Downloads

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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 20011
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 31423
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 15108
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 7049
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 5760
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 8040
Biocarta Pathways sets of proteins participating in pathways from Biocarta structural or functional annotations pathway 56226
BioGPS Cell Line Gene Expression Profiles mRNA expression profiles for the NCI-60 panel of cancer cell lines transcriptomics cell line 38737
BioGPS Human Cell Type and Tissue Gene Expression Profiles mRNA expression profiles for human tissues and cell types transcriptomics cell type or tissue 16852
BioGPS Mouse Cell Type and Tissue Gene Expression Profiles mRNA expression profiles for mouse tissues and cell types transcriptomics cell type or tissue 17871
Cancer Cell Line Encyclopedia Cell Line Gene CNV Profiles gene-level copy number variation profiles for cancer cell lines genomics cell line 30059
Cancer Cell Line Encyclopedia Cell Line Gene Expression Profiles mRNA microarray expression profiles for cancer cell lines transcriptomics cell line 102675
Cancer Cell Line Encyclopedia Cell Line Gene Mutation Profiles gene-level mutation profiles for cancer cell lines genomics cell line 30489
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 23222
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 62838
ClinVar Gene-Phenotype Associations SNP-phenotype associations curated by ClinVar users from various sources disease or phenotype associations phenotype 9293
Connectivity Map Signatures of Differentially Expressed Genes for Small Molecules mRNA expression profiles for cell lines following chemical perturbation transcriptomics small molecule perturbation 11651
COMPARTMENTS Curated Protein Localization Evidence Scores protein subcellular localization evidence scores by manual literature curation structural or functional annotations cellular component 5563
COMPARTMENTS Experimental Protein Localization Evidence Scores protein subcellular localization evidence scores by integrating experimental data proteomics cellular component 3246
COMPARTMENTS Text-mining Protein Localization Evidence Scores gene-cellular compartment co-occurrence scores from text-mining biomedical abstracts structural or functional annotations cellular component 6163
CORUM Protein Complexes proteins participating in complexes by manual literature curation structural or functional annotations protein complex 12421
Catalogue of Somatic Mutations In Cancer Cell Line Gene CNV Profiles gene-level copy number variation profiles for cancer cell lines genomics cell line 11342
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 22432
Comparative Toxicogenomics Database Gene-Chemical Interactions chemical-gene interactions curated from literature physical interactions chemical 15375
Comparative Toxicogenomics Database Gene-Disease Associations disease-gene interactions from manually curated literature disease or phenotype associations disease 27079
Database of Genotypes and Phenotypes Gene-Trait Associations gene-trait associations curated from genetic association studies disease or phenotype associations trait 6770
Dephosphorylation Database Substrates of Phosphatases phosphatase-substrate interactions manually curated from literature and databases of protein annotations or protein interactions physical interactions phosphatase 3298
DISEASES Curated Gene-Disease Assocation Evidence Scores disease gene evidence scores by manual literature curation disease or phenotype associations disease 6784
DISEASES Experimental Gene-Disease Assocation Evidence Scores disease gene evidence scores by integrating experimental data (GWAS) disease or phenotype associations disease 8939
DISEASES Text-mining Gene-Disease Assocation Evidence Scores gene-disease co-occurrence scores from text-mining biomedical abstracts disease or phenotype associations disease 32061
DrugBank Drug Targets sets of proteins targeted by drugs by manual literature curation physical interactions drug 24020
Encyclopedia of DNA Elements Histone Modification Site Profiles histone site modification profiles for cell lines from ENCODE genomics histone modification site profile 6235
Encyclopedia of DNA Elements Transcription Factor Binding Site Profiles transcription factor binding site profiles for cell lines genomics transcription factor binding site profile 15632
Encyclopedia of DNA Elements Transcription Factor Targets target genes of transcription factors from transcription factor binding site profiles genomics transcription factor 102437
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 4237
Genetic Association Database Gene-Disease Associations gene-disease associations curated from genetic association studies disease or phenotype associations disease 26039
Genetic Association Database High Level Gene-Disease Associations gene-disease associations curated from genetic association studies disease or phenotype associations disease 5673
Genomics of Drug Sensitivity in Cancer Cell Line Gene Expression Profiles mRNA microarray expression profiles for cancer cell lines transcriptomics cell line 13833
Gene Reference Into Function Biological Term Annotations statements describing functions of genes distilled from biomedical publications structural or functional annotations biological term 24429
GeneSigDB Published Gene Signatures gene signatures reported in the literature that were derived from analysis of transcriptomic or proteomic data transcriptomics PubMedID 6260
Gene Expression Omnibus Signatures of Differentially Expressed Genes for Diseases mRNA expression profiles for cell lines or tissues following disease perturbation transcriptomics disease perturbation 11668
