n", + " 'Ensembl': 'ENSMUSP00000059129',\n", + " 'score': 0.493,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000052837',\n", + " 'Ensembl': 'ENSMUSP00000064680',\n", + " 'score': 0.518,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000052684',\n", + " 'Ensembl': 'ENSMUSP00000102711',\n", + " 'score': 0.76,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000030087',\n", + " 'Ensembl': 'ENSMUSP00000144962',\n", + " 'score': 0.538,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 969: nan,\n", + " 970: nan,\n", + " 971: nan,\n", + " 972: nan,\n", + " 973: nan,\n", + " 974: [{'stringdb_link_to': 'ENSMUSG00000001627',\n", + " 'Ensembl': 'ENSMUSP00000001672',\n", + " 'score': 0.484,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000027858',\n", + " 'Ensembl': 'ENSMUSP00000029451',\n", + " 'score': 0.43,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000016559',\n", + " 'Ensembl': 'ENSMUSP00000102062',\n", + " 'score': 0.541,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000047407',\n", + " 'Ensembl': 'ENSMUSP00000130930',\n", + " 'score': 0.429,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 975: [{'stringdb_link_to': 'ENSMUSG00000039754',\n", + " 'Ensembl': 'ENSMUSP00000040403',\n", + " 'score': 0.866,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 976: [{'stringdb_link_to': 'ENSMUSG00000024413',\n", + " 'Ensembl': 'ENSMUSP00000025279',\n", + " 'score': 0.821,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000001700',\n", + " 'Ensembl': 'ENSMUSP00000157710',\n", + " 'score': 0.468,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 977: nan,\n", + " 978: nan,\n", + " 979: nan,\n", + " 980: [{'stringdb_link_to': nan,\n", + " 'Ensembl': nan,\n", + " 'score': nan,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 981: nan,\n", + " 982: nan,\n", + " 983: [{'stringdb_link_to': 'ENSMUSG00000032766',\n", + " 'Ensembl': 'ENSMUSP00000031670',\n", + " 'score': 0.688,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000032177',\n", + " 'Ensembl': 'ENSMUSP00000037025',\n", + " 'score': 0.764,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000048240',\n", + " 'Ensembl': 'ENSMUSP00000097061',\n", + " 'score': 0.732,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000021948',\n", + " 'Ensembl': 'ENSMUSP00000107830',\n", + " 'score': 0.918,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000021699',\n", + " 'Ensembl': 'ENSMUSP00000113488',\n", + " 'score': 0.75,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000032192',\n", + " 'Ensembl': 'ENSMUSP00000149938',\n", + " 'score': 0.677,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000064120',\n", + " 'Ensembl': 'ENSMUSP00000133694',\n", + " 'score': 0.808,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 984: nan,\n", + " 985: nan,\n", + " 986: [{'stringdb_link_to': nan,\n", + " 'Ensembl': nan,\n", + " 'score': nan,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 987: nan,\n", + " 988: nan,\n", + " 989: nan,\n", + " 990: [{'stringdb_link_to': 'ENSMUSG00000022009',\n", + " 'Ensembl': 'ENSMUSP00000022586',\n", + " 'score': 0.545,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000026743',\n", + " 'Ensembl': 'ENSMUSP00000028076',\n", + " 'score': 0.919,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000027829',\n", + " 'Ensembl': 'ENSMUSP00000029416',\n", + " 'score': 0.73,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000029313',\n", + " 'Ensembl': 'ENSMUSP00000031256',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000033323',\n", + " 'Ensembl': 'ENSMUSP00000038938',\n", + " 'score': 0.818,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None},\n", + " {'stringdb_link_to': 'ENSMUSG00000041328',\n", + " 'Ensembl': 'ENSMUSP00000113717',\n", + " 'score': 0.488,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 991: nan,\n", + " 992: nan,\n", + " 993: nan,\n", + " 994: nan,\n", + " 995: nan,\n", + " 996: [{'stringdb_link_to': nan,\n", + " 'Ensembl': nan,\n", + " 'score': nan,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 997: [{'stringdb_link_to': 'ENSMUSG00000038248',\n", + " 'Ensembl': 'ENSMUSP00000040072',\n", + " 'score': 0.424,\n", + " 'Uniprot-TrEMBL': None,\n", + " 'Uniprot-TrEMBL_link': None}],\n", + " 998: nan,\n", + " 999: nan,\n", + " ...}" + ] + }, + "execution_count": 55, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df[\"StringDB_ppi\"].