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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 | 5241 |
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 | 7524 |
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 | 2975 |
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 | 1840 |
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 | 1291 |
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 | 2222 |
Biocarta | Pathways | sets of proteins participating in pathways | structural or functional annotations | pathway | 6116 |
BioGPS | Cell Line Gene Expression Profiles | mRNA expression profiles for the NCI-60 panel of cancer cell lines | transcriptomics | cell line | 7929 |
BioGPS | Human Cell Type and Tissue Gene Expression Profiles | mRNA expression profiles for human tissues and cell types | transcriptomics | cell type or tissue | 3897 |
BioGPS | Mouse Cell Type and Tissue Gene Expression Profiles | mRNA expression profiles for mouse tissues and cell types | transcriptomics | cell type or tissue | 2958 |
Cancer Cell Line Encyclopedia | Cell Line Gene CNV Profiles | gene-level copy number variation profiles for cancer cell lines | genomics | cell line | 6996 |
Cancer Cell Line Encyclopedia | Cell Line Gene Expression Profiles | mRNA expression profiles for cancer cell lines | transcriptomics | cell line | 22891 |
Cancer Cell Line Encyclopedia | Cell Line Gene Mutation Profiles | gene-level mutation profiles for cancer cell lines | genomics | cell line | 6659 |
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 | 4769 |
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 | 8194 |
ClinVar | Gene-Phenotype Associations | SNP-phenotype associations curated by ClinVar users from various sources | disease or phenotype associations | phenotype | 1605 |
Connectivity Map | Signatures of Differentially Expressed Genes for Small Molecules | mRNA expression profiles for cell lines following chemical perturbation | transcriptomics | small molecule perturbation | 2748 |
COMPARTMENTS | Curated Protein Localization Evidence Scores | protein subcellular localization evidence scores by manual literature curation | structural or functional annotations | cellular component | 1092 |
COMPARTMENTS | Experimental Protein Localization Evidence Scores | protein subcellular localization evidence scores by integrating experimental data | proteomics | cellular component | 716 |
COMPARTMENTS | Text-mining Protein Localization Evidence Scores | gene-cellular compartment co-occurrence scores from text-mining biomedical abstracts | structural or functional annotations | cellular component | 1140 |
CORUM | Protein Complexes | proteins participating in complexes by manual literature curation | structural or functional annotations | protein complex | 1927 |
Catalogue of Somatic Mutations In Cancer | Cell Line Gene CNV Profiles | gene-level copy number variation profiles for cancer cell lines | genomics | cell line | 2647 |
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 | 7277 |
Comparative Toxicogenomics Database | Gene-Chemical Interactions | chemical-gene interactions curated from literature | physical interactions | chemical | 4515 |
Comparative Toxicogenomics Database | Gene-Disease Associations | disease-gene interactions curated from literature | disease or phenotype associations | disease | 7018 |
Database of Genotypes and Phenotypes | Gene-Trait Associations | gene-trait associations curated from genetic association studies | disease or phenotype associations | trait | 1475 |
Dephosphorylation Database | Substrates of Phosphatases | phosphatase-substrate interactions manually curated from literature and databases of protein annotations or protein interactions | physical interactions | phosphatase | 613 |
DISEASES | Curated Gene-Disease Assocation Evidence Scores | disease gene evidence scores by manual literature curation | disease or phenotype associations | disease | 1852 |
DISEASES | Experimental Gene-Disease Assocation Evidence Scores | disease gene evidence scores by integrating experimental data (GWAS) | disease or phenotype associations | disease | 1995 |
DISEASES | Text-mining Gene-Disease Assocation Evidence Scores | gene-disease co-occurrence scores from text-mining biomedical abstracts | disease or phenotype associations | disease | 7941 |
DrugBank | Drug Targets | targets of drugs by manual literature curation | physical interactions | drug | 4656 |
Encyclopedia of DNA Elements | Histone Modification Site Profiles | histone modification profiles for cell lines | genomics | histone modification site profile | 1202 |
Encyclopedia of DNA Elements | Transcription Factor Binding Site Profiles | transcription factor binding site profiles for cell lines | genomics | transcription factor binding site profile | 3081 |
Encyclopedia of DNA Elements | Transcription Factor Targets | target genes of transcription factors from transcription factor binding site profiles | genomics | transcription factor | 17027 |
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 | 1039 |
Genetic Association Database | Gene-Disease Associations | gene-disease associations curated from genetic association studies | disease or phenotype associations | disease | 4645 |
Genetic Association Database | High Level Gene-Disease Associations | gene-disease associations curated from genetic association studies | disease or phenotype associations | disease | 960 |
Genomics of Drug Sensitivity in Cancer | Cell Line Gene Expression Profiles | mRNA expression profiles for cancer cell lines | transcriptomics | cell line | 3469 |
Gene Reference Into Function | Biological Term Annotations | statements describing functions of genes distilled from biomedical publications | structural or functional annotations | biological term | 2506 |