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 5930
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 6074
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 4777
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 10166
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 6401
Gene Ontology Biological Process Annotations curated annotations of genes with biological processes structural or functional annotations biological process 10601
Gene Ontology Cellular Component Annotations curated annotations of genes with cellular components structural or functional annotations cellular component 6809
Gene Ontology Molecular Function Annotations curated annotations of genes with molecular functions structural or functional annotations molecular function 6637
Genotype Tissue Expression eQTL significance values for all gene-SNP pairs testing likelihood that SNP affects gene expression genomics SNP 5247
Genotype Tissue Expression Tissue Gene Expression Profiles gene expression profiles for tissues from GTEx by RNA-seq transcriptomics tissue 13108
Genotype Tissue Expression Tissue Sample Gene Expression Profiles RNA-seq gene expression profiles for tissue samples from GTEx transcriptomics tissue sample 7341
Guide to Pharmacology Chemical Ligands of Receptors chemical ligand-receptor interactions curated by experts physical interactions ligand (chemical) 6884
Guide to Pharmacology Protein Ligands of Receptors protein ligand-receptor interactions curated by experts physical interactions ligand (protein) 2728
GWAS Catalog SNP-Phenotype Associations SNP-phenotype association p-values curated from published GWAS disease or phenotype associations phenotype 8655
GWASdb SNP-Disease Associations SNP-disease association p-values curated from published GWAS disease or phenotype associations disease 21478
GWASdb SNP-Phenotype Associations SNP-phenotype association p-values curated from published GWAS disease or phenotype associations phenotype 7497
Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles mRNA expression profiles for breast cancer cell lines measured by microarray transcriptomics cell line 4991
Human Metabolome Database Metabolites of Enzymes biomolecular interactions between metabolites and proteins, such as processing enzymes, curated from literature physical interactions metabolite 6762
Human Protein Atlas Cell Line Gene Expression Profiles RNA-seq gene expression profiles for cell lines from HPA transcriptomics cell line 8696
Human Protein Atlas Tissue Gene Expression Profiles RNA-seq gene expression profiles for tissues from HPA transcriptomics tissue 10702
Human Protein Atlas Tissue Protein Expression Profiles semiquantitative protein expression profiles for tissues proteomics tissue 4228
Human Protein Atlas Tissue Sample Gene Expression Profiles RNA-seq gene expression profiles for tissue samples from HPA transcriptomics tissue sample 2894
Human Proteome Map Cell Type and Tissue Protein Expression Profiles protein expression profiles for tissues and cell types proteomics cell type or tissue 2911
Human Phenotype Ontology Gene-Disease Associations phenotype-causing gene mutations of human phenotypes from disease knowledgebases disease or phenotype associations phenotype 20600
Hub Proteins Protein-Protein Interactions sets of proteins interacting with hub proteins aggregated from data physical interactions hub protein 9513
HuGE Navigator Gene-Phenotype Associations gene-phenotype associations extracted from published GWAS by automated text-mining disease or phenotype associations phenotype 10543
HumanCyc Pathways sets of proteins participating in pathways from HumanCyc structural or functional annotations pathway 3751
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 10493
Jaspar PWMs Predicted Transcription Factor Targets target genes of transcription factors predicted using known transcription factor binding site motifs genomics transcription factor 27014
Kinase Enrichment Analysis Substrates of Kinases protein substrates of kinases from published low-throughput and high-throughput phosphoproteomics studies physical interactions kinase 6828
Kyoto Encyclopedia of Genes and Genomes Pathways sets of proteins participating in pathways from KEGG structural or functional annotations pathway 13150
LINCS Kinativ Kinase Inhibitor Bioactivity Profiles percent inhibition of kinases by small molecules measured in cell lysates physical interactions chemical bioactivity profile 1996
LINCS KinomeScan Kinase Inhibitor Targets kinase inhibitor targets from percent inhibition of kinases by small molecules measured using purified kinases physical interactions small molecule 3711
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles gene-level copy number variation profiles for cancer cell lines genomics cell line 7788
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles RNA-seq gene expression profiles for cancer cell lines transcriptomics cell line 9870
Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Mutation Profiles SNP gene mutations in cancer cell lines identified by microarray genomics cell line 6761
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 10816
LOCATE Curated Protein Localization Annotations subcellular localization of proteins from low-throughput or high-throughput protein localization assays proteomics cellular component 4827
MiRTarBase microRNA Targets target genes of microRNAs from published experiments physical interactions microRNA 14409
MotifMap Predicted Transcription Factor Targets target genes of transcription factors predicted using known transcription factor binding site motifs genomics transcription factor 17901
Mammalian Phenotype Ontology Gene-Phenotype Associations observed phenotypes of transgenic mice collected from mouse phenotyping studies disease or phenotype associations phenotype 10315
Molecular Signatures Database Cancer Gene Co-expression Modules computational signatures of genes co-expressed with cancer related genes transcriptomics co-expressed gene 6169
