Broad Updates Molecular Signatures Database

By Bio-IT World Staff

December 7, 2010 | Researchers at the Broad Institute have released MSigDB 3.0 (the website is now in version 3.3), the most comprehensive molecular signatures database to date. MSigDB is a database of annotated gene sets that has become a standard tool for gaining insights from the results of genomic studies. Since its first release in 2005, more than 21,000 researchers have registered to use MSigDB as a stand-alone resource or with its popular companion analysis software, Gene Set Enrichment Analysis (GSEA).

The database includes 6,796 gene sets divided into five major collections: positional gene sets, curated gene sets, motif gene sets, computational gene sets, and GO gene sets. Gene sets can be searched, browsed, and downloaded after registration, and new options allow users to display and download gene sets as Entrez Gene identifiers, in addition to gene names and microarray probe set identifiers.

The MSigDB 3.0 update includes more than 1,200 new gene sets drawn from review of key scientific journals and 430 new canonical pathway gene sets from a new collaboration with the providers of the Reactome pathway database (www.reactome.org). There have been new gene set annotations, including direct links to corresponding microarray datasets in Gene Expression Omnibus (GEO) and ArrayExpress, and direct links to chemical structures in NCBI PubChem.

The database is maintined by the Broad's GSEA team and welcomes user-submitted gene sets to genesets@broadinstitute.org.