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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 | 25257 | 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 | 39010 | 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 | 19658 | 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 | 9558 | 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 | 8575 | 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 | 10197 | false |
Biocarta | Pathways | Sets of proteins participating in pathways from Biocarta | structural or functional annotations | pathway | 77666 | false |
BioGPS | Cell Line Gene Expression Profiles | mRNA expression profiles for the NCI-60 panel of cancer cell lines | transcriptomics | cell line | 48763 | false |
BioGPS | Human Cell Type and Tissue Gene Expression Profiles | mRNA expression profiles for human tissues and cell types | transcriptomics | cell type or tissue | 21190 | false |
BioGPS | Mouse Cell Type and Tissue Gene Expression Profiles | mRNA expression profiles for mouse tissues and cell types | transcriptomics | cell type or tissue | 24955 | false |
Cancer Cell Line Encyclopedia (CCLE) | Cell Line Gene CNV Profiles | Gene-level copy number variation profiles for cancer cell lines | genomics | cell line | 37024 | false |
Cancer Cell Line Encyclopedia (CCLE) | Cell Line Gene Expression Profiles | mRNA microarray expression profiles for cancer cell lines | transcriptomics | cell line | 120880 | false |
Cancer Cell Line Encyclopedia (CCLE) | Cell Line Gene Mutation Profiles | Gene-level mutation profiles for cancer cell lines | genomics | cell line | 37484 | false |
ChIP-X Enrichment Analysis (ChEA) | 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 | 30976 | true |
ChIP-X Enrichment Analysis (ChEA) | 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 | 96280 | false |
ClinVar | Gene-Phenotype Associations | SNP-phenotype associations curated by ClinVar users from various sources | disease or phenotype associations | phenotype | 13556 | false |
Connectivity Map (CMAP) | Signatures of Differentially Expressed Genes for Small Molecules | mRNA expression profiles for cell lines following chemical perturbation | transcriptomics | small molecule perturbation | 15055 | false |
COMPARTMENTS | Curated Protein Localization Evidence Scores | Protein subcellular localization evidence scores by manual literature curation | structural or functional annotations | cellular component | 7666 | true |
COMPARTMENTS | Experimental Protein Localization Evidence Scores | Protein subcellular localization evidence scores by integrating experimental data | proteomics | cellular component | 4518 | true |
COMPARTMENTS | Text-mining Protein Localization Evidence Scores | Gene-cellular compartment co-occurrence scores from text-mining biomedical abstracts | structural or functional annotations | cellular component | 9260 | true |
CORUM | Protein Complexes | Proteins participating in complexes by manual literature curation | structural or functional annotations | protein complex | 17708 | false |
Catalogue of Somatic Mutations In Cancer (COSMIC) | Cell Line Gene CNV Profiles | Gene-level copy number variation profiles for cancer cell lines | genomics | cell line | 14617 | false |
Catalogue of Somatic Mutations In Cancer (COSMIC) | Cell Line Gene Mutation Profiles | Gene mutations in cancer cell lines from low-throughput or high-throughput studies | genomics | cell line | 27342 | false |
Comparative Toxicogenomics Database (CTD) | Gene-Chemical Interactions | Chemical-gene interactions curated from literature | physical interactions | chemical | 23655 | false |
Comparative Toxicogenomics Database (CTD) | Gene-Disease Associations | Disease-gene interactions from manually curated literature | disease or phenotype associations | disease | 33735 | false |
Database of Genotypes and Phenotypes (dbGAP) | Gene-Trait Associations | Gene-trait associations curated from genetic association studies | disease or phenotype associations | trait | 9000 | false |
Dephosphorylation Database (DEPOD) | Substrates of Phosphatases | Phosphatase-substrate interactions manually curated from literature and databases of protein annotations or protein interactions | physical interactions | phosphatase | 4601 | false |
DISEASES | Curated Gene-Disease Association Evidence Scores | Disease gene evidence scores by manual literature curation | disease or phenotype associations | disease | 8859 | true |
DISEASES | Experimental Gene-Disease Association Evidence Scores | Disease gene evidence scores by integrating experimental data (GWAS) | disease or phenotype associations | disease | 11454 | true |
