Downloads

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Resource Dataset Description Category Attribute Views Archived
Achilles Cell Line Gene Essentiality Profiles fitness scores for cell lines following single gene knockdowns disease or phenotype associations cell line 23607 false
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 36555 false
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 18306 false
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 9010 false
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 7891 false
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 9588 false
Biocarta Pathways sets of proteins participating in pathways from Biocarta structural or functional annotations pathway 68800 false
BioGPS Cell Line Gene Expression Profiles mRNA expression profiles for the NCI-60 panel of cancer cell lines transcriptomics cell line 45313 false
BioGPS Human Cell Type and Tissue Gene Expression Profiles mRNA expression profiles for human tissues and cell types transcriptomics cell type or tissue 19753 false
BioGPS Mouse Cell Type and Tissue Gene Expression Profiles mRNA expression profiles for mouse tissues and cell types transcriptomics cell type or tissue 22665 false
Cancer Cell Line Encyclopedia Cell Line Gene CNV Profiles gene-level copy number variation profiles for cancer cell lines genomics cell line 34828 false
Cancer Cell Line Encyclopedia Cell Line Gene Expression Profiles mRNA microarray expression profiles for cancer cell lines transcriptomics cell line 114519 false
Cancer Cell Line Encyclopedia Cell Line Gene Mutation Profiles gene-level mutation profiles for cancer cell lines genomics cell line 35104 false
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 28394 true
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 83283 false
ClinVar Gene-Phenotype Associations SNP-phenotype associations curated by ClinVar users from various sources disease or phenotype associations phenotype 11929 false
Connectivity Map Signatures of Differentially Expressed Genes for Small Molecules mRNA expression profiles for cell lines following chemical perturbation transcriptomics small molecule perturbation 13873 false
COMPARTMENTS Curated Protein Localization Evidence Scores protein subcellular localization evidence scores by manual literature curation structural or functional annotations cellular component 7006 false
COMPARTMENTS Experimental Protein Localization Evidence Scores protein subcellular localization evidence scores by integrating experimental data proteomics cellular component 4155 false
COMPARTMENTS Text-mining Protein Localization Evidence Scores gene-cellular compartment co-occurrence scores from text-mining biomedical abstracts structural or functional annotations cellular component 8606 false
CORUM Protein Complexes proteins participating in complexes by manual literature curation structural or functional annotations protein complex 16122 false
Catalogue of Somatic Mutations In Cancer Cell Line Gene CNV Profiles gene-level copy number variation profiles for cancer cell lines genomics cell line 13689 false
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 25756 false
Comparative Toxicogenomics Database Gene-Chemical Interactions chemical-gene interactions curated from literature physical interactions chemical 18170 false
Comparative Toxicogenomics Database Gene-Disease Associations disease-gene interactions from manually curated literature disease or phenotype associations disease 31237 false
Database of Genotypes and Phenotypes Gene-Trait Associations gene-trait associations curated from genetic association studies disease or phenotype associations trait 8240 false
Dephosphorylation Database Substrates of Phosphatases phosphatase-substrate interactions manually curated from literature and databases of protein annotations or protein interactions physical interactions phosphatase 4140 false
DISEASES Curated Gene-Disease Assocation Evidence Scores disease gene evidence scores by manual literature curation disease or phenotype associations disease 8214 false
DISEASES Experimental Gene-Disease Assocation Evidence Scores disease gene evidence scores by integrating experimental data (GWAS) disease or phenotype associations disease 10963 false
DISEASES Text-mining Gene-Disease Assocation Evidence Scores gene-disease co-occurrence scores from text-mining biomedical abstracts disease or phenotype associations disease 35549 false
DrugBank Drug Targets sets of proteins targeted by drugs by manual literature curation physical interactions drug 27827 false
Encyclopedia of DNA Elements Histone Modification Site Profiles histone site modification profiles for cell lines from ENCODE genomics histone modification site profile 8595 false
Encyclopedia of DNA Elements Transcription Factor Binding Site Profiles transcription factor binding site profiles for cell lines genomics transcription factor binding site profile 19438 false
Encyclopedia of DNA Elements Transcription Factor Targets target genes of transcription factors from transcription factor binding site profiles genomics transcription factor 124812 false
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 5738 false
Genetic Association Database Gene-Disease Associations gene-disease associations curated from genetic association studies disease or phenotype associations disease 33132 false
