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).

• Download the GSEA software and additional resources to analyze, annotate and interpret enrichment results.
• Explore the Molecular Signatures Database (MSigDB), a collection of annotated gene sets for use with GSEA software.
• View documentation describing GSEA and MSigDB.
• View guidelines for using RNA-seq datasets with GSEA.
• Use the GenePattern platform to run analyses, including classical GSEA and a variation designed for single-sample analysis (ssGSEA).

What's New

30-Jan-2026: MSigDB 2026.1 introduces the Human C9 collection of computational perturbation signature gene sets. The initial cohort of sets in this collection define the transcriptional signatures of various oncogene dependences. This release also provides collection updates for GO, Reactome, WikiPathways, and HPO, along with numerous new set additions for the Human and Mouse databases. Gene data has been updated to Ensembl 115. See the Human and Mouse release notes for details.

6-Jun-2025: MSigDB 2025.1 introduces the Mouse M7 collection of immunologic signature gene sets, comprising 787 sets curated from the Mouse Immune Dictionary (Cui et al. 2023). It also provides collection updates for GO, Reactome, and WikiPathways, along with numerous new set additions for the Human and Mouse databases. Gene data has been updated to Ensembl 114. See the Human and Mouse release notes for details.

8-Mar-2025: GSEA 4.4.0 released. This release updates GSEA for Java 21. It also addresses some issues launching on recent versions of MacOS. The algorithm and essential functionality remain unchanged. See the release notes for details.

13-Sep-2023: Our new publication describing the development of our Mouse-native MSigDB Collections is out now in Nature Methods! Go check it out!

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 supported by a grant from the National Cancer Institute of the NIH.