Harmonizome 3.0

From ChIP-X Enrichment Analysis

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

From Encyclopedia of DNA Elements

Transcription factor binding site profiles for cell lines

From Achilles

Fitness scores for cell lines following single gene knockdowns

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 BioGPS

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

From BioGPS

mRNA expression profiles for human tissues and cell types

From BioGPS

mRNA expression profiles for mouse tissues and cell types

From Cancer Cell Line Encyclopedia

Gene-level copy number variation profiles for cancer cell lines

From Cancer Cell Line Encyclopedia

mRNA microarray expression profiles for cancer cell lines

From Cancer Cell Line Encyclopedia

Gene-level mutation profiles for cancer cell lines

From ClinVar

SNP-phenotype associations curated by ClinVar users from various sources

From Catalogue of Somatic Mutations In Cancer

Gene-level copy number variation profiles for cancer cell lines

From Catalogue of Somatic Mutations In Cancer

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

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 Genomics of Drug Sensitivity in Cancer

mRNA microarray expression profiles for cancer cell lines

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 Heiser et al., PNAS, 2011

mRNA expression profiles for breast cancer cell lines measured by microarray

From Human Protein Atlas

RNA-seq gene expression profiles for cell lines from HPA

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 Klijn et al., Nat. Biotechnol., 2015

Gene-level copy number variation profiles for cancer cell lines

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

RNA-seq gene expression profiles for cancer cell lines

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

SNP gene mutations in cancer cell lines identified by microarray

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 Roadmap Epigenomics

mRNA expression profiles for primary cell types and tissues

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 Tabula Sapiens

Gene expression data from Tabula Sapiens scRNA-seq counts

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 CellMarker

Cell type markers across various tissues from human and mouse scRNA-seq

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 Replogle et al., Cell, 2022

Gene expression profiles in the K562 cell line following CRISPRi genetic perturbation

From Replogle et al., Cell, 2022

Gene expression profiles in the K562 cell line following CRISPRi genetic perturbation of essential genes

From Replogle et al., Cell, 2022

Gene expression profiles in the RPE1 cell line following CRISPRi genetic perturbation of essential genes

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 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