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 58, + "metadata": {}, + "outputs": [], + "source": [ + "filename_mice = \"data/mice/combined_df.pkl\"\n", + "\n", + "combined_df.to_pickle(filename_mice)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### graph" + ] + }, + { + "cell_type": "code", + "execution_count": 56, + "metadata": {}, + "outputs": [], + "source": [ + "filename_mice = \"data/mice/combined_df.pkl\"\n", + "with open(filename_mice, \"rb\") as f:\n", + " combined_df = pickle.load(f)" + ] + }, + { + "cell_type": "code", + "execution_count": 57, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "529" + ] + }, + "execution_count": 57, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Extract all 'NCBI.GeneID.TF' values into a single list\n", + "ncbi_gene_ids = (\n", + " combined_df[\"its_tf\"]\n", + " .apply(lambda x: [d[\"NCBI.GeneID.TF\"] for d in x] if isinstance(x, list) else [])\n", + " .explode()\n", + " .dropna()\n", + " .unique()\n", + " .tolist()\n", + ")\n", + "\n", + "len(ncbi_gene_ids)" + ] + }, + { + "cell_type": "code", + "execution_count": 59, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(755, 29)" + ] + }, + "execution_count": 59, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df_tf = combined_df[combined_df[\"target\"].isin(ncbi_gene_ids)]\n", + "combined_df_sig = combined_df[\n", + " (combined_df['padj_dea'] < 0.01) &\n", + " (\n", + " (combined_df['log2FoldChange_dea'] > 1) |\n", + " (combined_df['log2FoldChange_dea'] < -1)\n", + " )]\n", + "\n", + "\n", + "combined_df_sig = combined_df_sig[~combined_df_sig[\"target\"].isin(ncbi_gene_ids)]\n", + "combined_df_sig.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 60, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(1285, 29)" + ] + }, + "execution_count": 60, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df_tf_sig = pd.concat([combined_df_sig, combined_df_tf], axis=0, ignore_index=True)\n", + "combined_df_tf_sig.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 61, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "Series([], Name: its_tf, dtype: object)" + ] + }, + "execution_count": 61, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df_tf_sig[combined_df_tf_sig[\"GENE_SYMBOL_dea\"] == \"COQ10A\"][\"its_tf\"].apply(\n", + " lambda x: isinstance(x, list)\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 62, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{}" + ] + }, + "execution_count": 62, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df_tf_sig[combined_df_tf_sig[\"GENE_SYMBOL_dea\"] == \"COQ10A\"][\"its_tf\"].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 63, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_dea...g:Profiler_go:ccg:Profiler_go:mfg:Profiler_hpg:Profiler_keggg:Profiler_mirnag:Profiler_reacg:Profiler_tfg:Profiler_wpMitoCartaStringDB_ppi
1ENSMUSG00000059824Ensembl13170ncbi_gene_idDbp2816.783019-2.9852390.191760-15.5676141.208303e-54...[{'id': 'GO:0005667', 'name': 'transcription r...[{'id': 'GO:0000981', 'name': 'DNA-binding tra...NaN[{'id': 'KEGG:04710', 'name': 'Circadian rhyth...[{'id': 'MIRNA:mmu-miR-122-5p', 'name': 'mmu-m...NaN[{'id': 'TF:M03882', 'name': 'Factor: RelB:p50...NaNNaN[{'stringdb_link_to': 'ENSMUSG00000020893', 'E...
9ENSMUSG00000037465Ensembl21847ncbi_gene_idKlf102481.2085522.1897430.16681913.1264702.322309e-39...[{'id': 'GO:0005622', 'name': 'intracellular a...[{'id': 'GO:0005515', 'name': 'protein binding...NaNNaN[{'id': 'MIRNA:mmu-miR-301b-3p', 'name': 'mmu-...NaN[{'id': 'TF:M00002', 'name': 'Factor: E47; mot...NaNNaN[{'stringdb_link_to': 'ENSMUSG00000025880', 'E...
21ENSMUSG00000042292Ensembl223701ncbi_gene_idMkl11080.501466-2.2322130.191789-11.6388802.614271e-31...[{'id': 'GO:0005737', 'name': 'cytoplasm', 'p_...[{'id': 'GO:0005515', 'name': 'protein binding...[{'id': 'HP:0031378', 'name': 'Abnormal lympho...NaN[{'id': 'MIRNA:mmu-miR-1a-3p', 'name': 'mmu-mi...[{'id': 'REAC:R-MMU-162582', 'name': 'Signal T...[{'id': 'TF:M02024_1', 'name': 'Factor: mef-2A...NaNNaN[{'stringdb_link_to': 'ENSMUSG00000044167', 'E...
29ENSMUSG00000018143Ensembl17135ncbi_gene_idMafk2165.9859252.1097050.19389510.8806571.425327e-27...[{'id': 'GO:0005622', 'name': 'intracellular a...[{'id': 'GO:0005515', 'name': 'protein binding...NaNNaN[{'id': 'MIRNA:mmu-miR-3473c', 'name': 'mmu-mi...[{'id': 'REAC:R-MMU-9707616', 'name': 'Heme si...[{'id': 'TF:M10174_1', 'name': 'Factor: AR; mo...[{'id': 'WP:WP4265', 'name': 'Ethanol metaboli...NaN[{'stringdb_link_to': 'ENSMUSG00000025612', 'E...