DISEASES | Text-mining Gene-Disease Association Evidence Scores | Gene-disease co-occurrence scores from text-mining biomedical abstracts | disease or phenotype associations | disease | 36981 | true |
DrugBank | Drug Targets | Sets of proteins targeted by drugs by manual literature curation | physical interactions | drug | 36953 | false |
Encyclopedia of DNA Elements (ENCODE) | Histone Modification Site Profiles | Histone site modification profiles for cell lines from ENCODE | genomics | histone modification site profile | 9346 | false |
Encyclopedia of DNA Elements (ENCODE) | Transcription Factor Binding Site Profiles | Transcription factor binding site profiles for cell lines | genomics | transcription factor binding site profile | 21606 | false |
Encyclopedia of DNA Elements (ENCODE) | Transcription Factor Targets | Target genes of transcription factors from transcription factor binding site profiles | genomics | transcription factor | 137452 | 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 | 6188 | false |
Genetic Association Database (GAD) | Gene-Disease Associations | Gene-disease associations curated from genetic association studies | disease or phenotype associations | disease | 37778 | false |
Genetic Association Database (GAD) | High Level Gene-Disease Associations | Gene-disease associations curated from genetic association studies | disease or phenotype associations | disease | 7959 | false |
Genomics of Drug Sensitivity in Cancer (GDSC) | Cell Line Gene Expression Profiles | mRNA microarray expression profiles for cancer cell lines | transcriptomics | cell line | 17994 | false |
Gene Reference Into Function (GeneRIF) | Biological Term Annotations | Statements describing functions of genes distilled from biomedical publications | structural or functional annotations | biological term | 32042 | false |
GeneSigDB | Published Gene Signatures | Gene signatures reported in the literature that were derived from analysis of transcriptomic or proteomic data | transcriptomics | PubMedID | 8749 | false |
Gene Expression Omnibus (GEO) | Signatures of Differentially Expressed Genes for Diseases | mRNA expression profiles for cell lines or tissues following disease perturbation | transcriptomics | disease perturbation | 15711 | false |
Gene Expression Omnibus (GEO) | 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 | 8980 | false |
Gene Expression Omnibus (GEO) | 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 | 8724 | false |
Gene Expression Omnibus (GEO) | Signatures of Differentially Expressed Genes for Small Molecules | mRNA expression profiles for cell lines or tissues following small molecule perturbation | transcriptomics | small molecule perturbation | 7544 | false |
Gene Expression Omnibus (GEO) | 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 | 13360 | false |
Gene Expression Omnibus (GEO) | Signatures of Differentially Expressed Genes for Viral Infections | mRNA expression profiles for cell lines or tissues following viral infection | transcriptomics | virus perturbation | 9300 | false |
Gene Ontology (GO) | Biological Process Annotations 2015 | Curated annotations of genes with biological processes | structural or functional annotations | biological process | 14824 | true |
Gene Ontology (GO) | Cellular Component Annotations 2015 | Curated annotations of genes with cellular components | structural or functional annotations | cellular component | 8952 | true |
Gene Ontology (GO) | Molecular Function Annotations 2015 | Curated annotations of genes with molecular functions | structural or functional annotations | molecular function | 8703 | true |
Genotype Tissue Expression (GTEx) | eQTL | Significance values for all gene-SNP pairs testing likelihood that SNP affects gene expression | genomics | SNP | 7585 | true |
Genotype Tissue Expression (GTEx) | Tissue Gene Expression Profiles | Gene expression profiles for tissues from GTEx by RNA-seq | transcriptomics | tissue | 16696 | true |
Genotype Tissue Expression (GTEx) | Tissue Sample Gene Expression Profiles | RNA-seq gene expression profiles for tissue samples from GTEx | transcriptomics | tissue sample | 11462 | false |
Guide to Pharmacology | Chemical Ligands of Receptors | Chemical ligand-receptor interactions curated by experts | physical interactions | ligand (chemical) | 12394 | false |
Guide to Pharmacology | Protein Ligands of Receptors | Protein ligand-receptor interactions curated by experts | physical interactions | ligand (protein) | 3331 | false |
GWAS Catalog | SNP-Phenotype Associations | SNP-phenotype association p-values curated from published GWAS | disease or phenotype associations | phenotype | 11277 | false |