Genetic Association Database High Level Gene-Disease Associations gene-disease associations curated from genetic association studies disease or phenotype associations disease 7046 false
Genomics of Drug Sensitivity in Cancer Cell Line Gene Expression Profiles mRNA microarray expression profiles for cancer cell lines transcriptomics cell line 16432 false
Gene Reference Into Function Biological Term Annotations statements describing functions of genes distilled from biomedical publications structural or functional annotations biological term 29221 false
GeneSigDB Published Gene Signatures gene signatures reported in the literature that were derived from analysis of transcriptomic or proteomic data transcriptomics PubMedID 8052 false
Gene Expression Omnibus Signatures of Differentially Expressed Genes for Diseases mRNA expression profiles for cell lines or tissues following disease perturbation transcriptomics disease perturbation 14354 false
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 7945 false
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 7880 false
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 6550 false
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 12431 false
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 8356 false
Gene Ontology Biological Process Annotations curated annotations of genes with biological processes structural or functional annotations biological process 13593 true
Gene Ontology Cellular Component Annotations curated annotations of genes with cellular components structural or functional annotations cellular component 8556 true
Gene Ontology Molecular Function Annotations curated annotations of genes with molecular functions structural or functional annotations molecular function 8049 true
Genotype Tissue Expression eQTL significance values for all gene-SNP pairs testing likelihood that SNP affects gene expression genomics SNP 6672 false
Genotype Tissue Expression Tissue Gene Expression Profiles gene expression profiles for tissues from GTEx by RNA-seq transcriptomics tissue 15412 true
Genotype Tissue Expression Tissue Sample Gene Expression Profiles RNA-seq gene expression profiles for tissue samples from GTEx transcriptomics tissue sample 9836 false
Guide to Pharmacology Chemical Ligands of Receptors chemical ligand-receptor interactions curated by experts physical interactions ligand (chemical) 8914 false
Guide to Pharmacology Protein Ligands of Receptors protein ligand-receptor interactions curated by experts physical interactions ligand (protein) 3026 false
GWAS Catalog SNP-Phenotype Associations SNP-phenotype association p-values curated from published GWAS disease or phenotype associations phenotype 10397 false
GWASdb SNP-Disease Associations SNP-disease association p-values curated from published GWAS disease or phenotype associations disease 26672 false
GWASdb SNP-Phenotype Associations SNP-phenotype association p-values curated from published GWAS disease or phenotype associations phenotype 9816 false
Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles mRNA expression profiles for breast cancer cell lines measured by microarray transcriptomics cell line 6126 false
Human Metabolome Database Metabolites of Enzymes biomolecular interactions between metabolites and proteins, such as processing enzymes, curated from literature physical interactions metabolite 9594 false
Human Protein Atlas Cell Line Gene Expression Profiles RNA-seq gene expression profiles for cell lines from HPA transcriptomics cell line 10546 false
Human Protein Atlas Tissue Gene Expression Profiles RNA-seq gene expression profiles for tissues from HPA transcriptomics tissue 12580 false
Human Protein Atlas Tissue Protein Expression Profiles semiquantitative protein expression profiles for tissues proteomics tissue 5449 false
Human Protein Atlas Tissue Sample Gene Expression Profiles RNA-seq gene expression profiles for tissue samples from HPA transcriptomics tissue sample 4414 false
Human Proteome Map Cell Type and Tissue Protein Expression Profiles protein expression profiles for tissues and cell types proteomics cell type or tissue 3897 false
Human Phenotype Ontology Gene-Disease Associations phenotype-causing gene mutations of human phenotypes from disease knowledgebases disease or phenotype associations phenotype 24439 false
Hub Proteins Protein-Protein Interactions sets of proteins interacting with hub proteins aggregated from data physical interactions hub protein 11793 false
HuGE Navigator Gene-Phenotype Associations gene-phenotype associations extracted from published GWAS by automated text-mining disease or phenotype associations phenotype 13198 false
HumanCyc Pathways sets of proteins participating in pathways from HumanCyc structural or functional annotations pathway 4821 false
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 13480 false
Jaspar PWMs Predicted Transcription Factor Targets target genes of transcription factors predicted using known transcription factor binding site motifs genomics transcription factor 35911 false
Kinase Enrichment Analysis Substrates of Kinases protein substrates of kinases from published low-throughput and high-throughput phosphoproteomics studies physical interactions kinase 8893 false
Kyoto Encyclopedia of Genes and Genomes Pathways sets of proteins participating in pathways from KEGG structural or functional annotations pathway 16422 false
