The Molecular Signatures Database (MSigDB) 3.0, released in September 2010, is an updated version of the widely used repository of gene sets for enrichment analysis. This new version includes over 6700 gene sets, a complete revision of canonical pathways and experimental signatures from publications, enhanced annotations, and upgrades to the web interface. MSigDB is freely available for non-commercial use and is integrated with the Gene Set Enrichment Analysis (GSEA) software. The database covers a diverse range of gene set sources and types, including signatures from original research publications and collections from resources like GO, KEGG, TRANSFAC, and L2L. The gene sets are curated manually and computationally, ensuring unique and stable identifiers. The MSigDB website allows users to view annotated gene sets, perform simple searches, and use online analysis tools for overlap computation, heat map visualization, and gene family categorization. The database is maintained by the Broad Institute of MIT and Harvard, with funding from the National Cancer Institute.The Molecular Signatures Database (MSigDB) 3.0, released in September 2010, is an updated version of the widely used repository of gene sets for enrichment analysis. This new version includes over 6700 gene sets, a complete revision of canonical pathways and experimental signatures from publications, enhanced annotations, and upgrades to the web interface. MSigDB is freely available for non-commercial use and is integrated with the Gene Set Enrichment Analysis (GSEA) software. The database covers a diverse range of gene set sources and types, including signatures from original research publications and collections from resources like GO, KEGG, TRANSFAC, and L2L. The gene sets are curated manually and computationally, ensuring unique and stable identifiers. The MSigDB website allows users to view annotated gene sets, perform simple searches, and use online analysis tools for overlap computation, heat map visualization, and gene family categorization. The database is maintained by the Broad Institute of MIT and Harvard, with funding from the National Cancer Institute.