Molecular Signatures Database v4.0

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 ANGIOGENESIS 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 any of the three provided public expression compendia.

Registration

Please register to download the GSEA software 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 v4.0 updated May 31, 2013. Release notes.
GSEA/MSigDB web site v4.02 released Jan 18, 2014

Contributors

The MSigDB is maintained by the GSEA team with the support of our MSigDB Scientific Advisory Board. We also welcome and appreciate contributions to this shared resource and encourage users to submit their gene sets to genesets@broadinstitute.org. Our thanks to our many contributors.

Funded by: National Cancer Institute, National Institutes of Health, National Institute of General Medical Sciences.

Collections

The MSigDB gene sets are divided into 7 major collections:

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 signatures  defined directly from microarray gene expression data from cancer gene perturbations.

c7 immunologic signatures  defined directly from microarray gene expression data from immunologic studies.

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 also the source for the gene set as listed on the gene set page.

Contact Us

If you have comments or questions, please contact us: gsea@broadinstitute.org.