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 4835
Nuclear Receptor Signaling Atlas Protein Complexes proteins identified in complexes isolated from cultured cells proteomics protein complex 8580
Nuclear Receptor Signaling Atlas Protein-Protein Interactions protein-protein interactions inferred from membership in complexes proteomics interacting protein 6909
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 15600
PANTHER Pathways sets of proteins participating in pathways from PANTHER structural or functional annotations pathway 7432
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 42624
Phosphosite Textmining Biological Term Annotations occurrence frequencies for biological terms in abstracts of publications describing phosphosites structural or functional annotations biological term 2614
PhosphoSitePlus Substrates of Kinases kinase-substrate interactions curated from low-throughput or high-throughput phosphoproteomics studies physical interactions kinase 7798
Pathway Interaction Database Pathways sets of proteins participating in pathways from PID structural or functional annotations pathway 12152
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 9413
Reactome Pathways sets of proteins participating in pathways from Reactome structural or functional annotations pathway 8382
Roadmap Epigenomics Cell and Tissue DNA Accessibility Profiles DNA accessibility profiles for primary cell types and tissues genomics cell type or tissue 1662
Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles DNA methylation profiles for primary cell types and tissues genomics cell type or tissue 4897
Roadmap Epigenomics Cell and Tissue Gene Expression Profiles mRNA expression profiles for primary cell types and tissues transcriptomics cell type or tissue 4334
Roadmap Epigenomics Histone Modification Site Profiles histone modification profiles for primary cells and tissues genomics histone modification site profile 4162
SILAC Phosphoproteomics Signatures of Differentially Phosphorylated Proteins for Drugs phosphorylation levels of proteins in cell lines following drug treatment proteomics drug perturbation 3033
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 1611
SILAC Phosphoproteomics Signatures of Differentially Phosphorylated Proteins for Protein Ligands phosphorylation levels of proteins in cell lines following ligand treatment proteomics ligand (protein) perturbation 2627
TargetScan Predicted Conserved microRNA Targets target genes of microRNAs predicted by searching genes for sites matching conserved miRNA seed regions genomics microRNA 5091
The Cancer Genome Atlas Signatures of Differentially Expressed Genes for Tumors mRNA expression profiles for tumor and normal tissue samples transcriptomics tissue sample 14140
TISSUES Curated Tissue Protein Expression Evidence Scores protein tissue expression evidence scores by manual literature curation structural or functional annotations tissue 6183
TISSUES Experimental Tissue Protein Expression Evidence Scores protein tissue expression evidence scores by integrating experimental data proteomics tissue 4611
TISSUES Text-mining Tissue Protein Expression Evidence Scores gene-tissue co-occurrence scores from text-mining biomedical abstracts structural or functional annotations tissue 14719
Virus MINT Protein-Viral Protein Interactions interactions between viral and human proteins manually curated from literature physical interactions viral protein 4609
Wikipathways Pathways sets of proteins participating in pathways from Wikipathways structural or functional annotations pathway 11267
Virus MINT Protein-Virus Interactions interactions between viruses and human proteins manually curated from literature physical interactions virus 2890
LOCATE Predicted Protein Localization Annotations subcellular localization of proteins by sequence similarity to localization sequences proteomics cellular component 3355
TargetScan Predicted Nonconserved microRNA Targets target genes of microRNAs predicted by searching genes for sites matching nonconserved miRNA seed regions genomics microRNA 5104
PhosphoSitePlus Phosphosite-Disease Associations disease-phosphosite associations curated from literature disease or phenotype associations disease 2313
Sanger Cancer Dependency Map Cancer Cell Line Proteomics Protein intensity values acquired using data-independent acquisition mass spectrometry (DIA-MS). proteomics cell line 318
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 428
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 201
DeepCoverMOA Drug Mechanisms of Action protein expression profiles in HCT116 cell line following drug treatment proteomics small molecule perturbation 334
Tabula Sapiens Gene-Cell Associations gene expression data from Tabula Sapiens scRNA-seq counts transcriptomics cell type 206
DisGeNET Gene-Disease Associations gene-disease associations sourced from curated repositories, GWAS catalogues, animal models and the scientific literature disease or phenotype associations disease 728
DisGeNET Gene-Phenotype Associations gene-phenotype associations sourced from curated repositories, GWAS catalogues, animal models and the scientific literature disease or phenotype associations phenotype 298
Gene Ontology Biological Process Annotations 2023 curated annotations of genes with biological processes structural or functional annotations biological process 392
Gene Ontology Cellular Component Annotations 2023 curated annotations of genes with cellular components structural or functional annotations cellular component 140
Gene Ontology Molecular Function Annotations 2023 curated annotations of genes with molecular functions structural or functional annotations molecular function 185
Wikipathways PFOCR sets of genes extracted from pathway figure using optical character recognition structural or functional annotations pathway 403
Funding