GWASdb | SNP-Disease Associations | SNP-disease association p-values curated from published GWAS | disease or phenotype associations | disease | 29971 | false |
GWASdb | SNP-Phenotype Associations | SNP-phenotype association p-values curated from published GWAS | disease or phenotype associations | phenotype | 10685 | 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 | 6570 | false |
Human Metabolome Database | Metabolites of Enzymes | Biomolecular interactions between metabolites and proteins, such as processing enzymes, curated from literature | physical interactions | metabolite | 11181 | false |
Human Protein Atlas (HPA) | Cell Line Gene Expression Profiles | RNA-seq gene expression profiles for cell lines from HPA | transcriptomics | cell line | 11598 | false |
Human Protein Atlas (HPA) | Tissue Gene Expression Profiles | RNA-seq gene expression profiles for tissues from HPA | transcriptomics | tissue | 13381 | false |
Human Protein Atlas (HPA) | Tissue Protein Expression Profiles | Semiquantitative protein expression profiles for tissues | proteomics | tissue | 6014 | false |
Human Protein Atlas (HPA) | Tissue Sample Gene Expression Profiles | RNA-seq gene expression profiles for tissue samples from HPA | transcriptomics | tissue sample | 5274 | false |
Human Proteome Map (HPM) | Cell Type and Tissue Protein Expression Profiles | Protein expression profiles for tissues and cell types | proteomics | cell type or tissue | 4360 | false |
Human Phenotype Ontology (HPO) | Gene-Disease Associations | Phenotype-causing gene mutations of human phenotypes from disease knowledgebases | disease or phenotype associations | phenotype | 27235 | false |
Hub Proteins | Protein-Protein Interactions | Sets of proteins interacting with hub proteins aggregated from data | physical interactions | hub protein | 12941 | false |
HuGE Navigator | Gene-Phenotype Associations | Gene-phenotype associations extracted from published GWAS by automated text-mining | disease or phenotype associations | phenotype | 13968 | false |
HumanCyc | Pathways | Sets of proteins participating in pathways from HumanCyc | structural or functional annotations | pathway | 5395 | 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 | 15063 | false |
Jaspar PWMs | Predicted Transcription Factor Targets | Target genes of transcription factors predicted using known transcription factor binding site motifs | genomics | transcription factor | 41173 | false |
Kinase Enrichment Analysis (KEA) | Substrates of Kinases | Protein substrates of kinases from published low-throughput and high-throughput phosphoproteomics studies | physical interactions | kinase | 10056 | false |
Kyoto Encyclopedia of Genes and Genomes (KEGG) | Pathways | Sets of proteins participating in pathways from KEGG | structural or functional annotations | pathway | 18588 | false |
LINCS Kinativ | Kinase Inhibitor Bioactivity Profiles | Percent inhibition of kinases by small molecules measured in cell lysates | physical interactions | chemical bioactivity profile | 3142 | 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 | 5653 | 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 | 9135 | false |
Klijn et al., Nat. Biotechnol., 2015 | Cell Line Gene Expression Profiles | RNA-seq gene expression profiles for cancer cell lines | transcriptomics | cell line | 13911 | 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 | 8718 | false |
LINCS L1000 Connectivity Map (L1000 CMAP) | Signatures of Differentially Expressed Genes for Small Molecules | mRNA expression profiles for cell lines following small molecule perturbation | transcriptomics | small molecule perturbation | 14778 | true |
LOCATE | Curated Protein Localization Annotations | Subcellular localization of proteins from low-throughput or high-throughput protein localization assays | proteomics | cellular component | 7217 | false |
MiRTarBase | microRNA Targets | Target genes of microRNAs from published experiments | physical interactions | microRNA | 18569 | false |
MotifMap | Predicted Transcription Factor Targets | Target genes of transcription factors predicted using known transcription factor binding site motifs | genomics | transcription factor | 26899 | false |
Mammalian Phenotype Ontology (MPO) | Gene-Phenotype Associations | Observed phenotypes of transgenic mice collected from mouse phenotyping studies | disease or phenotype associations | phenotype | 14833 | true |
Molecular Signatures Database (MSigDB) | Cancer Gene Co-expression Modules | Computational signatures of genes co-expressed with cancer related genes | transcriptomics | co-expressed gene | 8373 | false |
