Downloads

Click on a dataset to access its downloads. Click on a column header to sort the table by that column. Type in the search bar to filter.

To download the data programmatically, use the API or this Python script.

Resource Dataset Description Category Attribute Views
Achilles Cell Line Gene Essentiality Profiles fitness scores for cell lines following single gene knockdowns disease or phenotype associations cell line 3992
Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles mRNA expression profiles for 6 adult human brain tissue samples spanning ~300 brain structures transcriptomics tissue 5952
Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles mRNA expression profiles for adult mouse brain tissues spanning ~2000 anatomically defined brain structures transcriptomics tissue 2349
Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray mRNA expression profiles for human brain tissue samples spanning 27 time points and 26 brain structures transcriptomics tissue sample 1471
Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq mRNA expression profiles for human brain tissue samples spanning 31 time points and 26 brain structures transcriptomics tissue sample 997
Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles mRNA expression profiles for 4 human prenatal brain tissue samples spanning 4 time points and ~300 brain structures transcriptomics tissue 1775
Biocarta Pathways sets of proteins participating in pathways structural or functional annotations pathway 3948
BioGPS Cell Line Gene Expression Profiles mRNA expression profiles for the NCI-60 panel of cancer cell lines transcriptomics cell line 5331
BioGPS Human Cell Type and Tissue Gene Expression Profiles mRNA expression profiles for human tissues and cell types transcriptomics cell type or tissue 2849
BioGPS Mouse Cell Type and Tissue Gene Expression Profiles mRNA expression profiles for mouse tissues and cell types transcriptomics cell type or tissue 2070
Cancer Cell Line Encyclopedia Cell Line Gene CNV Profiles gene-level copy number variation profiles for cancer cell lines genomics cell line 5029
Cancer Cell Line Encyclopedia Cell Line Gene Expression Profiles mRNA expression profiles for cancer cell lines transcriptomics cell line 15713
Cancer Cell Line Encyclopedia Cell Line Gene Mutation Profiles gene-level mutation profiles for cancer cell lines genomics cell line 4588
ChIP-X Enrichment Analysis Transcription Factor Binding Site Profiles transcription factor binding site profiles from published ChIP-chip, ChIP-seq, and other transcription factor functional studies genomics transcription factor binding site profile 3657
ChIP-X Enrichment Analysis Transcription Factor Targets target genes of transcription factors from published ChIP-chip, ChIP-seq, and other transcription factor binding site profiling studies genomics transcription factor 5762
ClinVar Gene-Phenotype Associations SNP-phenotype associations curated by ClinVar users from various sources disease or phenotype associations phenotype 1222
Connectivity Map Signatures of Differentially Expressed Genes for Small Molecules mRNA expression profiles for cell lines following chemical perturbation transcriptomics small molecule perturbation 2156
COMPARTMENTS Curated Protein Localization Evidence Scores protein subcellular localization evidence scores by manual literature curation structural or functional annotations cellular component 839
COMPARTMENTS Experimental Protein Localization Evidence Scores protein subcellular localization evidence scores by integrating experimental data proteomics cellular component 548
COMPARTMENTS Text-mining Protein Localization Evidence Scores gene-cellular compartment co-occurrence scores from text-mining biomedical abstracts structural or functional annotations cellular component 840
CORUM Protein Complexes proteins participating in complexes by manual literature curation structural or functional annotations protein complex 1424
Catalogue of Somatic Mutations In Cancer Cell Line Gene CNV Profiles gene-level copy number variation profiles for cancer cell lines genomics cell line 1985
Catalogue of Somatic Mutations In Cancer Cell Line Gene Mutation Profiles gene mutations in cancer cell lines from low-throughput or high-throughput studies genomics cell line 4925
Comparative Toxicogenomics Database Gene-Chemical Interactions chemical-gene interactions curated from literature physical interactions chemical 3805
Comparative Toxicogenomics Database Gene-Disease Associations disease-gene interactions curated from literature disease or phenotype associations disease 5448
Database of Genotypes and Phenotypes Gene-Trait Associations gene-trait associations curated from genetic association studies disease or phenotype associations trait 1133
Dephosphorylation Database Substrates of Phosphatases phosphatase-substrate interactions manually curated from literature and databases of protein annotations or protein interactions physical interactions phosphatase 461
DISEASES Curated Gene-Disease Assocation Evidence Scores disease gene evidence scores by manual literature curation disease or phenotype associations disease 1397