GeneSigDB | Published Gene Signatures | gene signatures reported in the literature that were derived from analysis of transcriptomic or proteomic data | transcriptomics | PubMedID | 997 |
Gene Expression Omnibus | Signatures of Differentially Expressed Genes for Diseases | mRNA expression profiles for cell lines or tissues following disease perturbation | transcriptomics | disease perturbation | 2594 |
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 | 1557 |
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 | 2113 |
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 | 1285 |
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 | 1740 |
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 | 1488 |
Gene Ontology | Biological Process Annotations | curated annotations of genes with biological processes | structural or functional annotations | biological process | 1682 |
Gene Ontology | Cellular Component Annotations | curated annotations of genes with cellular components | structural or functional annotations | cellular component | 832 |
Gene Ontology | Molecular Function Annotations | curated annotations of genes with molecular functions | structural or functional annotations | molecular function | 1275 |
Genotype Tissue Expression | eQTL | significance values for all gene-SNP pairs testing likelihood that SNP affects gene expression | genomics | SNP | 1188 |
Genotype Tissue Expression | Tissue Gene Expression Profiles | mRNA expression profiles for tissues | transcriptomics | tissue | 3157 |
Genotype Tissue Expression | Tissue Sample Gene Expression Profiles | mRNA expression profiles for tissue samples | transcriptomics | tissue sample | 1203 |
Guide to Pharmacology | Chemical Ligands of Receptors | ligand-receptor interactions curated by experts | physical interactions | ligand (chemical) | 1747 |
Guide to Pharmacology | Protein Ligands of Receptors | ligand-receptor interactions curated by experts | physical interactions | ligand (protein) | 526 |
GWAS Catalog | SNP-Phenotype Associations | SNP-phenotype association p-values curated from published GWAS | disease or phenotype associations | phenotype | 1707 |
GWASdb | SNP-Disease Associations | SNP-disease association p-values curated from published GWAS | disease or phenotype associations | disease | 3199 |
GWASdb | SNP-Phenotype Associations | SNP-phenotype association p-values curated from published GWAS | disease or phenotype associations | phenotype | 1732 |
Heiser et al., PNAS, 2011 | Cell Line Gene Expression Profiles | mRNA expression profiles for breast cancer cell lines measured by microarray | transcriptomics | cell line | 1182 |
Human Metabolome Database | Metabolites of Enzymes | biomolecular interactions between metabolites and proteins, such as processing enzymes, curated from literature | physical interactions | metabolite | 1006 |
Human Protein Atlas | Cell Line Gene Expression Profiles | mRNA expression profiles for cell lines | transcriptomics | cell line | 2387 |
Human Protein Atlas | Tissue Gene Expression Profiles | mRNA expression profiles for tissues | transcriptomics | tissue | 2190 |
Human Protein Atlas | Tissue Protein Expression Profiles | semiquantitative protein expression profiles for tissues | proteomics | tissue | 908 |
Human Protein Atlas | Tissue Sample Gene Expression Profiles | mRNA expression profiles for tissue samples | transcriptomics | tissue sample | 523 |
Human Proteome Map | Cell Type and Tissue Protein Expression Profiles | protein expression profiles for tissues and cell types | proteomics | cell type or tissue | 480 |
Human Phenotype Ontology | Gene-Disease Associations | phenotype-causing gene mutations of human phenotypes from disease knowledgebases | disease or phenotype associations | phenotype | 6521 |
Hub Proteins | Protein-Protein Interactions | sets of proteins interacting with hub proteins | physical interactions | hub protein | 1717 |
HuGE Navigator | Gene-Phenotype Associations | gene-phenotype associations extracted from published GWAS by automated text-mining | disease or phenotype associations | phenotype | 2862 |
HumanCyc | Pathways | sets of proteins participating in pathways | structural or functional annotations | pathway | 790 |
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 | 1766 |
Jaspar PWMs | Predicted Transcription Factor Targets | target genes of transcription factors predicted using known transcription factor binding site motifs | genomics | transcription factor | 3644 |
Kinase Enrichment Analysis | Substrates of Kinases | protein substrates of kinases from published low-throughput and high-throughput phosphoproteomics studies | physical interactions | kinase | 1321 |
Kyoto Encyclopedia of Genes and Genomes | Pathways | sets of proteins participating in pathways | structural or functional annotations | pathway | 1574 |
LINCS Kinativ | Kinase Inhibitor Bioactivity Profiles | percent inhibition of kinases by small molecules measured in cell lysates | physical interactions | chemical bioactivity profile | 591 |
LINCS KinomeScan | Kinase Inhibitor Targets | kinase inhibitor targets from percent inhibition of kinases by small molecules measured using purified kinases | physical interactions | small molecule | 968 |
Klijn et al., Nat. Biotechnol., 2015 | Cell Line Gene CNV Profiles | gene-level copy number variation profiles for cancer cell lines | genomics | cell line | 2258 |
Klijn et al., Nat. Biotechnol., 2015 | Cell Line Gene Expression Profiles | mRNA expression profiles for cancer cell lines | transcriptomics | cell line | 3047 |
Klijn et al., Nat. Biotechnol., 2015 | Cell Line Gene Mutation Profiles | gene mutations in cancer cell lines | genomics | cell line | 2173 |