34ENSMUSG00000040943Ensembl214133ncbi_gene_idTet2841.4636381.3217980.12581910.5055438.145301e-26...[{'id': 'GO:0005622', 'name': 'intracellular a...[{'id': 'GO:0005515', 'name': 'protein binding...[{'id': 'HP:0030386', 'name': 'Abnormal propor...NaN[{'id': 'MIRNA:mmu-miR-466d-5p', 'name': 'mmu-...NaN[{'id': 'TF:M03882', 'name': 'Factor: RelB:p50...NaNNaN[{'stringdb_link_to': 'ENSMUSG00000022346', 'E...
..................................................................
11084ENSMUSG00000000440Ensembl19016ncbi_gene_idPparg104.582903-0.0129340.259905-0.0497639.603111e-01...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
11131ENSMUSG00000055866Ensembl18627ncbi_gene_idPer21058.6823230.0068020.2079560.0327079.739080e-01...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
11136ENSMUSG00000033249Ensembl26386ncbi_gene_idHsf4367.7848050.0050860.1620260.0313919.749574e-01...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
11143ENSMUSG00000026021Ensembl22218ncbi_gene_idSumo11372.979132-0.0027330.094426-0.0289419.769115e-01...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
11225ENSMUSG00000005718Ensembl83383ncbi_gene_idTfap4274.276267-0.0006430.251716-0.0025569.979610e-01...NaNNaNNaNNaNNaNNaNNaNNaNNaNNaN
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530 rows × 29 columns

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[{'id': 'GO:0005667', 'name': 'transcription r... \n", + "9 2.322309e-39 ... [{'id': 'GO:0005622', 'name': 'intracellular a... \n", + "21 2.614271e-31 ... [{'id': 'GO:0005737', 'name': 'cytoplasm', 'p_... \n", + "29 1.425327e-27 ... [{'id': 'GO:0005622', 'name': 'intracellular a... \n", + "34 8.145301e-26 ... [{'id': 'GO:0005622', 'name': 'intracellular a... \n", + "... ... ... ... \n", + "11084 9.603111e-01 ... NaN \n", + "11131 9.739080e-01 ... NaN \n", + "11136 9.749574e-01 ... NaN \n", + "11143 9.769115e-01 ... NaN \n", + "11225 9.979610e-01 ... 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{'NCBI.GeneID.Target': '51673',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000159713',\n", + " 'Name.Target': 'TPPP3',\n", + " 'UniprotID.Target': 'Q9BW30',\n", + " 'Target.TFLink.ortho': 'Dr:E7FG48;Mm:Q9CRB6;Rn:Q5PPN5',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '84448',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000163995',\n", + " 'Name.Target': 'ABLIM2',\n", + " 'UniprotID.Target': 'Q6H8Q1',\n", + " 'Target.TFLink.ortho': 'Dr:U3JA30;Rn:A0A0G2JXC7',\n", + " 'Target.nonTFLink.ortho': 'Mm:E9Q4K0',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '83636',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000131943',\n", + " 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'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '6390',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000117118',\n", + " 'Name.Target': 'SDHB',\n", + " 'UniprotID.Target': 'P21912',\n", + " 'Target.TFLink.ortho': 'Ce:Q09545;Dm:P21914;Dr:A5PL98;Mm:Q9CQA3;Rn:P21913;Sc:P21801',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '57462',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000164976',\n", + " 'Name.Target': 'MYORG',\n", + " 'UniprotID.Target': 'Q6NSJ0',\n", + " 'Target.TFLink.ortho': 'Dr:E7F1U0;Mm:Q69ZQ1;Rn:D4AE63',\n", + " 'Target.nonTFLink.ortho': 'Dm:Q9VBR6;Dr:A0A0R4IJD4',\n", + " 'Detection.method': 'chromatin 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'Target.TFLink.ortho': 'Dm:Q9VS54;Mm:Q9WTN0;Rn:Q6F596;Sc:Q12051',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '150274',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000100209',\n", + " 'Name.Target': 'HSCB',\n", + " 'UniprotID.Target': 'Q8IWL3',\n", + " 'Target.TFLink.ortho': 'Ce:Q21324;Dm:A8JNT7;Mm:A0A0R4J0T0;Rn:D3ZME7;Sc:P53193',\n", + " 'Target.nonTFLink.ortho': 'Dr:B0V1J6',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '2653',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000140905',\n", + " 'Name.Target': 'GCSH',\n", + " 'UniprotID.Target': 'P23434',\n", + " 'Target.TFLink.ortho': 'Ce:Q20634;Ce:O62122;Dm:Q9U616;Dr:Q6DGX4;Mm:Q91WK5;Sc:P39726',\n", + " 'Target.nonTFLink.ortho': 'Dr:F1QRR5',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '51619',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000078967',\n", + " 'Name.Target': 