Gene Disease Associations

Open Targets gene-disease associations per datatype and per datasource

gene_disease_associations.csv.gz

Number of rows x columns: 2,405,594 rows x 33 columns

This file is a dump of the Open Targets database summarising all the gene-disease associations per type of evidence (genetics, somatic mutations, transcriptomic studies, clinical trials, affected pathways, disease relevant animal model, text-mining) and per source of evidence (Expression Atlas,uniprot,gwas catalog,PheWAS Catalog,eva,Uniprot literature,Genomics England, gene2phenotype, Reactome,SlapEnrich,PROGENy, Phenodigm, cancer gene census, EVA somatic, UniProt Somatic, Intogen, ChEMBL, Europe PMC)

Column name	Description
target_indication	target-disease pair
ensembl_gene_id	Ensembl gene identifier
symbol	gene symbol
disease_id	disease identifier
disease_label	disease/GWAS trait/phenotype name
therapeutic_area	therapeutic area for this disease/trait/phenotype, e.g., metabolic disease; genetic disorder
is_direct	Is the association drawn from a direct evidence or propagated based on the disease classification?
overall_score	overall score of the association (aggregate the others)
genetic_association	genetic association score
somatic_mutation	somatic mutation score (from all somatic datasources)
known_drug	Clinical trial score based on ChEMBL evidence
rna_expression	mRNA differential expression score
affected_pathway	Affected pathways score (combines Reactome and SlapEnrich)
animal_model	Animal model score based on Phenodigm
literature	Europe PMC score
expression_atlas	Expression Atlas association score
uniprot	UniProt genetic score
gwas_catalog	GWAS Catalog genetic score
phewas_catalog	PheWAS Catalog genetic score
eva	EVA (ClinVar) genetic score
uniprot_literature	UniProt literature curated genetic score
genomics_england	Genomics England PanelApp genetic score
gene2phenotype	Gene2Phenotype genetic score
reactome	Reactome affected pathways score
slapenrich	SlapEnrich cancer affected pathways score
progeny	PROGENy signaling pathways score
phenodigm	Phenodigm (Animal model) score
cancer_gene_census	Cancer Gene Census score
eva_somatic	EVA (ClinVar) somatic mutations score
uniprot_somatic	UniProt somatic mutations score
intogen	InToGEN cancer driver gene score
chembl	ChEMBL clinical trial score
europepmc	EuroPMC literature score

head -10 gene_disease_associations.csv
key,ensembl_gene_id,symbol,disease_id,disease_label,therapeutic_area,is_direct,overall_score,genetic_association,somatic_mutation,known_drug,rna_expression,affected_pathway,animal_model,literature,expression_atlas,uniprot,gwas_catalog,phewas_catalog,eva,uniprot_literature,genomics_england,gene2phenotype,reactome,slapenrich,progeny,phenodigm,cancer_gene_census,eva_somatic,uniprot_somatic,intogen,chembl,europepmc
ENSG00000065485-Orphanet_3389,ENSG00000065485,PDIA5,Orphanet_3389,Tuberculosis,infectious disease,True,5.7590800000000004e-05,0.0,0.0,0.0,5.7590800000000004e-05,0.0,0.0,0.0,5.7590800000000004e-05,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
ENSG00000145431-HP_0001392,ENSG00000145431,PDGFC,HP_0001392,Abnormality of the liver,phenotype,False,0.03802784199546485,0.0,0.0,0.0,0.0,0.0,0.0,0.03802784199546485,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.03802784199546485
ENSG00000113231-EFO_0000546,ENSG00000113231,PDE8B,EFO_0000546,injury,other disease,True,0.2,0.0,0.0,0.2,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.2,0.0
ENSG00000163114-Orphanet_98497,ENSG00000163114,PDHA2,Orphanet_98497,Genetic peripheral neuropathy,genetic disorder,False,0.03431711111111112,0.0,0.0,0.0,0.0,0.0,0.0,0.03431711111111112,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.03431711111111112
ENSG00000160613-HP_0000707,ENSG00000160613,PCSK7,HP_0000707,abnormality of the nervous system,phenotype,False,0.028066930555555553,0.0,0.0,0.0,0.0,0.0,0.0,0.028066930555555553,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.028066930555555553
ENSG00000154678-EFO_0002970,ENSG00000154678,PDE1C,EFO_0002970,muscular disease,skeletal system disease,False,0.125,0.0,0.0,0.125,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.125,0.0
ENSG00000160191-EFO_0000712,ENSG00000160191,PDE9A,EFO_0000712,stroke,cardiovascular disease; other disease,True,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.0
ENSG00000154678-EFO_0004247,ENSG00000154678,PDE1C,EFO_0004247,mood disorder,nervous system disease; other disease,False,1.0,0.0,0.0,1.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1,0.0
ENSG00000163114-Orphanet_68367,ENSG00000163114,PDHA2,Orphanet_68367,Inborn errors of metabolism,metabolic disease; genetic disorder,False,0.03431711111111112,0.0,0.0,0.0,0.0,0.0,0.0,0.03431711111111112,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.03431711111111112