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 | 2112 |
LOCATE | Curated Protein Localization Annotations | subcellular localization of proteins from low-throughput or high-throughput protein localization assays | proteomics | cellular component | 592 |
MiRTarBase | microRNA Targets | target genes of microRNAs from published experiments | physical interactions | microRNA | 2262 |
MotifMap | Predicted Transcription Factor Targets | target genes of transcription factors predicted using known transcription factor binding site motifs | genomics | transcription factor | 2848 |
Mammalian Phenotype Ontology | Gene-Phenotype Associations | observed phenotypes of transgenic mice collected from mouse phenotyping studies | disease or phenotype associations | phenotype | 1923 |
Molecular Signatures Database | Cancer Gene Co-expression Modules | computational signatures of genes co-expressed with cancer related genes | transcriptomics | co-expressed gene | 1592 |
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 | 1509 |
Nuclear Receptor Signaling Atlas | Protein Complexes | proteins identified in complexes isolated from cultured cells | proteomics | protein complex | 2333 |
Nuclear Receptor Signaling Atlas | Protein-Protein Interactions | protein-protein interactions inferred from membership in complexes | proteomics | interacting protein | 1525 |
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 | 4154 |
PANTHER | Pathways | sets of proteins participating in pathways | structural or functional annotations | pathway | 1168 |
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 | 8449 |
Phosphosite Textmining | Biological Term Annotations | occurrence frequencies for biological terms in abstracts of publications describing phosphosites | structural or functional annotations | biological term | 567 |
PhosphoSitePlus | Substrates of Kinases | kinase-substrate interactions curated from low-throughput or high-throughput phosphoproteomics studies | physical interactions | kinase | 1102 |
Pathway Interaction Database | Pathways | sets of proteins participating in pathways | structural or functional annotations | pathway | 2452 |
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 | 1205 |
Reactome | Pathways | sets of proteins participating in pathways | structural or functional annotations | pathway | 1436 |
Roadmap Epigenomics | Cell and Tissue DNA Accessibility Profiles | DNA accessibility profiles for primary cell types and tissues | genomics | cell type or tissue | 373 |
Roadmap Epigenomics | Cell and Tissue DNA Methylation Profiles | DNA methylation profiles for primary cell types and tissues | genomics | cell type or tissue | 1190 |
Roadmap Epigenomics | Cell and Tissue Gene Expression Profiles | mRNA expression profiles for primary cell types and tissues | transcriptomics | cell type or tissue | 1055 |
Roadmap Epigenomics | Histone Modification Site Profiles | histone modification profiles for primary cells and tissues | genomics | histone modification site profile | 765 |
SILAC Phosphoproteomics | Signatures of Differentially Phosphorylated Proteins for Drugs | phosphorylation levels of proteins in cell lines following drug treatment | proteomics | drug perturbation | 803 |
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 | 340 |
SILAC Phosphoproteomics | Signatures of Differentially Phosphorylated Proteins for Protein Ligands | phosphorylation levels of proteins in cell lines following ligand treatment | proteomics | ligand (protein) perturbation | 571 |
TargetScan | Predicted Conserved microRNA Targets | target genes of microRNAs predicted by searching genes for sites matching conserved miRNA seed regions | genomics | microRNA | 918 |
The Cancer Genome Atlas | Signatures of Differentially Expressed Genes for Tumors | mRNA expression profiles for tumor and normal tissue samples | transcriptomics | tissue sample | 2618 |
TISSUES | Curated Tissue Protein Expression Evidence Scores | protein tissue expression evidence scores by manual literature curation | structural or functional annotations | tissue | 1272 |
TISSUES | Experimental Tissue Protein Expression Evidence Scores | protein tissue expression evidence scores by integrating experimental data | proteomics | tissue | 988 |
TISSUES | Text-mining Tissue Protein Expression Evidence Scores | gene-tissue co-occurrence scores from text-mining biomedical abstracts | structural or functional annotations | tissue | 3391 |
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 | 4595 |
TRANSFAC | Predicted Transcription Factor Targets | target genes of transcription factors predicted using known transcription factor binding site motifs | genomics | transcription factor | 6174 |
Virus MINT | Protein-Viral Protein Interactions | interactions between viral and human proteins manually curated from literature | physical interactions | viral protein | 1128 |
Wikipathways | Pathways | sets of proteins participating in pathways | structural or functional annotations | pathway | 2131 |
Virus MINT | Protein-Virus Interactions | interactions between viruses and human proteins manually curated from literature | physical interactions | virus | 670 |
LOCATE | Predicted Protein Localization Annotations | subcellular localization of proteins by sequence similarity to localization sequences | proteomics | cellular component | 669 |
TargetScan | Predicted Nonconserved microRNA Targets | target genes of microRNAs predicted by searching genes for sites matching nonconserved miRNA seed regions | genomics | microRNA | 703 |
PhosphoSitePlus | Phosphosite-Disease Associations | disease-phosphosite associations curated from literature | disease or phenotype associations | disease | 639 |