Name

Hub Proteins Protein-Protein Interactions Dataset

From Hub Proteins

sets of proteins interacting with hub proteins

NURSA Protein-Protein Interactions Dataset

From Nuclear Receptor Signaling Atlas

protein-protein interactions inferred from membership in complexes

Virus MINT Protein-Viral Protein Interactions Dataset

From Virus MINT

interactions between viral and human proteins manually curated from literature

Achilles Cell Line Gene Essentiality Profiles Dataset

From Achilles

fitness scores for cell lines following single gene knockdowns

Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles Dataset

From Allen Brain Atlas

mRNA expression profiles for 6 adult human brain tissue samples spanning ~300 brain structures

Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles Dataset

From Allen Brain Atlas

mRNA expression profiles for adult mouse brain tissues spanning ~2000 anatomically defined brain structures

Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray Dataset

From Allen Brain Atlas

mRNA expression profiles for human brain tissue samples spanning 27 time points and 26 brain structures

Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq Dataset

From Allen Brain Atlas

mRNA expression profiles for human brain tissue samples spanning 31 time points and 26 brain structures

Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles Dataset

From Allen Brain Atlas

mRNA expression profiles for 4 human prenatal brain tissue samples spanning 4 time points and ~300 brain structures

Biocarta Pathways Dataset

From Biocarta

sets of proteins participating in pathways

BioGPS Cell Line Gene Expression Profiles Dataset

From BioGPS

mRNA expression profiles for the NCI-60 panel of cancer cell lines

BioGPS Human Cell Type and Tissue Gene Expression Profiles Dataset

From BioGPS

mRNA expression profiles for human tissues and cell types

BioGPS Mouse Cell Type and Tissue Gene Expression Profiles Dataset

From BioGPS

mRNA expression profiles for mouse tissues and cell types

CCLE Cell Line Gene CNV Profiles Dataset

From Cancer Cell Line Encyclopedia

gene-level copy number variation profiles for cancer cell lines

CCLE Cell Line Gene Expression Profiles Dataset

From Cancer Cell Line Encyclopedia

mRNA expression profiles for cancer cell lines

CCLE Cell Line Gene Mutation Profiles Dataset

From Cancer Cell Line Encyclopedia

gene-level mutation profiles for cancer cell lines

CHEA Transcription Factor Binding Site Profiles Dataset

From ChIP-X Enrichment Analysis

transcription factor binding site profiles from published ChIP-chip, ChIP-seq, and other transcription factor functional studies

COMPARTMENTS Curated Protein Localization Evidence Scores Dataset

From COMPARTMENTS

protein subcellular localization evidence scores by manual literature curation

COMPARTMENTS Experimental Protein Localization Evidence Scores Dataset

From COMPARTMENTS

protein subcellular localization evidence scores by integrating experimental data

COMPARTMENTS Text-mining Protein Localization Evidence Scores Dataset

From COMPARTMENTS

gene-cellular compartment co-occurrence scores from text-mining biomedical abstracts

CORUM Protein Complexes Dataset

From CORUM

proteins participating in complexes by manual literature curation

COSMIC Cell Line Gene CNV Profiles Dataset

From Catalogue of Somatic Mutations In Cancer

gene-level copy number variation profiles for cancer cell lines

COSMIC Cell Line Gene Mutation Profiles Dataset

From Catalogue of Somatic Mutations In Cancer

gene mutations in cancer cell lines from low-throughput or high-throughput studies

DEPOD Substrates of Phosphatases Dataset

From Dephosphorylation Database

phosphatase-substrate interactions manually curated from literature and databases of protein annotations or protein interactions

ENCODE Histone Modification Site Profiles Dataset

From Encyclopedia of DNA Elements

histone modification profiles for cell lines

ENCODE Transcription Factor Binding Site Profiles Dataset

From Encyclopedia of DNA Elements

transcription factor binding site profiles for cell lines

ESCAPE Omics Signatures of Genes and Proteins for Stem Cells Dataset

From ESCAPE

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

GDSC Cell Line Gene Expression Profiles Dataset

From Genomics of Drug Sensitivity in Cancer

mRNA expression profiles for cancer cell lines

GeneSigDB Published Gene Signatures Dataset

From GeneSigDB

gene signatures reported in the literature that were derived from analysis of transcriptomic or proteomic data