'UBE2D4',\n", + " 'UniprotID.Target': 'Q9Y2X8',\n", + " 'Target.TFLink.ortho': 'Dr:A4QNX5',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '123624',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000273540',\n", + " 'Name.Target': 'AGBL1',\n", + " 'UniprotID.Target': 'Q96MI9',\n", + " 'Target.TFLink.ortho': '-',\n", + " 'Target.nonTFLink.ortho': 'Mm:D3Z1M2;Rn:A0A0G2JV75',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '2954',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000100577',\n", + " 'Name.Target': 'GSTZ1',\n", + " 'UniprotID.Target': 'O43708',\n", + " 'Target.TFLink.ortho': '-',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '171425',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000125246',\n", + " 'Name.Target': 'CLYBL',\n", + " 'UniprotID.Target': 'Q8N0X4',\n", + " 'Target.TFLink.ortho': 'Ce:Q93167;Dr:Q1JPT8;Mm:Q8R4N0;Rn:Q5I0K3',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '4839',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000111641',\n", + " 'Name.Target': 'NOP2',\n", + " 'UniprotID.Target': 'P46087',\n", + " 'Target.TFLink.ortho': 'Dr:F1QWP7;Mm:E9QN31;Rn:D4ACW1',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '64682',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000153107',\n", + " 'Name.Target': 'ANAPC1',\n", + " 'UniprotID.Target': 'Q9H1A4',\n", + " 'Target.TFLink.ortho': 'Dm:Q9VXV3;Dr:A0A2R8QA59;Mm:P53995;Rn:F1M801',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '8637',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000243056',\n", + " 'Name.Target': 'EIF4EBP3',\n", + " 'UniprotID.Target': 'O60516',\n", + " 'Target.TFLink.ortho': 'Dr:Q98TT6;Mm:Q80VV3',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '285440',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000145476',\n", + " 'Name.Target': 'CYP4V2',\n", + " 'UniprotID.Target': 'Q6ZWL3',\n", + " 'Target.TFLink.ortho': 'Ce:G5EGT6;Dm:Q9VA27;Dr:A0JMQ6;Mm:Q9DBW0;Rn:A2RRT9',\n", + " 'Target.nonTFLink.ortho': 'Dr:A0JMN1',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '36',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000196177',\n", + " 'Name.Target': 'ACADSB',\n", + " 'UniprotID.Target': 'P45954',\n", + " 'Target.TFLink.ortho': 'Ce:O44549;Ce:H2KZG6;Dm:Q9VVU1;Dr:F1QFQ7;Mm:Q9DBL1;Rn:A0A0A0MY00',\n", + " 'Target.nonTFLink.ortho': 'Ce:A0A0K3AQR2',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '7112',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000120802',\n", + " 'Name.Target': 'TMPO',\n", + " 'UniprotID.Target': 'P42166',\n", + " 'Target.TFLink.ortho': '-',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '287',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000145362',\n", + " 'Name.Target': 'ANK2',\n", + " 'UniprotID.Target': 'Q01484',\n", + " 'Target.TFLink.ortho': '-',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '11112',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000106049',\n", + " 'Name.Target': 'HIBADH',\n", + " 'UniprotID.Target': 'P31937',\n", + " 'Target.TFLink.ortho': 'Ce:Q9XTI0;Dm:Q9V8M5;Dr:F1QE62;Dr:A0A0R4IA23;Mm:Q99L13;Rn:P29266',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '206358',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000123643',\n", + " 'Name.Target': 'SLC36A1',\n", + " 'UniprotID.Target': 'Q7Z2H8',\n", + " 'Target.TFLink.ortho': 'Mm:Q8K4D3;Rn:Q924A5;Sc:P36062',\n", + " 'Target.nonTFLink.ortho': 'Dr:E7F5P8',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '518',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000154518',\n", + " 'Name.Target': 'ATP5MC3',\n", + " 'UniprotID.Target': 'P48201',\n", + " 'Target.TFLink.ortho': 'Dr:Q7ZYW7;Mm:Q9CR84;Mm:P56384;Rn:Q499S2',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '22985',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000100813',\n", + " 'Name.Target': 'ACIN1',\n", + " 'UniprotID.Target': 'Q9UKV3',\n", + " 'Target.TFLink.ortho': 'Dr:F1Q511;Mm:Q9JIX8;Rn:E9PST5',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '3625',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000163083',\n", + " 'Name.Target': 'INHBB',\n", + " 'UniprotID.Target': 'P09529',\n", + " 'Target.TFLink.ortho': 'Mm:Q04999;Rn:A0A0G2K0C6',\n", + " 'Target.nonTFLink.ortho': 