Molecular Signatures Database (MSigDB) | Signatures of Differentially Expressed Genes for Cancer Gene Perturbations | Oncogenic signatures of genes differentially expressed following cancer gene perturbations | transcriptomics | gene perturbation | 7370 | false |
Nuclear Receptor Signaling Atlas (NURSA) | Protein Complexes | Proteins identified in complexes isolated from cultured cells | proteomics | protein complex | 11876 | false |
Nuclear Receptor Signaling Atlas (NURSA) | Protein-Protein Interactions | Protein-protein interactions inferred from membership in complexes | proteomics | interacting protein | 9032 | false |
Online Mendelian Inheritance in Man (OMIM) | Gene-Disease Associations | Disease- or phenotype-causing gene mutations for heritable human diseases or phenotypes curated from biomedical publications | disease or phenotype associations | phenotype | 20478 | false |
PANTHER | Pathways | Sets of proteins participating in pathways from PANTHER | structural or functional annotations | pathway | 10482 | false |
Pathway Commons (PC) | 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 | 54321 | false |
Phosphosite Textmining | Biological Term Annotations | Occurrence frequencies for biological terms in abstracts of publications describing phosphosites | structural or functional annotations | biological term | 3654 | false |
PhosphoSitePlus | Substrates of Kinases | Kinase-substrate interactions curated from low-throughput or high-throughput phosphoproteomics studies | physical interactions | kinase | 11323 | false |
Pathway Interaction Database (PID) | Pathways | Sets of proteins participating in pathways from PID | structural or functional annotations | pathway | 16269 | false |
Proteomics Database (ProteomicsDB) | 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 | 13110 | false |
Reactome | Pathways 2014 | Sets of proteins participating in pathways from Reactome | structural or functional annotations | pathway | 12676 | true |
Roadmap Epigenomics | Cell and Tissue DNA Methylation Profiles | DNA methylation profiles for primary cell types and tissues | genomics | cell type or tissue | 9250 | false |
Roadmap Epigenomics | Cell and Tissue Gene Expression Profiles | mRNA expression profiles for primary cell types and tissues | transcriptomics | cell type or tissue | 6512 | false |
Roadmap Epigenomics | Histone Modification Site Profiles | Histone modification profiles for primary cells and tissues | genomics | histone modification site profile | 7191 | false |
SILAC Phosphoproteomics | Signatures of Differentially Phosphorylated Proteins for Drugs | Phosphorylation levels of proteins in cell lines following drug treatment | proteomics | drug perturbation | 4385 | 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 | 2769 | 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 | 3646 | false |
TargetScan | Predicted Conserved microRNA Targets | Target genes of microRNAs predicted by searching genes for sites matching conserved miRNA seed regions | genomics | microRNA | 6895 | false |
The Cancer Genome Atlas (TCGA) | Signatures of Differentially Expressed Genes for Tumors | mRNA expression profiles for tumor and normal tissue samples | transcriptomics | tissue sample | 18496 | false |
TISSUES | Curated Tissue Protein Expression Evidence Scores | Protein tissue expression evidence scores by manual literature curation | structural or functional annotations | tissue | 8917 | true |
TISSUES | Experimental Tissue Protein Expression Evidence Scores | Protein tissue expression evidence scores by integrating experimental data | proteomics | tissue | 7212 | true |
TISSUES | Text-mining Tissue Protein Expression Evidence Scores | Gene-tissue co-occurrence scores from text-mining biomedical abstracts | structural or functional annotations | tissue | 20455 | true |
Virus MINT | Protein-Viral Protein Interactions | Interactions between viral and human proteins manually curated from literature | physical interactions | viral protein | 6646 | false |
WikiPathways | Pathways 2014 | Sets of proteins participating in pathways from WikiPathways | structural or functional annotations | pathway | 14214 | true |
Virus MINT | Protein-Virus Interactions | Interactions between viruses and human proteins manually curated from literature | physical interactions | virus | 4332 | false |
LOCATE | Predicted Protein Localization Annotations | Subcellular localization of proteins by sequence similarity to localization sequences | proteomics | cellular component | 4951 | false |