GEO Signatures of Differentially Expressed Genes for Gene Perturbations Dataset

From Gene Expression Omnibus

mRNA expression profiles for cell lines or tissues following genetic perturbation (knockdown, knockout, over-expression, mutation)

GEO Signatures of Differentially Expressed Genes for Kinase Perturbations Dataset

From Gene Expression Omnibus

mRNA expression profiles for cell lines or tissues following kinase perturbation (inhibition, activation, knockdown, knockout, over-expression, mutation)

GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations Dataset

From Gene Expression Omnibus

mRNA expression profiles for cell lines or tissues following transcription factor perturbation (inhibition, activation, knockdown, knockout, over-expression, mutation)

GO Biological Process Annotations Dataset

From Gene Ontology

curated annotations of genes with biological processes

GTEx Tissue Gene Expression Profiles Dataset

From Genotype Tissue Expression

mRNA expression profiles for tissues

GTEx Tissue Sample Gene Expression Profiles Dataset

From Genotype Tissue Expression

mRNA expression profiles for tissue samples

Guide to Pharmacology Chemical Ligands of Receptors Dataset

From Guide to Pharmacology

ligand-receptor interactions curated by experts

Guide to Pharmacology Protein Ligands of Receptors Dataset

From Guide to Pharmacology

ligand-receptor interactions curated by experts

GWAS Catalog SNP-Phenotype Associations Dataset

From GWAS Catalog

SNP-phenotype association p-values curated from published GWAS

GWASdb SNP-Phenotype Associations Dataset

From GWASdb

SNP-phenotype association p-values curated from published GWAS

Heiser et al., PNAS, 2011 Cell Line Gene Expression Profiles Dataset

From Heiser et al., PNAS, 2011

mRNA expression profiles for breast cancer cell lines measured by microarray

HPA Cell Line Gene Expression Profiles Dataset

From Human Protein Atlas

mRNA expression profiles for cell lines

HPA Tissue Gene Expression Profiles Dataset

From Human Protein Atlas

mRNA expression profiles for tissues

HPA Tissue Protein Expression Profiles Dataset

From Human Protein Atlas

semiquantitative protein expression profiles for tissues

HPA Tissue Sample Gene Expression Profiles Dataset

From Human Protein Atlas

mRNA expression profiles for tissue samples

HPM Cell Type and Tissue Protein Expression Profiles Dataset

From Human Proteome Map

protein expression profiles for tissues and cell types

HuGE Navigator Gene-Phenotype Associations Dataset

From HuGE Navigator

gene-phenotype associations extracted from published GWAS by automated text-mining

HumanCyc Pathways Dataset

From HumanCyc

sets of proteins participating in pathways

InterPro Predicted Protein Domain Annotations Dataset

From InterPro

protein domains predicted for gene products based on sequence similarity to known domain signatures

JASPAR Predicted Transcription Factor Targets Dataset

From Jaspar PWMs

target genes of transcription factors predicted using known transcription factor binding site motifs

KEGG Pathways Dataset

From Kyoto Encyclopedia of Genes and Genomes

sets of proteins participating in pathways

LINCS Kinativ Kinase Inhibitor Bioactivity Profiles Dataset

From LINCS Kinativ

percent inhibition of kinases by small molecules measured in cell lysates

Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles Dataset

From Klijn et al., Nat. Biotechnol., 2015

gene-level copy number variation profiles for cancer cell lines

Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Expression Profiles Dataset

From Klijn et al., Nat. Biotechnol., 2015

mRNA expression profiles for cancer cell lines

Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene Mutation Profiles Dataset

From Klijn et al., Nat. Biotechnol., 2015

gene mutations in cancer cell lines

LOCATE Curated Protein Localization Annotations Dataset

From LOCATE

subcellular localization of proteins from low-throughput or high-throughput protein localization assays

MotifMap Predicted Transcription Factor Targets Dataset

From MotifMap

target genes of transcription factors predicted using known transcription factor binding site motifs

MPO Gene-Phenotype Associations Dataset

From Mammalian Phenotype Ontology

observed phenotypes of transgenic mice collected from mouse phenotyping studies

MSigDB Signatures of Differentially Expressed Genes for Cancer Gene Perturbations Dataset

