Molecular Signatures Database

Overview

The Molecular Signatures Database (MSigDB) is a resource of tens of thousands of annotated gene sets for use with GSEA software, divided into Human and Mouse collections. From this web site, you can

  • Examine a gene set and its annotations. See, for example, the HALLMARK_APOPTOSIS human gene set page.
  • Browse gene sets by name or collection.
  • Search for gene sets by keyword.
  • Investigate gene sets:
    • Compute overlaps between your gene set and gene sets in MSigDB.
    • Categorize members of a gene set by gene families.
    • View the expression profile of a gene set in a provided public expression compendia.
    • Investigate the gene set in the online biological network repository NDEx
  • Download gene sets.

License Terms

GSEA and MSigDB are available for use under these license terms.

Please register to download the GSEA software and the MSigDB gene sets, and to use our web tools. After registering, you can log in at any time using your email address. Registration is free. Its only purpose is to help us track usage for reports to our funding agencies.

Current Version

Human MSigDB v2025.1.Hs updated June 2025. Release notes.

Mouse MSigDB v2025.1.Mm updated June 2025. Release notes.

Citing the MSigDB

To cite your use of the Molecular Signatures Database (MSigDB), a joint project of UC San Diego and Broad Institute, please reference Subramanian, Tamayo, et al. (2005, PNAS) and one or more of the following as appropriate: Liberzon, et al. (2011, Bioinformatics), Liberzon, et al. (2015, Cell Systems), and also the source for the gene set as listed on the gene set page. If you use Mouse MSigDB, please also cite Castanza, et al. (2023, Nature Methods).

Funding

GSEA and MSigDB are currently funded by a grant from NCI's Informatics Technology for Cancer Research (ITCR)

Human Collections

H hallmark gene sets  are coherently expressed signatures derived by aggregating many MSigDB gene sets to represent well-defined biological states or processes.
C5 ontology gene sets  consist of genes annotated by the same ontology term.
C1 positional gene sets   corresponding to human chromosome cytogenetic bands.
C6 oncogenic signature gene sets  defined directly from microarray gene expression data from cancer gene perturbations.
C2 curated gene sets  from online pathway databases, publications in PubMed, and knowledge of domain experts.
C7 immunologic signature gene sets  represent cell states and perturbations within the immune system.
C3 regulatory target gene sets  based on gene target predictions for microRNA seed sequences and predicted transcription factor binding sites.
C8 cell type signature gene sets  curated from cluster markers identified in single-cell sequencing studies of human tissue.
C4 computational gene sets  defined by mining large collections of cancer-oriented expression data.

Mouse Collections

MH mouse-ortholog hallmark gene sets  are versions of gene sets in the MSigDB Hallmarks collection mapped to their mouse orthologs.
M5 ontology gene sets  consist of genes annotated by the same ontology term.
M1 positional gene sets   corresponding to mouse chromosome cytogenetic bands.
M7 immunologic signature gene sets  represent cell states and perturbations within the immune system.
M2 curated gene sets  from online pathway databases, publications in PubMed, and knowledge of domain experts.
M8 cell type signature gene sets  curated from cluster markers identified in single-cell sequencing studies of mouse tissue.
M3 regulatory target gene sets  based on gene target predictions for microRNA seed sequences and predicted transcription factor binding sites.

Other Gene Set Resources

If you would like to suggest or contribute new gene sets, please contact us at genesets@broadinstitute.org.