LINCS Kinativ Kinase Inhibitor Bioactivity Profiles percent inhibition of kinases by small molecules measured in cell lysates physical interactions chemical bioactivity profile 2727 false
LINCS KinomeScan Kinase Inhibitor Targets kinase inhibitor targets from percent inhibition of kinases by small molecules measured using purified kinases physical interactions small molecule 5078 false
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles gene-level copy number variation profiles for cancer cell lines genomics cell line 8564 false
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles RNA-seq gene expression profiles for cancer cell lines transcriptomics cell line 12739 false
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Mutation Profiles SNP gene mutations in cancer cell lines identified by microarray genomics cell line 8127 false
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 13601 true
LOCATE Curated Protein Localization Annotations subcellular localization of proteins from low-throughput or high-throughput protein localization assays proteomics cellular component 6310 false
MiRTarBase microRNA Targets target genes of microRNAs from published experiments physical interactions microRNA 16447 false
MotifMap Predicted Transcription Factor Targets target genes of transcription factors predicted using known transcription factor binding site motifs genomics transcription factor 23636 false
Mammalian Phenotype Ontology Gene-Phenotype Associations observed phenotypes of transgenic mice collected from mouse phenotyping studies disease or phenotype associations phenotype 13297 true
Molecular Signatures Database Cancer Gene Co-expression Modules computational signatures of genes co-expressed with cancer related genes transcriptomics co-expressed gene 7640 false
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 6567 false
Nuclear Receptor Signaling Atlas Protein Complexes proteins identified in complexes isolated from cultured cells proteomics protein complex 10968 false
Nuclear Receptor Signaling Atlas Protein-Protein Interactions protein-protein interactions inferred from membership in complexes proteomics interacting protein 8222 false
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 18402 false
PANTHER Pathways sets of proteins participating in pathways from PANTHER structural or functional annotations pathway 9362 false
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 50307 false
Phosphosite Textmining Biological Term Annotations occurrence frequencies for biological terms in abstracts of publications describing phosphosites structural or functional annotations biological term 3309 false
PhosphoSitePlus Substrates of Kinases kinase-substrate interactions curated from low-throughput or high-throughput phosphoproteomics studies physical interactions kinase 9831 false
Pathway Interaction Database Pathways sets of proteins participating in pathways from PID structural or functional annotations pathway 14625 false
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 11884 false
Reactome Pathways sets of proteins participating in pathways from Reactome structural or functional annotations pathway 11723 false
Roadmap Epigenomics Cell and Tissue DNA Accessibility Profiles DNA accessibility profiles for primary cell types and tissues genomics cell type or tissue 2580 false
Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles DNA methylation profiles for primary cell types and tissues genomics cell type or tissue 8332 false
Roadmap Epigenomics Cell and Tissue Gene Expression Profiles mRNA expression profiles for primary cell types and tissues transcriptomics cell type or tissue 5843 false
Roadmap Epigenomics Histone Modification Site Profiles histone modification profiles for primary cells and tissues genomics histone modification site profile 6101 false
SILAC Phosphoproteomics Signatures of Differentially Phosphorylated Proteins for Drugs phosphorylation levels of proteins in cell lines following drug treatment proteomics drug perturbation 3919 false
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 2521 false
SILAC Phosphoproteomics Signatures of Differentially Phosphorylated Proteins for Protein Ligands phosphorylation levels of proteins in cell lines following ligand treatment proteomics ligand (protein) perturbation 3292 false
TargetScan Predicted Conserved microRNA Targets target genes of microRNAs predicted by searching genes for sites matching conserved miRNA seed regions genomics microRNA 6296 false
The Cancer Genome Atlas Signatures of Differentially Expressed Genes for Tumors mRNA expression profiles for tumor and normal tissue samples transcriptomics tissue sample 16725 false
TISSUES Curated Tissue Protein Expression Evidence Scores protein tissue expression evidence scores by manual literature curation structural or functional annotations tissue 8097 false
TISSUES Experimental Tissue Protein Expression Evidence Scores protein tissue expression evidence scores by integrating experimental data proteomics tissue 6361 false
TISSUES Text-mining Tissue Protein Expression Evidence Scores gene-tissue co-occurrence scores from text-mining biomedical abstracts structural or functional annotations tissue 18833 false
Virus MINT Protein-Viral Protein Interactions interactions between viral and human proteins manually curated from literature physical interactions viral protein 5951 false
Wikipathways Pathways sets of proteins participating in pathways from Wikipathways structural or functional annotations pathway 13302 false