DISEASES Experimental Gene-Disease Assocation Evidence Scores disease gene evidence scores by integrating experimental data (GWAS) disease or phenotype associations disease 1410
DISEASES Text-mining Gene-Disease Assocation Evidence Scores gene-disease co-occurrence scores from text-mining biomedical abstracts disease or phenotype associations disease 6012
DrugBank Drug Targets targets of drugs by manual literature curation physical interactions drug 3455
Encyclopedia of DNA Elements Histone Modification Site Profiles histone modification profiles for cell lines genomics histone modification site profile 941
Encyclopedia of DNA Elements Transcription Factor Binding Site Profiles transcription factor binding site profiles for cell lines genomics transcription factor binding site profile 2380
Encyclopedia of DNA Elements Transcription Factor Targets target genes of transcription factors from transcription factor binding site profiles genomics transcription factor 11916
ESCAPE Omics Signatures of Genes and Proteins for Stem Cells sets of target genes of transcription factors from published ChIP-chip, ChIP-seq, and other transcription factor binding site profiling studies;sets of differentially expressed genes following perturbation of a protein from gene expression data in GEO; sets of interacting proteins from high- and low-throughput protein-protein interaction studies; sets of targets of microRNAs from public databases, computationally predicted or experimentally verified transcriptomics PubMedID 847
Genetic Association Database Gene-Disease Associations gene-disease associations curated from genetic association studies disease or phenotype associations disease 3275
Genetic Association Database High Level Gene-Disease Associations gene-disease associations curated from genetic association studies disease or phenotype associations disease 697
Genomics of Drug Sensitivity in Cancer Cell Line Gene Expression Profiles mRNA expression profiles for cancer cell lines transcriptomics cell line 2802
Gene Reference Into Function Biological Term Annotations statements describing functions of genes distilled from biomedical publications structural or functional annotations biological term 1419
GeneSigDB Published Gene Signatures gene signatures reported in the literature that were derived from analysis of transcriptomic or proteomic data transcriptomics PubMedID 769
Gene Expression Omnibus Signatures of Differentially Expressed Genes for Diseases mRNA expression profiles for cell lines or tissues following disease perturbation transcriptomics disease perturbation 1920
Gene Expression Omnibus Signatures of Differentially Expressed Genes for Gene Perturbations mRNA expression profiles for cell lines or tissues following genetic perturbation (knockdown, knockout, over-expression, mutation) transcriptomics gene perturbation 1243
Gene Expression Omnibus Signatures of Differentially Expressed Genes for Kinase Perturbations mRNA expression profiles for cell lines or tissues following kinase perturbation (inhibition, activation, knockdown, knockout, over-expression, mutation) transcriptomics kinase perturbation 1695
Gene Expression Omnibus Signatures of Differentially Expressed Genes for Small Molecules mRNA expression profiles for cell lines or tissues following small molecule perturbation transcriptomics small molecule perturbation 1024
Gene Expression Omnibus Signatures of Differentially Expressed Genes for Transcription Factor Perturbations mRNA expression profiles for cell lines or tissues following transcription factor perturbation (inhibition, activation, knockdown, knockout, over-expression, mutation) transcriptomics transcription factor perturbation 1311
Gene Expression Omnibus Signatures of Differentially Expressed Genes for Viral Infections mRNA expression profiles for cell lines or tissues following viral infection transcriptomics virus perturbation 1184
Gene Ontology Biological Process Annotations curated annotations of genes with biological processes structural or functional annotations biological process 1310
Gene Ontology Cellular Component Annotations curated annotations of genes with cellular components structural or functional annotations cellular component 635
Gene Ontology Molecular Function Annotations curated annotations of genes with molecular functions structural or functional annotations molecular function 975
Genotype Tissue Expression eQTL significance values for all gene-SNP pairs testing likelihood that SNP affects gene expression genomics SNP 929
Genotype Tissue Expression Tissue Gene Expression Profiles mRNA expression profiles for tissues transcriptomics tissue 2234
Genotype Tissue Expression Tissue Sample Gene Expression Profiles mRNA expression profiles for tissue samples transcriptomics tissue sample 955
Guide to Pharmacology Chemical Ligands of Receptors ligand-receptor interactions curated by experts physical interactions ligand (chemical) 1313
Guide to Pharmacology Protein Ligands of Receptors ligand-receptor interactions curated by experts physical interactions ligand (protein) 423