'Dr:A0A0G2KD75',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '5191',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000112357',\n", + " 'Name.Target': 'PEX7',\n", + " 'UniprotID.Target': 'O00628',\n", + " 'Target.TFLink.ortho': 'Dm:Q9VSN7;Dr:F1QFW8;Mm:P97865;Rn:Q498S5;Sc:P39108',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '2668',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000168621',\n", + " 'Name.Target': 'GDNF',\n", + " 'UniprotID.Target': 'P39905',\n", + " 'Target.TFLink.ortho': '-',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '64061',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000184205',\n", + " 'Name.Target': 'TSPYL2',\n", + " 'UniprotID.Target': 'Q9H2G4',\n", + " 'Target.TFLink.ortho': 'Mm:Q7TQI8;Rn:A0A096MJ32',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '2926',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000132463',\n", + " 'Name.Target': 'GRSF1',\n", + " 'UniprotID.Target': 'Q12849',\n", + " 'Target.TFLink.ortho': 'Dr:F8W4V6;Mm:Q8C5Q4',\n", + " 'Target.nonTFLink.ortho': 'Rn:F1LRK4',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '201562',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000206527',\n", + " 'Name.Target': 'HACD2',\n", + " 'UniprotID.Target': 'Q6Y1H2',\n", + " 'Target.TFLink.ortho': 'Ce:O17040;Dr:B0V199;Mm:Q9D3B1;Rn:D3ZHG0',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '23632',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000118298',\n", + " 'Name.Target': 'CA14',\n", + " 'UniprotID.Target': 'Q9ULX7',\n", + " 'Target.TFLink.ortho': 'Mm:Q9WVT6;Rn:A2IBE0',\n", + " 'Target.nonTFLink.ortho': 'Dr:F8W4I7',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285',\n", + " 'Source.database': 'ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '1160',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000131730',\n", + " 'Name.Target': 'CKMT2',\n", + " 'UniprotID.Target': 'P17540',\n", + " 'Target.TFLink.ortho': 'Mm:Q6P8J7',\n", + " 'Target.nonTFLink.ortho': 'Dm:Q9VF23;Rn:A0A0G2JVQ1',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '54948',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000166902',\n", + " 'Name.Target': 'MRPL16',\n", + " 'UniprotID.Target': 'Q9NX20',\n", + " 'Target.TFLink.ortho': 'Ce:Q22140;Dm:Q9W547;Mm:Q99N93;Rn:Q5M818',\n", + " 'Target.nonTFLink.ortho': 'Dr:F1R2K1',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '8604',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000115840',\n", + " 'Name.Target': 'SLC25A12',\n", + " 'UniprotID.Target': 'O75746',\n", + " 'Target.TFLink.ortho': 'Mm:Q8BH59;Rn:F1LX07',\n", + " 'Target.nonTFLink.ortho': 'Dr:A0A0R4II73',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '2037',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000079819',\n", + " 'Name.Target': 'EPB41L2',\n", + " 'UniprotID.Target': 'O43491',\n", + " 'Target.TFLink.ortho': 'Mm:O70318',\n", + " 'Target.nonTFLink.ortho': 'Rn:D3ZM69',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '6391',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000143252',\n", + " 'Name.Target': 'SDHC',\n", + " 'UniprotID.Target': 'Q99643',\n", + " 'Target.TFLink.ortho': 'Ce:P41956;Dm:Q9VGS3;Mm:Q9CZB0;Rn:Q641Z9',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '141',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000144843',\n", + " 'Name.Target': 'ADPRH',\n", + " 'UniprotID.Target': 'P54922',\n", + " 'Target.TFLink.ortho': 'Mm:P54923;Rn:Q02589',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '400451',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000185442',\n", + " 'Name.Target': 'FAM174B',\n", + " 'UniprotID.Target': 'Q3ZCQ3',\n", + " 'Target.TFLink.ortho': 'Mm:Q8K064',\n", + " 'Target.nonTFLink.ortho': 'Rn:D4A4W1',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '23596',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000203668',\n", + " 'Name.Target': 'OPN3',\n", + " 'UniprotID.Target': 'Q9H1Y3',\n", + " 'Target.TFLink.ortho': 'Dr:A9NJI7;Mm:Q9WUK7;Rn:D3ZFS1',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '54715',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000078328',\n", + " 'Name.Target': 'RBFOX1',\n", + " 'UniprotID.Target': 'Q9NWB1',\n", + " 'Target.TFLink.ortho': 'Dr:Q642J5;Mm:Q9JJ43;Rn:D3ZSL1',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '10105',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000108179',\n", + " 