TargetScan | Predicted Nonconserved microRNA Targets | Target genes of microRNAs predicted by searching genes for sites matching nonconserved miRNA seed regions | genomics | microRNA | 6688 | false |
PhosphoSitePlus | Phosphosite-Disease Associations | Disease-phosphosite associations curated from literature | disease or phenotype associations | disease | 4171 | false |
Sanger Cancer Dependency Map (DepMap) | Cancer Cell Line Proteomics | Protein intensity values acquired using data-independent acquisition mass spectrometry (DIA-MS). | proteomics | cell line | 2421 | 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 | 2784 | 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 | 2349 | false |
DeepCoverMOA | Drug Mechanisms of Action | Protein expression profiles in HCT116 cell line following drug treatment | proteomics | small molecule perturbation | 2413 | false |
Tabula Sapiens | Gene-Cell Associations | Gene expression data from Tabula Sapiens scRNA-seq counts | transcriptomics | cell type | 1670 | 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 | 6543 | 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 | 3746 | false |
Gene Ontology (GO) | Biological Process Annotations 2023 | Curated annotations of genes with biological processes | structural or functional annotations | biological process | 4524 | true |
Gene Ontology (GO) | Cellular Component Annotations 2023 | Curated annotations of genes with cellular components | structural or functional annotations | cellular component | 2139 | true |
Gene Ontology (GO) | Molecular Function Annotations 2023 | Curated annotations of genes with molecular functions | structural or functional annotations | molecular function | 2282 | true |
Pathway Figure Optical Character Recognition (PFOCR) | Pathway Figure Associations 2023 | Sets of genes/proteins extracted from pathway figures in research publications using optical character recognition | structural or functional annotations | pathway | 2928 | true |
Cancer Cell Line Encyclopedia (CCLE) | Cell Line Proteomics | Protein intensity values acquired using mass spectrometry across human cancerous cell lines | proteomics | cell line | 1611 | false |
Cancer Dependency Map (DepMap) | CRISPR Gene Dependency | Dependency scores for cell lines following single gene knockdowns | disease or phenotype associations | cell line | 1400 | false |
ChIP-X Enrichment Analysis (ChEA) | Transcription Factor Targets 2022 | Target genes of transcription factors from published ChIP-chip, ChIP-seq, and other transcription factor binding site profiling studies | genomics | transcription factor | 4935 | false |
Mammalian Phenotype Ontology (MPO) | Mouse Phenotype Associations 2023 | Observed phenotypes of transgenic mice collected from mouse phenotyping studies | disease or phenotype associations | phenotype | 1632 | false |
LINCS L1000 Connectivity Map (L1000 CMAP) | CRISPR Knockout Consensus Signatures | Gene association consensus signatures following CRISPR gene knockout | transcriptomics | gene perturbation | 3503 | false |
Molecular Transducers of Physical Activity Consortium (MoTrPAC) | Rat Endurance Exercise Training Transcriptomics | RNA-seq gene expression profiles for rat tissue samples across 4 time points and 19 tissues | transcriptomics | tissue sample | 598 | false |
GlyGen | Glycosylated Proteins | Proteins glycosylated by saccharide ligands from glycosylation site citations | proteomics | glycan | 949 | false |
International Mouse Phenotyping Consortium (IMPC) | Knockout Mouse Phenotypes | Observed phenotypes of mice following gene knockout | disease or phenotype associations | phenotype | 763 | false |
Metabolomics Workbench (MW) | Enzyme Metabolite Associations | Biomolecular interactions between metabolites and proteins curated from experimental studies | physical interactions | metabolite | 671 | false |
LINCS L1000 Connectivity Map (L1000 CMAP) | Chemical Perturbations Consensus Signatures | Gene association consensus signatures following small molecule perturbation | transcriptomics | small molecule perturbation | 1671 | false |
Genotype Tissue Expression (GTEx) | Tissue Gene Expression Profiles 2023 | Gene expression profiles for tissues from GTEx by RNA-seq | transcriptomics | tissue | 774 | false |
Genotype Tissue Expression (GTEx) | Tissue-Specific Aging Signatures | Tissue-specific aging signatures createed from GTEx RNA-seq gene expression profiles | transcriptomics | tissue sample | 1285 | false |
The Human BioMolecular Atlas Program (HuBMAP) | Azimuth Cell Type Annotations | Gene-cell type annotations from integrated reference scRNA-seq gene expression profiles | transcriptomics | cell type | 887 | false |
