Harmonizome 3.0

From Hub Proteins

Sets of proteins interacting with hub proteins aggregated from data

From Nuclear Receptor Signaling Atlas

Protein-protein interactions inferred from membership in complexes

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

From Virus MINT

Interactions between viral and human proteins manually curated from literature

From COMPARTMENTS

Protein subcellular localization evidence scores by manual literature curation

From COMPARTMENTS

Protein subcellular localization evidence scores by integrating experimental data

From COMPARTMENTS

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

From CORUM

Proteins participating in complexes by manual literature curation

From Guide to Pharmacology

Protein ligand-receptor interactions curated by experts

From Human Protein Atlas

Semiquantitative protein expression profiles for tissues

From InterPro

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

From LOCATE

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

From Nuclear Receptor Signaling Atlas

Proteins identified in complexes isolated from cultured cells

From SILAC Phosphoproteomics

Phosphorylation levels of proteins in cell lines following ligand treatment

From TISSUES

Protein tissue expression evidence scores by manual literature curation

From TISSUES

Protein tissue expression evidence scores by integrating experimental data

From TISSUES

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

From Virus MINT

Interactions between viruses and human proteins manually curated from literature

From LOCATE

Subcellular localization of proteins by sequence similarity to localization sequences

From TISSUES

Protein tissue expression evidence scores by manual literature curation

From TISSUES

Protein tissue expression evidence scores by integrating experimental data

From TISSUES

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

From COMPARTMENTS

Protein subcellular localization evidence scores by manual literature curation

From COMPARTMENTS

Protein subcellular localization evidence scores by integrating experimental data

From COMPARTMENTS

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

From Allen Brain Atlas

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

From Allen Brain Atlas

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

From Allen Brain Atlas

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

From Allen Brain Atlas

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

From Allen Brain Atlas

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

From ClinVar

SNP-phenotype associations curated by ClinVar users from various sources

From Comparative Toxicogenomics Database

Chemical-gene interactions curated from literature

From Comparative Toxicogenomics Database

Disease-gene interactions from manually curated literature

From Database of Genotypes and Phenotypes

Gene-trait associations curated from genetic association studies

From DISEASES

Disease gene evidence scores by manual literature curation

From DISEASES

Disease gene evidence scores by integrating experimental data (GWAS)

From DISEASES

Gene-disease co-occurrence scores from text-mining biomedical abstracts

From Genetic Association Database

Gene-disease associations curated from genetic association studies

From Genetic Association Database

Gene-disease associations curated from genetic association studies

From GeneSigDB

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

From Gene Expression Omnibus

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

From Genotype Tissue Expression

Gene expression profiles for tissues from GTEx by RNA-seq

From Genotype Tissue Expression

RNA-seq gene expression profiles for tissue samples from GTEx

From Human Protein Atlas

RNA-seq gene expression profiles for tissues from HPA

From Human Protein Atlas

RNA-seq gene expression profiles for tissue samples from HPA

From Human Phenotype Ontology

Phenotype-causing gene mutations of human phenotypes from disease knowledgebases

From HuGE Navigator

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

From Mammalian Phenotype Ontology

Observed phenotypes of transgenic mice collected from mouse phenotyping studies

From Molecular Signatures Database

Computational signatures of genes co-expressed with cancer related genes

From Molecular Signatures Database

Oncogenic signatures of genes differentially expressed following cancer gene perturbations

From Online Mendelian Inheritance in Man

Disease- or phenotype-causing gene mutations for heritable human diseases or phenotypes curated from biomedical publications

From SILAC Phosphoproteomics

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

From knockTF

Gene expression profiles for cell lines or tissues following transcription factor perturbation (knockdown/knockout)

From DisGeNET

Gene-disease associations sourced from curated repositories, GWAS catalogues, animal models and the scientific literature

From DisGeNET

Gene-phenotype associations sourced from curated repositories, GWAS catalogues, animal models and the scientific literature

From Cancer Dependency Map

Dependency scores for cell lines following single gene knockdowns

From Genotype Tissue Expression

Gene expression profiles for tissues from GTEx by RNA-seq

From SynGO

Curated annotations of genes with synaptic processes and components

From PerturbAtlas

Gene expression profiles for cell lines, cell types, tissues, and models following genetic perturbation (knockdown, knockout, knockin, over-expression, mutation, and multi-condition)

From PerturbAtlas

Gene expression profiles for cell lines, cell types, tissues, and models following genetic perturbation (knockdown, knockout, knockin, over-expression, mutation, and multi-condition)

From RummaGEO

Single gene perturbation signatures produced by querying RummaGEO metadata for knockouts, knockdowns, and over-expression conditions

From DISEASES

Disease gene evidence scores by manual literature curation

From DISEASES

Disease gene evidence scores by integrating experimental data (GWAS)

From DISEASES

Gene-disease co-occurrence scores from text-mining biomedical abstracts

From Novartis Institutes for Biomedical Research

Drug perturbation signatures created by profiling 4343 small molecules in the U2-OS cell line with the DRUG-seq platform

From ClinVar

SNP-phenotype associations curated by ClinVar users from various sources

From Allen Brain Atlas

mRNA expression profiles for dementia and traumatic brain injuries (TBI) from aging brain tissue

From Cell Maps for AI

Gene expression profiles in the KOLF2.1J cell line following CRISPRi genetic perturbation

From Human Protein Atlas

RNA-seq gene expression profiles for cell lines from HPA

From Gene Expression Omnibus

mRNA expression profiles for cell lines or tissues following disease perturbation

From Gene Expression Omnibus

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

From Gene Expression Omnibus

mRNA expression profiles for cell lines or tissues following small molecule perturbation

From Gene Expression Omnibus

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

From Gene Expression Omnibus

mRNA expression profiles for cell lines or tissues following viral infection

From Gene Ontology

Curated annotations of genes with biological processes

From Gene Ontology

Curated annotations of genes with cellular components

From Gene Ontology

Curated annotations of genes with molecular functions

From Gene Ontology

Curated annotations of genes with biological processes

From Gene Ontology

Curated annotations of genes with cellular components

From Gene Ontology

Curated annotations of genes with molecular functions

From Gene Ontology

curated annotations of genes with biological processes

From Gene Ontology

curated annotations of genes with cellular components

From Gene Ontology

curated annotations of genes with molecular functions

From Gene Reference Into Function

Statements describing functions of genes distilled from biomedical publications

From Drug-Gene Interaction Database

Sets of proteins targeted by drugs by data aggregation