GWAS Catalog SNP-Phenotype Associations SNP-phenotype association p-values curated from published GWAS disease or phenotype associations phenotype 1224
GWASdb SNP-Disease Associations SNP-disease association p-values curated from published GWAS disease or phenotype associations disease 2231
GWASdb SNP-Phenotype Associations SNP-phenotype association p-values curated from published GWAS disease or phenotype associations phenotype 1315
Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles mRNA expression profiles for breast cancer cell lines measured by microarray transcriptomics cell line 918
Human Metabolome Database Metabolites of Enzymes biomolecular interactions between metabolites and proteins, such as processing enzymes, curated from literature physical interactions metabolite 773
Human Protein Atlas Cell Line Gene Expression Profiles mRNA expression profiles for cell lines transcriptomics cell line 1824
Human Protein Atlas Tissue Gene Expression Profiles mRNA expression profiles for tissues transcriptomics tissue 1311
Human Protein Atlas Tissue Protein Expression Profiles semiquantitative protein expression profiles for tissues proteomics tissue 626
Human Protein Atlas Tissue Sample Gene Expression Profiles mRNA expression profiles for tissue samples transcriptomics tissue sample 388
Human Proteome Map Cell Type and Tissue Protein Expression Profiles protein expression profiles for tissues and cell types proteomics cell type or tissue 360
Human Phenotype Ontology Gene-Disease Associations phenotype-causing gene mutations of human phenotypes from disease knowledgebases disease or phenotype associations phenotype 5294
Hub Proteins Protein-Protein Interactions sets of proteins interacting with hub proteins physical interactions hub protein 1237
HuGE Navigator Gene-Phenotype Associations gene-phenotype associations extracted from published GWAS by automated text-mining disease or phenotype associations phenotype 2190
HumanCyc Pathways sets of proteins participating in pathways structural or functional annotations pathway 575
InterPro Predicted Protein Domain Annotations protein domains predicted for gene products based on sequence similarity to known domain signatures structural or functional annotations protein domain 1325
Jaspar PWMs Predicted Transcription Factor Targets target genes of transcription factors predicted using known transcription factor binding site motifs genomics transcription factor 2689
Kinase Enrichment Analysis Substrates of Kinases protein substrates of kinases from published low-throughput and high-throughput phosphoproteomics studies physical interactions kinase 920
Kyoto Encyclopedia of Genes and Genomes Pathways sets of proteins participating in pathways structural or functional annotations pathway 1156
LINCS Kinativ Kinase Inhibitor Bioactivity Profiles percent inhibition of kinases by small molecules measured in cell lysates physical interactions chemical bioactivity profile 470
LINCS KinomeScan Kinase Inhibitor Targets kinase inhibitor targets from percent inhibition of kinases by small molecules measured using purified kinases physical interactions small molecule 796
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles gene-level copy number variation profiles for cancer cell lines genomics cell line 1699
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles mRNA expression profiles for cancer cell lines transcriptomics cell line 2385
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Mutation Profiles gene mutations in cancer cell lines genomics cell line 1683
LINCS L1000 Connectivity Map Signatures of Differentially Expressed Genes for Small Molecules mRNA expression profiles for cell lines following small molecule perturbation transcriptomics small molecule perturbation 1512
LOCATE Curated Protein Localization Annotations subcellular localization of proteins from low-throughput or high-throughput protein localization assays proteomics cellular component 408
MiRTarBase microRNA Targets target genes of microRNAs from published experiments physical interactions microRNA 1784
MotifMap Predicted Transcription Factor Targets target genes of transcription factors predicted using known transcription factor binding site motifs genomics transcription factor 2195
Mammalian Phenotype Ontology Gene-Phenotype Associations observed phenotypes of transgenic mice collected from mouse phenotyping studies disease or phenotype associations phenotype 1540
Molecular Signatures Database Cancer Gene Co-expression Modules computational signatures of genes co-expressed with cancer related genes transcriptomics co-expressed gene 1182
Molecular Signatures Database Signatures of Differentially Expressed Genes for Cancer Gene Perturbations oncogenic signatures of genes differentially expressed following cancer gene perturbations transcriptomics gene perturbation 1205
Nuclear Receptor Signaling Atlas Protein Complexes proteins identified in complexes isolated from cultured cells proteomics protein complex 1847
Nuclear Receptor Signaling Atlas Protein-Protein Interactions protein-protein interactions inferred from membership in complexes proteomics interacting protein 1169