SynGO | Synaptic Gene Annotations | Curated annotations of genes with synaptic processes and components | structural or functional annotations | biological term | 583 | false |
CellMarker | Gene-Cell Type Associations | Cell type markers across various tissues from human and mouse scRNA-seq | transcriptomics | cell type | 2185 | false |
Kinase Library | Tyrosine Kinome Atlas | A phosphoproteomics atlas detailing phosphorylation of protein substrates by 93 canonical and non-canonical tyrosine kinases in the human kinome. | proteomics | kinase | 457 | false |
Pathway Figure Optical Character Recognition (PFOCR) | Pathway Figure Associations 2024 | Sets of genes/proteins extracted from pathway figures in research publications using optical character recognition, updated for 2024 | structural or functional annotations | pathway | 1608 | false |
WikiPathways | Pathways 2024 | Sets of proteins participating in pathways from WikiPathways updated for 2024 | structural or functional annotations | pathway | 951 | false |
Reactome | Pathways 2024 | Sets of proteins participating in pathways from Reactome, updated for 2024 | structural or functional annotations | pathway | 1099 | false |
The Human BioMolecular Atlas Program (HuBMAP) | ASCT+B Annotations | Anatomical structure and cell type biomarker annotations from the HuBMAP ASCT+B tables | structural or functional annotations | cell type | 388 | false |
The Human BioMolecular Atlas Program (HuBMAP) | ASCT+B Augmented with RNA-seq Coexpression | Anatomical structure and cell type biomarker annotations from the HuBMAP ASCT+B tables, augmented with RNA-seq coexpression data from ARCHS4 | structural or functional annotations | cell type | 131 | false |
Gene Ontology (GO) | Biological Process Annotations 2025 | curated annotations of genes with biological processes | structural or functional annotations | biological process | 272 | false |
Gene Ontology (GO) | Cellular Component Annotations 2025 | curated annotations of genes with cellular components | structural or functional annotations | cellular component | 255 | false |
Gene Ontology (GO) | Molecular Function Annotations 2025 | curated annotations of genes with molecular functions | structural or functional annotations | molecular function | 119 | false |
DISEASES | Curated Gene-Disease Assocation Evidence Scores 2025 | Disease gene evidence scores by manual literature curation | disease or phenotype associations | disease | 8839 | false |
DISEASES | Experimental Gene-Disease Association Evidence Scores 2025 | Disease gene evidence scores by integrating experimental data (GWAS) | disease or phenotype associations | disease | 11450 | false |
DISEASES | Text-mining Gene-Disease Association Evidence Scores 2025 | Gene-disease co-occurrence scores from text-mining biomedical abstracts | disease or phenotype associations | disease | 36912 | false |
Novartis Institutes for Biomedical Research (NIBR) | DRUG-seq U2OS MoA Box | Drug perturbation signatures created by profiling 4343 small molecules in the U2-OS cell line with the DRUG-seq platform | transcriptomics | drug perturbation | 75 | false |
Genotype Tissue Expression (GTEx) | eQTL 2025 | Significance values for all gene-SNP pairs testing likelihood that SNP affects gene expression | genomics | SNP | 7559 | false |
TISSUES | Curated Tissue Protein Expression Evidence Scores 2025 | Protein tissue expression evidence scores by manual literature curation | structural or functional annotations | tissue | 8930 | false |
TISSUES | Experimental Tissue Protein Expression Evidence Scores 2025 | Protein tissue expression evidence scores by integrating experimental data | proteomics | cell type or tissue | 7196 | false |
TISSUES | Text-mining Tissue Protein Expression Evidence Scores 2025 | Gene-tissue co-occurrence scores from text-mining biomedical abstracts | structural or functional annotations | cell type or tissue | 20451 | false |
COMPARTMENTS | Curated Protein Localization Evidence Scores 2025 | Protein subcellular localization evidence scores by manual literature curation | structural or functional annotations | cellular component | 38 | false |
COMPARTMENTS | Experimental Protein Localization Evidence Scores 2025 | Protein subcellular localization evidence scores by integrating experimental data | proteomics | cellular component | 22 | false |
COMPARTMENTS | Text-mining Protein Localization Evidence Scores 2025 | Gene-cellular compartment co-occurrence scores from text-mining biomedical abstracts | structural or functional annotations | cellular component | 9271 | false |