Cancer Program Publication

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
ProjectBioinformatics & Computational Biology
Abstract 
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.
AuthorsAravind Subramanian, Pablo Tamayo, Vamsi K. Mootha, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda Paulovich, Scott L. Pomeroy, Todd R. Golub, Eric S. Lander, and Jill P. Mesirov.
Publication Date09/30/2005
Contact emails lander@broad.mit.edu
mesirov@broad.mit.edu
Publication URLhttp://www.pnas.org/cgi/content/abstract/0506580102v1
KeywordsGSEA,KS,Kolmogorov-Smirnov,gene set, MSigDB, signatures, enrichment
 
Supplemental Information
URLs
NameURL
GSEA websitehttp://www.broad.mit.edu/gsea/
Nature Review article that discusses GSEAhttp://www.nature.com/nrg/journal/v7/n1/full/nrg1749.html