The Molecular Signatures Database (MSigDB) 3.0 is a comprehensive resource for gene sets used in the analysis of genomic data. It includes over 6700 gene sets, revised canonical pathways, and enhanced annotations. MSigDB is freely available for non-commercial use at http://www.broadinstitute.org/msigdb. It is specifically designed for enrichment analysis methods and is natively integrated with the Gene Set Enrichment Analysis (GSEA) software. MSigDB covers a wide range of gene set sources, including those derived from original research publications, specialized resources like GO, KEGG, TRANSFAC, and L2L, as well as those obtained through manual curation and computational methods. The database includes gene sets from human genes, some model organisms, and provides annotations with HUGO gene symbols and human Entrez Gene IDs. MSigDB 3.0 includes more detailed annotations, including links to external resources such as PubMed, GEO, ArrayExpress, PubChem, and Entrez Gene. The database also provides online tools for searching and analyzing gene sets, including computing overlaps between gene sets, viewing heat maps, and categorizing genes by gene families. The online resource allows users to find gene sets by searching for keywords in the annotations and provides detailed information on each gene set. The MSigDB web site has been updated to include more detailed information on gene sets and their annotations. The database is supported by the National Cancer Institute and has no conflicts of interest.The Molecular Signatures Database (MSigDB) 3.0 is a comprehensive resource for gene sets used in the analysis of genomic data. It includes over 6700 gene sets, revised canonical pathways, and enhanced annotations. MSigDB is freely available for non-commercial use at http://www.broadinstitute.org/msigdb. It is specifically designed for enrichment analysis methods and is natively integrated with the Gene Set Enrichment Analysis (GSEA) software. MSigDB covers a wide range of gene set sources, including those derived from original research publications, specialized resources like GO, KEGG, TRANSFAC, and L2L, as well as those obtained through manual curation and computational methods. The database includes gene sets from human genes, some model organisms, and provides annotations with HUGO gene symbols and human Entrez Gene IDs. MSigDB 3.0 includes more detailed annotations, including links to external resources such as PubMed, GEO, ArrayExpress, PubChem, and Entrez Gene. The database also provides online tools for searching and analyzing gene sets, including computing overlaps between gene sets, viewing heat maps, and categorizing genes by gene families. The online resource allows users to find gene sets by searching for keywords in the annotations and provides detailed information on each gene set. The MSigDB web site has been updated to include more detailed information on gene sets and their annotations. The database is supported by the National Cancer Institute and has no conflicts of interest.