From Molecular Signatures Database

oncogenic signatures of genes differentially expressed following cancer gene perturbations

NURSA Protein Complexes Dataset

From Nuclear Receptor Signaling Atlas

proteins identified in complexes isolated from cultured cells

PANTHER Pathways Dataset

From PANTHER

sets of proteins participating in pathways

Pathway Commons Protein-Protein Interactions Dataset

From Pathway Commons

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

Phosphosite Textmining Biological Term Annotations Dataset

From Phosphosite Textmining

occurrence frequencies for biological terms in abstracts of publications describing phosphosites

PhosphoSitePlus Substrates of Kinases Dataset

From PhosphoSitePlus

kinase-substrate interactions curated from low-throughput or high-throughput phosphoproteomics studies

PID Pathways Dataset

From Pathway Interaction Database

sets of proteins participating in pathways

ProteomicsDB Cell Type and Tissue Protein Expression Profiles Dataset

From Proteomics Database

protein expression profiles for tissues and cell types reprocessed from many proteomics datasets

Reactome Pathways Dataset

From Reactome

sets of proteins participating in pathways

Roadmap Epigenomics Cell and Tissue DNA Accessibility Profiles Dataset

From Roadmap Epigenomics

DNA accessibility profiles for primary cell types and tissues

Roadmap Epigenomics Cell and Tissue DNA Methylation Profiles Dataset

From Roadmap Epigenomics

DNA methylation profiles for primary cell types and tissues

Roadmap Epigenomics Cell and Tissue Gene Expression Profiles Dataset

From Roadmap Epigenomics

mRNA expression profiles for primary cell types and tissues

Roadmap Epigenomics Histone Modification Site Profiles Dataset

From Roadmap Epigenomics

histone modification profiles for primary cells and tissues

SILAC Phosphoproteomics Signatures of Differentially Phosphorylated Proteins for Drugs Dataset

From SILAC Phosphoproteomics

phosphorylation levels of proteins in cell lines following drug treatment

SILAC Phosphoproteomics Signatures of Differentially Phosphorylated Proteins for Gene Perturbations Dataset

From SILAC Phosphoproteomics

phosphorylation levels of proteins in cell lines following genetic perturbation (knockdown, knockout, over-expression, mutation)

SILAC Phosphoproteomics Signatures of Differentially Phosphorylated Proteins for Protein Ligands Dataset

From SILAC Phosphoproteomics

phosphorylation levels of proteins in cell lines following ligand treatment

TargetScan Predicted Conserved microRNA Targets Dataset

From TargetScan

target genes of microRNAs predicted by searching genes for sites matching conserved miRNA seed regions

TISSUES Curated Tissue Protein Expression Evidence Scores Dataset

From TISSUES

protein tissue expression evidence scores by manual literature curation

TISSUES Experimental Tissue Protein Expression Evidence Scores Dataset

From TISSUES

protein tissue expression evidence scores by integrating experimental data

TISSUES Text-mining Tissue Protein Expression Evidence Scores Dataset

From TISSUES

gene-tissue co-occurrence scores from text-mining biomedical abstracts

TRANSFAC Predicted Transcription Factor Targets Dataset

From TRANSFAC

target genes of transcription factors predicted using known transcription factor binding site motifs

Wikipathways Pathways Dataset

From Wikipathways

sets of proteins participating in pathways

Virus MINT Protein-Virus Interactions Dataset

From Virus MINT

interactions between viruses and human proteins manually curated from literature

LOCATE Predicted Protein Localization Annotations Dataset

From LOCATE

subcellular localization of proteins by sequence similarity to localization sequences

TargetScan Predicted Nonconserved microRNA Targets Dataset

From TargetScan

target genes of microRNAs predicted by searching genes for sites matching nonconserved miRNA seed regions

PhosphoSitePlus Phosphosite-Disease Associations Dataset

From PhosphoSitePlus

disease-phosphosite associations curated from literature

ClinVar Gene-Phenotype Associations Dataset

From ClinVar

SNP-phenotype associations curated by ClinVar users from various sources

dbGAP Gene-Trait Associations Dataset

From Database of Genotypes and Phenotypes

gene-trait associations curated from genetic association studies

HPO Gene-Disease Associations Dataset

From Human Phenotype Ontology

phenotype-causing gene mutations of human phenotypes from disease knowledgebases