'Name.Target': 'PPIF',\n", + " 'UniprotID.Target': 'P30405',\n", + " 'Target.TFLink.ortho': 'Dm:Q7K2I4;Dm:P25007;Mm:Q99KR7;Rn:P29117',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '23408',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000124523',\n", + " 'Name.Target': 'SIRT5',\n", + " 'UniprotID.Target': 'Q9NXA8',\n", + " 'Target.TFLink.ortho': 'Mm:Q8K2C6;Rn:Q68FX9',\n", + " 'Target.nonTFLink.ortho': 'Dr:Q6DHI5',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '29126285;27924024',\n", + " 'Source.database': 'GTRD;ReMap',\n", + " 'Small-scale.evidence': 'No'},\n", + " {'NCBI.GeneID.Target': '81796',\n", + " 'Ensembl.GeneID.Target': 'ENSG00000137571',\n", + " 'Name.Target': 'SLCO5A1',\n", + " 'UniprotID.Target': 'Q9H2Y9',\n", + " 'Target.TFLink.ortho': 'Dr:E7F2I7;Mm:E9PVD9;Rn:D3ZZM7',\n", + " 'Target.nonTFLink.ortho': '-',\n", + " 'Detection.method': 'chromatin immunoprecipitation assay',\n", + " 'PubmedID': '27924024',\n", + " 'Source.database': 'GTRD',\n", + " 'Small-scale.evidence': 'No'}]}" + ] + }, + "execution_count": 57, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df_tf_sig[combined_df_tf_sig[\"identifier\"] == \"ENSG00000001167\"][\"its_target\"].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 65, + "metadata": {}, + "outputs": [], + "source": [ + "combined_df_tf_sig[\"its_target\"][10]" + ] + }, + { + "cell_type": "code", + "execution_count": 66, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "0" + ] + }, + "execution_count": 66, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "# Extract all targets for NFYA ('NCBI.GeneID.TF')\n", + "ncbi_gene_ids_NFYA_targets = (\n", + " combined_df_tf_sig[combined_df_tf_sig[\"identifier\"] == \"ENSG00000001167\"][\"its_target\"]\n", + " .apply(lambda x: [d[\"NCBI.GeneID.Target\"] for d in x] if isinstance(x, list) else [])\n", + " .explode()\n", + " .dropna()\n", + " .unique()\n", + " .tolist()\n", + ")\n", + "\n", + "len(ncbi_gene_ids_NFYA_targets)" + ] + }, + { + "cell_type": "code", + "execution_count": 50, + "metadata": {}, + "outputs": [], + "source": [ + "# combined_df = combine_sources(\n", + "# merged_df_mice,\n", + "# [\n", + "# ppi_df,\n", + "# ],\n", + "# )" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "metadata": {}, + "outputs": [], + "source": [ + "# combined_metadata = create_or_append_to_metadata(\n", + "# bridgedb_metadata_mice,\n", + "# [\n", + "# ppi_metadata,\n", + "# get_data_versions(\"hsapiens\")\n", + "# ],\n", + "# )" + ] + }, + { + "cell_type": "code", + "execution_count": 55, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "[{'datasource': 'StringDB',\n", + " 'metadata': {'source_version': {'source_version': '12.0'}},\n", + " 'query': {'size': 222,\n", + " 'input_type': 'HGNC',\n", + " 'number_of_added_edges': 532,\n", + " 'time': '0:00:00.651298',\n", + " 'date': '2024-12-18 14:43:18',\n", + " 'url': 'https://string-db.org/api'}},\n", + " {'biomart': 'Ensembl',\n", + " 'biomart_version': '111',\n", + " 'display_name': 'Human',\n", + " 'genebuild': 'GRCh38.p14',\n", + " 'gprofiler_version': 'e111_eg58_p18_f463989d',\n", + " 'organism': 'hsapiens',\n", + " 'sources': {'CORUM': {'name': 'CORUM protein complexes',\n", + " 'version': '28.11.2022 Corum 4.1'},\n", + " 'GO:BP': {'name': 'biological process',\n", + " 'version': 'annotations: BioMart\\nclasses: releases/2024-01-17'},\n", + " 'GO:CC': {'name': 'cellular component',\n", + " 'version': 'annotations: BioMart\\nclasses: releases/2024-01-17'},\n", + " 'GO:MF': {'name': 'molecular function',\n", + " 'version': 'annotations: BioMart\\nclasses: releases/2024-01-17'},\n", + " 'HP': {'name': 'Human Phenotype Ontology',\n", + " 'version': 'annotations: 01.2024\\nclasses: None'},\n", + " 'HPA': {'name': 'Human Protein Atlas',\n", + " 'version': 'annotations: HPA website: 23-07-17\\nclasses: script: 24-01-02'},\n", + " 'KEGG': {'name': 'Kyoto Encyclopedia of Genes and Genomes',\n", + " 'version': 'KEGG FTP Release 2024-01-22'},\n", + " 'MIRNA': {'name': 'miRTarBase', 'version': 'Release 9.0'},\n", + " 'REAC': {'name': 'Reactome',\n", + " 'version': 'annotations: BioMart\\nclasses: 2024-1-25'},\n", + " 'TF': {'name': 'Transfac',\n", + " 'version': 'annotations: TRANSFAC Release 