Molecular Signatures Database v7.0

Overview

The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. From this web site, you can

  • Search for gene sets by keyword.
  • Browse gene sets by name or collection.
  • Examine a gene set and its annotations. See, for example, the GO_NOTCH_SIGNALING_PATHWAY gene set page.
  • Download gene sets.
  • 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.

License Terms

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

Please register to download the GSEA software, access our web tools, and view the MSigDB gene sets. 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

MSigDB database v7.0 updated August 2019. Release notes.

Gene Sets from Community Contributors

We welcome community contributions of gene sets to this shared resource. We also appreciate information about external collections of gene sets that are not part of MSigDB but may be useful for certain analyses. We encourage users to contact us at genesets@broadinstitute.org.

Funding

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

Collections

The MSigDB gene sets are divided into 8 major collections:
H hallmark gene sets  are coherently expressed signatures derived by aggregating many MSigDB gene sets to represent well-defined biological states or processes.
C1 positional gene sets  for each human chromosome and cytogenetic band.
C2 curated gene sets  from online pathway databases, publications in PubMed, and knowledge of domain experts.
C3 motif gene sets  based on conserved cis-regulatory motifs from a comparative analysis of the human, mouse, rat, and dog genomes.
C4 computational gene sets  defined by mining large collections of cancer-oriented microarray data.
C5 GO gene sets  consist of genes annotated by the same GO terms.
C6 oncogenic gene sets  defined directly from microarray gene expression data from cancer gene perturbations.
C7 immunologic gene sets  defined directly from microarray gene expression data from immunologic studies.

Supplementary Gene Sets for Single Cell Identities

The MSigDB team has developed a preliminary collection of cell identity marker gene sets from single-cell sequencing data of primarily normal human tissues.

Citing the MSigDB

To cite your use of the Molecular Signatures Database (MSigDB), please reference Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550) and one or more of the following as appropriate: Liberzon, et al. (2011, Bionformatics), Liberzon, et al. (2015, Cell Systems), and also the source for the gene set as listed on the gene set page.