Harmonizome 3.0

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 Pathway Figure Optical Character Recognition

Sets of genes/proteins extracted from pathway figures in research publications using optical character recognition

From Pathway Figure Optical Character Recognition

Sets of genes/proteins extracted from pathway figures in research publications using optical character recognition, updated for 2024

From Connectivity Map

mRNA expression profiles for cell lines following chemical perturbation

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

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 genetic perturbation (knockdown, knockout, over-expression, mutation)

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 LINCS L1000 Connectivity Map

mRNA expression profiles for cell lines following small molecule perturbation

From Molecular Signatures Database

Oncogenic signatures of genes differentially expressed following cancer gene perturbations

From The Cancer Genome Atlas

mRNA expression profiles for tumor and normal tissue samples

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 Kyoto Encyclopedia of Genes and Genomes

Sets of proteins participating in pathways from KEGG

From Kyoto Encyclopedia of Genes and Genomes

Sets of proteins participating in pathways from KEGG

From Pathway Interaction Database

Sets of proteins participating in pathways from PID