Data sources versions

Release v3

Data sources and versions

Core features

• Ensembl Release 79 (March 2015): Core data for all species are built from Ensembl v79, so **_Homo sapiens_** uses now assembly GRCh38.p2 and GENCODE 22, you can query the rest of assemblies at [**Ensembl table of assemblies**](http://www.ensembl.org/info/website/archives/assembly.html). These includes genome sequence, gene sets, variation and regulation. Ensembl Release 75 (Feb 2014) is used only for keeping old **_Homo sapiens_ GRCh37** assembly.

Protein

• UniProt (Release March 2015)
• InterPro v50 v50 (Release Feb 2015)
• Polyphen2/Sift from Ensembl v79

Variation

• Ensembl v79 Variation (dbSNP 142)
• Population frequencies: 1000 genomes project, ESP (ExAC in preparation).

Regulatory

• Ensembl v79 Regulatory
• miRNAs:
• miRBase (Release 21)
• miRTarBase (Release 4.5)
• TargetScan (Release 6.0)

Clinical association

• ClinVar (Release March 2015)
• GWAS Catalog
• COSMIC v71 (Release March 2015)

Conservation scores

• PhastCons
• PhyloP
• (GERP++ in preparation)

Systems biology

• IntAct (Release March 2015)
• (Reactome 51 in preparation)

Others

• Gene Expression Atlas
• Gene disease association: DisGeNET
• DGIdb: http://dgidb.genome.wustl.edu/

Available species