GSEA | MSigDB

MSigDB needs your support! Many of you take advantage of the Hallmark collection of MSigDB to aid your interpretation of GSEA results. We are now preparing a research proposal to obtain funding to expand and enhance the collection. Our goal is to develop a new approach that will better elucidate and annotate component processes, thereby generating more coherent, accurate gene sets.

So, once again we ask for your help by sending us a short email telling us how you use MSigDB in your work, especially if you have found the Hallmarks collection useful. Please send your emails to [e-mail] on or before Friday September 28, 2018.

We're hiring! We are looking for a curator to join the GSEA-MSigDB project in the Mesirov Lab at UC San Diego.

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 v6.2 updated July 2018. Release notes.
GSEA/MSigDB web site v6.3 released January 2018

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.

Contributors

The MSigDB is maintained by the GSEA team. We also welcome and appreciate contributions to this shared resource and encourage users to submit their gene sets to [e-mail]. Our thanks to our many contributors.

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

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.

Gene Sets from Community Contributors

We have begun gathering gene sets from community contributors. These are not part of MSigDB but may be useful for certain analyses.