Virus MINT Protein-Virus Interactions interactions between viruses and human proteins manually curated from literature physical interactions virus 3865 false
LOCATE Predicted Protein Localization Annotations subcellular localization of proteins by sequence similarity to localization sequences proteomics cellular component 4431 false
TargetScan Predicted Nonconserved microRNA Targets target genes of microRNAs predicted by searching genes for sites matching nonconserved miRNA seed regions genomics microRNA 6251 false
PhosphoSitePlus Phosphosite-Disease Associations disease-phosphosite associations curated from literature disease or phenotype associations disease 3512 false
Sanger Cancer Dependency Map Cancer Cell Line Proteomics Protein intensity values acquired using data-independent acquisition mass spectrometry (DIA-MS). proteomics cell line 1551 false
knockTF Gene Expression Profiles with Transcription Factor Perturtbations Gene expression profiles for cell lines or tissues following transcription factor perturbation (knockdown/knockout) transcriptomics transcription factor perturbation 1789 false
Kinase Library Serine Threonine Kinome Atlas A phosphoproteomics atlas detailing phosphorylation of protein substrates by 303 serine/threonine kinases in the human kinome. proteomics kinase 1302 false
DeepCoverMOA Drug Mechanisms of Action protein expression profiles in HCT116 cell line following drug treatment proteomics small molecule perturbation 1548 false
Tabula Sapiens Gene-Cell Associations gene expression data from Tabula Sapiens scRNA-seq counts transcriptomics cell type 1004 false
DisGeNET Gene-Disease Associations gene-disease associations sourced from curated repositories, GWAS catalogues, animal models and the scientific literature disease or phenotype associations disease 2827 false
DisGeNET Gene-Phenotype Associations gene-phenotype associations sourced from curated repositories, GWAS catalogues, animal models and the scientific literature disease or phenotype associations phenotype 1615 false
Gene Ontology Biological Process Annotations 2023 curated annotations of genes with biological processes structural or functional annotations biological process 2291 false
Gene Ontology Cellular Component Annotations 2023 curated annotations of genes with cellular components structural or functional annotations cellular component 1252 false
Gene Ontology Molecular Function Annotations 2023 curated annotations of genes with molecular functions structural or functional annotations molecular function 1344 false
Wikipathways PFOCR sets of genes extracted from pathway figure using optical character recognition structural or functional annotations pathway 1590 false
Cancer Cell Line Encyclopedia Cell Line Proteomics Protein intensity values acquired using mass spectrometry across human cancerous cell lines proteomics cell line 273 false
Cancer Dependency Map CRISPR Gene Dependency dependency scores for cell lines following single gene knockdowns disease or phenotype associations cell line 315 false
ChIP-X Enrichment Analysis Transcription Factor Binding Site Profiles 2022 transcription factor binding site profiles from published ChIP-chip, ChIP-seq, and other transcription factor functional studies genomics transcription factor binding site profile 574 false
Mammalian Phenotype Ontology Mouse Phenotype Associations 2023 observed phenotypes of transgenic mice collected from mouse phenotyping studies disease or phenotype associations phenotype 261 false
LINCS L1000 Connectivity Map CRISPR Knockout Consensus Signatures gene association consensus signatures following CRISPR gene knockout transcriptomics gene perturbation 420 false
Molecular Transducers of Physical Activity Consortium Rat Endurance Exercise Training Transcriptomics RNA-seq gene expression profiles for rat tissue samples across 4 time points and 19 tissues transcriptomics tissue sample 83 false
GlyGen Glycosylated Proteins proteins glycosylated by saccharide ligands from glycosylation site citations proteomics glycan 148 false
International Mouse Phenotyping Consortium Knockout Mouse Phenotypes observed phenotypes of mice following gene knockout disease or phenotype associations phenotype 168 false
Metabolomics Workbench Gene Metabolite Associations biomolecular interactions between metabolites and proteinscurated from experimental studies physical interactions metabolite 109 false
LINCS L1000 Connectivity Map Chemical Perturbations Consensus Signatures gene association consensus signatures following small molecule perturbation transcriptomics small molecule perturbation 282 false
Genotype Tissue Expression Tissue Gene Expression Profiles 2023 gene expression profiles for tissues from GEx by RNA-seq transcriptomics tissue 139 false
Genotype Tissue Expression Tissue-Specific Aging Signatures tissue-specific aging signatures createed from GTEx RNA-seq gene expression profiles transcriptomics tissue sample 139 false
The Human BioMolecular Atlas Program Azimuth Cell Type Annotations gene-cell type annotations from integrated reference scRNA-seq gene expression profiles transcriptomics cell type 146 false
SynGO Synaptic Gene Annotations curated annotations of genes with synaptic terms structural or functional annotations biological term 180 false
CellMarker Gene-Cell Type Associations cell type markers across various tissues from human and mouse scRNA-seq transcriptomics cell type 406 false