Overview

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically
significant, concordant differences between two biological states
(e.g. phenotypes).

What's New

24-Mar-2023: With the release of MSigDB 2023.1 we are introducing a SQLite database for the gene sets in both the Human (2023.1.Hs) and the Mouse (2023.1.Mm) resources. This new format brings the MSigDB contents and metadata with all of the searchability and manipulative power of a full relational database. See our documentation for more details on the contents and usage.

3-Mar-2023: MSigDB 2023.1 released. Updated to gene data from Ensembl 109. Human and Mouse collections for Reactome, GO, and WikiPathways have been updated, as well as HPO, Lung atlas sets from He et al. have been added to C8, and Uterine cell types from Zhang et al to M8, plus new user-submitted sets for C2 and M2 CGP. See the release notes for details.

2-Oct-2022: GSEA 4.3.2 released. This is a minor release to fix a bug on the species consistency check. See the release notes for details.

7-Sep-2022: Announcing the first release of Mouse MSigDB (v2022.1.Mm) with ~16,000 gene sets that can be used directly for GSEA analysis of mouse datasets without the need for orthology conversion. A new release of Human MSigDB (v2022.1.Hs) includes updates to Reactome, GO, HPO, and WikiPathways. See the 2022.1.Hs release notes and 2022.1.Mm release notes for details.

7-Sep-2022: GSEA 4.3.0 released. Adds support for convenient access to the new Mouse MSigDB database and makes adjustments for our new versioning scheme. See the release notes for details.

29-Mar-2022: MSigDB gene sets are now available as JSON bundles. Check our Downloads page for the full collections. Smaller bundles as well as extended metadata in TSV format are available from our Search page.

1-Mar-2022: GSEA 4.2.3 released. There is a new correlation metric (Spearman) and a new collapse mode (Absolute Max), plus better handling of missing values and many other fixes in 4.2.x. Log4J has been removed entirely from the code to avoid vulnerability concerns. All users are encouraged to update! See the release notes for details.

We need your help: Update on GSEA/MSigDB funding support

Last November we submitted a proposal to NCI's Information Technology for Cancer Research (ITCR) program for the continued funding of GSEA and MSigDB. Unfortunately, our proposal was not funded in this round, but we were encouraged to resubmit for the next one. This funding is critical for our continuing support and enhancement of the GSEA-MSigDB resource.

For our original submission many of you sent us emails of support, an important requirement for these grants. We now ask for your help again. We would greatly appreciate a short email message from you describing how the resource has been of value to your work and any concerns you may have about its continued availability.

Please send us your message of support to gsea-los@broadinstitute.org on or before Monday June 5, 2023.

Thanks in advance for your help and support.
The GSEA/MSigDB Team.


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.

Citing GSEA

To cite your use of the GSEA software, a joint project of UC San Diego and Broad Institute, please reference Subramanian, Tamayo, et al. (2005, PNAS) and Mootha, Lindgren, et al. (2003, Nature Genetics).

Funding

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