2023.2\\nclasses: v2'},\n", + " 'WP': {'name': 'WikiPathways', 'version': '20240101'}},\n", + " 'taxonomy_id': '9606'},\n", + " {'datasource': 'BridgeDb',\n", + " 'metadata': {'source_version': {'java.version': '11.0.16',\n", + " 'bridgedb.version': '3.0.25',\n", + " 'webservice.version': '2.1.7'},\n", + " 'data_version': ['DATASOURCENAME: Ensembl',\n", + " 'BUILDDATE: 20230311',\n", + " 'SERIES: Homo sapiens genes and proteins',\n", + " 'DATATYPE: GeneProduct',\n", + " 'DATASOURCEVERSION: 108',\n", + " 'SCHEMAVERSION: 3',\n", + " 'DATASOURCENAME: Wikidata',\n", + " 'BUILDDATE: 20211127',\n", + " 'SERIES: humancorona',\n", + " 'DATATYPE: GeneProduct',\n", + " 'DATASOURCEVERSION: 1.0.0',\n", + " 'SCHEMAVERSION: 3',\n", + " 'DATASOURCENAME: Wikidata',\n", + " 'BUILDDATE: 20230209',\n", + " 'SERIES: Complexes',\n", + " 'DATATYPE: Complexes',\n", + " 'DATASOURCEVERSION: 1.0.0',\n", + " 'SCHEMAVERSION: 3',\n", + " 'DATASOURCENAME: Wikidata',\n", + " 'BUILDDATE: 20230506',\n", + " 'SERIES: Homo sapiens genes and proteins',\n", + " 'DATATYPE: GeneProduct',\n", + " 'DATASOURCEVERSION: 1.0.0',\n", + " 'SCHEMAVERSION: 3',\n", + " 'DATASOURCENAME: EBI-RHEA',\n", + " 'BUILDDATE: 20210109',\n", + " 'SERIES: standard-interaction',\n", + " 'DATATYPE: Interaction',\n", + " 'DATASOURCEVERSION: 115',\n", + " 'SCHEMAVERSION: 3',\n", + " 'DATASOURCENAME: HMDB-CHEBI-WIKIDATA',\n", + " 'BUILDDATE: 20220707',\n", + " 'DATATYPE: Metabolite',\n", + " 'SERIES: standard_metabolite',\n", + " 'DATASOURCEVERSION: HMDB5.0.20211102-CHEBI211-WIKIDATA20220707',\n", + " 'SCHEMAVERSION: 3',\n", + " 'DATASOURCENAME: Wikidata',\n", + " 'BUILDDATE: 20211211',\n", + " 'SERIES: pathways',\n", + " 'DATATYPE: Pathways',\n", + " 'DATASOURCEVERSION: 1.0.0',\n", + " 'BRIDGEDBVERSION: 3.0.10',\n", + " 'SCHEMAVERSION: 3',\n", + " 'DATASOURCENAME: Wikidata',\n", + " 'BUILDDATE: 20230428',\n", + " 'SERIES: publications',\n", + " 'DATATYPE: Article',\n", + " 'DATASOURCEVERSION: 1.0.0',\n", + " 'BRIDGEDBVERSION: 3.0.22-SNAPSHOT',\n", + " 'SCHEMAVERSION: 3']},\n", + " 'query': {'size': 12322,\n", + " 'input_type': 'Ensembl',\n", + " 'time': '0:00:05.538243',\n", + " 'date': '2024-12-18 14:39:58',\n", + " 'url': 'https://webservice.bridgedb.org/Human/xrefsBatch',\n", + " 'request_string': 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" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [identifier, identifier.source, target, target.source, GENE_SYMBOL_dea, baseMean_dea, log2FoldChange_dea, lfcSE_dea, stat_dea, pvalue_dea, padj_dea, minus_log10_pvalue_dea, is_tf, is_target, its_target, its_tf, intersections, g:Profiler_corum, g:Profiler_go:bp, g:Profiler_go:cc, g:Profiler_go:mf, g:Profiler_hp, g:Profiler_kegg, g:Profiler_mirna, g:Profiler_reac, g:Profiler_tf, g:Profiler_wp, MitoCarta, StringDB_ppi]\n", + "Index: []\n", + "\n", + "[0 rows x 29 columns]" + ] + }, + "execution_count": 70, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df[combined_df[\"GENE_SYMBOL_dea\"] == \"MT-ND4\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 63, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{10722: [{'stringdb_link_to': 'ENSG00000010256',\n", + " 'Ensembl': 'ENSP00000203407',\n", + " 'score': 0.971,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000108179',\n", + " 'Ensembl': 'ENSP00000225174',\n", + " 'score': 0.404,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000110955',\n", + " 'Ensembl': 'ENSP00000262030',\n", + " 'score': 0.553,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000154518',\n", + " 'Ensembl': 'ENSP00000284727',\n", + " 'score': 0.513,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000005700',\n", + " 'Ensembl': 'ENSP00000305721',\n", + " 'score': 0.457,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000198804',\n", + " 'Ensembl': 'ENSP00000354499',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000198727',\n", + " 'Ensembl': 'ENSP00000354554',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000198899',\n", + " 'Ensembl': 'ENSP00000354632',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000198888',\n", + " 'Ensembl': 'ENSP00000354687',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000198712',\n", + " 'Ensembl': 'ENSP00000354876',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000101247',\n", + " 