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Proc Natl Acad Sci U S A DOI:10.1073/pnas.0506580102

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

Publication TypeJournal Article
Year of Publication2005
AuthorsSubramanian, A, Tamayo, P, Mootha, VK, Mukherjee, S, Ebert, BL, Gillette, MA, Paulovich, A, Pomeroy, SL, Golub, TR, Lander, ES, Mesirov, JP
JournalProc Natl Acad Sci U S A
Volume102
Issue43
Pages15545-50
Date Published2005 Oct 25
ISSN0027-8424
KeywordsCell Line, Tumor, Female, Gene Expression Profiling, Genes, p53, Genome, Humans, Leukemia, Myeloid, Acute, Lung Neoplasms, Male, Oligonucleotide Array Sequence Analysis, Precursor Cell Lymphoblastic Leukemia-Lymphoma
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.

URLhttp://www.pnas.org/cgi/pmidlookup?view=long&pmid=16199517
DOI10.1073/pnas.0506580102
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/16199517?dopt=Abstract

Alternate JournalProc. Natl. Acad. Sci. U.S.A.
PubMed ID16199517
PubMed Central IDPMC1239896
Grant ListT32 CA009172 / CA / NCI NIH HHS / United States