Online Mendelian Inheritance in Man Gene-Disease Associations disease- or phenotype-causing gene mutations for heritable human diseases or phenotypes curated from biomedical publications disease or phenotype associations phenotype 3299
PANTHER Pathways sets of proteins participating in pathways structural or functional annotations pathway 793
Pathway Commons Protein-Protein Interactions protein-protein interactions from low-throughput or high-throughput studies aggregated by Pathway Commons from the following databases: Reactome, NCI Pathways, PhosphoSite, HumanCyc, HPRD, PANTHER, DIP, BioGRID, IntAct, BIND, Transfac, MiRTarBase, Drugbank, Recon X, Comparative Toxicogenomics Database, and KEGG physical interactions interacting protein 6521
Phosphosite Textmining Biological Term Annotations occurrence frequencies for biological terms in abstracts of publications describing phosphosites structural or functional annotations biological term 451
PhosphoSitePlus Substrates of Kinases kinase-substrate interactions curated from low-throughput or high-throughput phosphoproteomics studies physical interactions kinase 812
Pathway Interaction Database Pathways sets of proteins participating in pathways structural or functional annotations pathway 1777
Proteomics Database Cell Type and Tissue Protein Expression Profiles protein expression profiles for tissues and cell types reprocessed from many proteomics datasets proteomics cell type or tissue 876
Reactome Pathways sets of proteins participating in pathways structural or functional annotations pathway 1105
Roadmap Epigenomics Cell and Tissue DNA Accessibility Profiles DNA accessibility profiles for primary cell types and tissues genomics cell type or tissue 316
Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles DNA methylation profiles for primary cell types and tissues genomics cell type or tissue 995
Roadmap Epigenomics Cell and Tissue Gene Expression Profiles mRNA expression profiles for primary cell types and tissues transcriptomics cell type or tissue 783
Roadmap Epigenomics Histone Modification Site Profiles histone modification profiles for primary cells and tissues genomics histone modification site profile 627
SILAC Phosphoproteomics Signatures of Differentially Phosphorylated Proteins for Drugs phosphorylation levels of proteins in cell lines following drug treatment proteomics drug perturbation 645
SILAC Phosphoproteomics Signatures of Differentially Phosphorylated Proteins for Gene Perturbations phosphorylation levels of proteins in cell lines following genetic perturbation (knockdown, knockout, over-expression, mutation) proteomics gene perturbation 275
SILAC Phosphoproteomics Signatures of Differentially Phosphorylated Proteins for Protein Ligands phosphorylation levels of proteins in cell lines following ligand treatment proteomics ligand (protein) perturbation 458
TargetScan Predicted Conserved microRNA Targets target genes of microRNAs predicted by searching genes for sites matching conserved miRNA seed regions genomics microRNA 659
The Cancer Genome Atlas Signatures of Differentially Expressed Genes for Tumors mRNA expression profiles for tumor and normal tissue samples transcriptomics tissue sample 1960
TISSUES Curated Tissue Protein Expression Evidence Scores protein tissue expression evidence scores by manual literature curation structural or functional annotations tissue 924
TISSUES Experimental Tissue Protein Expression Evidence Scores protein tissue expression evidence scores by integrating experimental data proteomics tissue 744
TISSUES Text-mining Tissue Protein Expression Evidence Scores gene-tissue co-occurrence scores from text-mining biomedical abstracts structural or functional annotations tissue 2377
TRANSFAC Curated Transcription Factor Targets target genes of transcription factors manually curated from low-throughput or high-throughput transcription factor functional studies genomics transcription factor 3406
TRANSFAC Predicted Transcription Factor Targets target genes of transcription factors predicted using known transcription factor binding site motifs genomics transcription factor 4712
Virus MINT Protein-Viral Protein Interactions interactions between viral and human proteins manually curated from literature physical interactions viral protein 870
Wikipathways Pathways sets of proteins participating in pathways structural or functional annotations pathway 1552
Virus MINT Protein-Virus Interactions interactions between viruses and human proteins manually curated from literature physical interactions virus 521
LOCATE Predicted Protein Localization Annotations subcellular localization of proteins by sequence similarity to localization sequences proteomics cellular component 543
TargetScan Predicted Nonconserved microRNA Targets target genes of microRNAs predicted by searching genes for sites matching nonconserved miRNA seed regions genomics microRNA 533
PhosphoSitePlus Phosphosite-Disease Associations disease-phosphosite associations curated from literature disease or phenotype associations disease 513
Funding