'Ensembl': 'Ensembl:ENSP00000367346',\n", + " 'score': 0.587,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000152234',\n", + " 'Ensembl': 'Ensembl:ENSP00000381736',\n", + " 'score': 0.654,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000143252',\n", + " 'Ensembl': 'Ensembl:ENSP00000356953',\n", + " 'score': 0.696,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000117118',\n", + " 'Ensembl': 'Ensembl:ENSP00000364649',\n", + " 'score': 0.958,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000023228',\n", + " 'Ensembl': 'Ensembl:ENSP00000392709',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'},\n", + " {'stringdb_link_to': 'ENSG00000198763',\n", + " 'Ensembl': 'Ensembl:ENSP00000355046',\n", + " 'score': 0.999,\n", + " 'Uniprot-TrEMBL': 'MT-ND4'}]}" + ] + }, + "execution_count": 63, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df[combined_df[\"identifier\"] == \"ENSG00000198886\"][\"StringDB_ppi\"].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 64, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{81: [{'stringdb_link_to': 'ENSG00000198886',\n", + " 'Ensembl': 'Ensembl:ENSP00000354961',\n", + " 'score': 0.457,\n", + " 'Uniprot-TrEMBL': 'IBTK'}]}" + ] + }, + "execution_count": 64, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df[combined_df[\"identifier\"] == \"ENSG00000005700\"][\"StringDB_ppi\"].to_dict()" + ] + }, + { + "cell_type": "code", + "execution_count": 65, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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identifieridentifier.sourcetargettarget.sourceGENE_SYMBOL_deabaseMean_dealog2FoldChange_dealfcSE_deastat_deapvalue_dea...g:Profiler_go:mfg:Profiler_hpg:Profiler_hpag:Profiler_keggg:Profiler_mirnag:Profiler_reacg:Profiler_tfg:Profiler_wpMitoCartaStringDB_ppi
2558ENSG00000108387Ensembl5414ncbi_gene_id2004-09-01 00:00:00193.4710210.0734770.134930.5445560.586059...NaNNaNNaNNaNNaNNaNNaNNaN[{'gene_description': 'septin 4', 'evidence': ...NaN
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1 rows × 30 columns

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" + ], + "text/plain": [ + " identifier identifier.source target target.source \\\n", + "2558 ENSG00000108387 Ensembl 5414 ncbi_gene_id \n", + "\n", + " GENE_SYMBOL_dea baseMean_dea log2FoldChange_dea lfcSE_dea \\\n", + "2558 2004-09-01 00:00:00 193.471021 0.073477 0.13493 \n", + "\n", + " stat_dea pvalue_dea ... g:Profiler_go:mf g:Profiler_hp \\\n", + "2558 0.544556 0.586059 ... NaN NaN \n", + "\n", + " g:Profiler_hpa g:Profiler_kegg g:Profiler_mirna g:Profiler_reac \\\n", + "2558 NaN NaN NaN NaN \n", + "\n", + " g:Profiler_tf g:Profiler_wp \\\n", + "2558 NaN NaN \n", + "\n", + " MitoCarta StringDB_ppi \n", + "2558 [{'gene_description': 'septin 4', 'evidence': ... NaN \n", + "\n", + "[1 rows x 30 columns]" + ] + }, + "execution_count": 65, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "combined_df[combined_df[\"identifier\"] == \"ENSG00000108387\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 67, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Combined DataFrame saved in ./data/mice/graph_mice/graph_mice_df.pkl\n", + "Metadata saved in ./data/mice/graph_mice/graph_mice_metadata.pkl\n", + "Building graph: 100%|██████████| 1285/1285 [00:04<00:00, 303.40it/s]\n", + "Graph is built successfully\n", + "Graph saved in ./data/mice/graph_mice/graph_mice_graph.pkl and ./data/mice/graph_mice/graph_mice_graph.gml\n" + ] + } + ], + "source": [ + "pygraph = generator.save_graph(\n", + " combined_df=combined_df_tf_sig,\n", + " combined_metadata=bridgedb_metadata_mice,\n", + " graph_name=\"graph_mice\",\n", + " graph_dir=\"./data/mice\",\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": 68, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "MultiDiGraph with 17327 nodes and 275684 edges\n" + ] + } + ], + "source": [ + "print(pygraph)" + ] + }, + { + "cell_type": "code", + "execution_count": 69, + "metadata": {}, + "outputs": [], + "source": [ + "from pyBiodatafuse.graph import neo4j\n", + "\n", + "neo4j.save_graph_to_graphml(pygraph, \"data/mice/graph_mice/networkx_graph_mice.graphml\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.13" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +}