Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.


Journal Article

Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.

Full Text

Cited Authors

  • Subramanian, A; Tamayo, P; Mootha, VK; Mukherjee, S; Ebert, BL; Gillette, MA; Paulovich, A; Pomeroy, SL; Golub, TR; Lander, ES; Mesirov, JP

Published Date

  • October 2005

Published In

Volume / Issue

  • 102 / 43

Start / End Page

  • 15545 - 15550

PubMed ID

  • 16199517

Pubmed Central ID

  • 16199517

Electronic International Standard Serial Number (EISSN)

  • 1091-6490

International Standard Serial Number (ISSN)

  • 0027-8424

Digital Object Identifier (DOI)

  • 10.1073/pnas.0506580102


  • eng