Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50. Epub 2005 Sep 30.

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

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

Source

Broad Institute of Massachusetts Institute of Technology and Harvard, 320 Charles Street, Cambridge, MA 02141, USA.

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.

Comment in

Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15278-9.

PMID:: 16199517; [PubMed - indexed for MEDLINE]
PMCID: PMC1239896

Free PMC Article

Images from this publication.See all images (3) Free text

MeSH Terms

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Related citations

Improving gene set analysis of microarray data by SAM-GS. [BMC Bioinformatics. 2007]
Improving gene set analysis of microarray data by SAM-GS.
Dinu I, Potter JD, Mueller T, Liu Q, Adewale AJ, Jhangri GS, Einecke G, Famulski KS, Halloran P, Yasui Y. BMC Bioinformatics. 2007 Jul 5; 8:242. Epub 2007 Jul 5.
Comparative evaluation of gene-set analysis methods. [BMC Bioinformatics. 2007]
Comparative evaluation of gene-set analysis methods.
Liu Q, Dinu I, Adewale AJ, Potter JD, Yasui Y. BMC Bioinformatics. 2007 Nov 7; 8:431. Epub 2007 Nov 7.
GAGE: generally applicable gene set enrichment for pathway analysis. [BMC Bioinformatics. 2009]
GAGE: generally applicable gene set enrichment for pathway analysis.
Luo W, Friedman MS, Shedden K, Hankenson KD, Woolf PJ. BMC Bioinformatics. 2009 May 27; 10:161. Epub 2009 May 27.
Review Current status of gene expression profiling in the diagnosis and management of acute leukaemia. [Br J Haematol. 2009]
Review Current status of gene expression profiling in the diagnosis and management of acute leukaemia.
Bacher U, Kohlmann A, Haferlach T. Br J Haematol. 2009 Jun; 145(5):555-68. Epub 2009 Mar 16.
Review Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts. [J Clin Oncol. 2006]
Review Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts.
Hayes DN, Monti S, Parmigiani G, Gilks CB, Naoki K, Bhattacharjee A, Socinski MA, Perou C, Meyerson M. J Clin Oncol. 2006 Nov 1; 24(31):5079-90.

See reviews... See all...

Cited by over 100 PubMed Central articles

Pathway-Wide Association Study Implicates Multiple Sterol Transport and Metabolism Genes in HDL Cholesterol Regulation. [Front Genet. 2011]
Pathway-Wide Association Study Implicates Multiple Sterol Transport and Metabolism Genes in HDL Cholesterol Regulation.
Wang K, Edmondson AC, Li M, Gao F, Qasim AN, Devaney JM, Burnett MS, Waterworth DM, Mooser V, Grant SF, et al. Front Genet. 2011; 2:41. Epub 2011 Jul 5.
MicroRNA Signatures in Tumor Tissue Related to Angiogenesis in Non-Small Cell Lung Cancer. [PLoS One. 2012]
MicroRNA Signatures in Tumor Tissue Related to Angiogenesis in Non-Small Cell Lung Cancer.
Donnem T, Fenton CG, Lonvik K, Berg T, Eklo K, Andersen S, Stenvold H, Al-Shibli K, Al-Saad S, Bremnes RM, et al. PLoS One. 2012; 7(1):e29671. Epub 2012 Jan 25.
Single sample expression-anchored mechanisms predict survival in head and neck cancer. [PLoS Comput Biol. 2012]
Single sample expression-anchored mechanisms predict survival in head and neck cancer.
Yang X, Regan K, Huang Y, Zhang Q, Li J, Seiwert TY, Cohen EE, Xing HR, Lussier YA. PLoS Comput Biol. 2012 Jan; 8(1):e1002350. Epub 2012 Jan 26.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Gene set enrichment analysis: a knowledge-based approach for interpreting genome...
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Proc Natl Acad Sci U S A. 2005 Oct 25 ;102(43):15545-50. Epub 2005 Sep 30 .

PubMed
20-Hz whole body vibration training fails to counteract the decrease in leg musc...
20-Hz whole body vibration training fails to counteract the decrease in leg muscle volume caused by 14 days of 6 degrees head down tilt bed rest.
Eur J Appl Physiol. 2009 Jan ;105(2):271-7. Epub 2008 Oct 30 .

PubMed
Meta-analysis of the association between the monoamine oxidase-A gene and mood d...
Meta-analysis of the association between the monoamine oxidase-A gene and mood disorders.
Psychiatr Genet. 2010 Feb ;20(1):1-7.

PubMed
Microbial degradation pathways of the herbicide dichlobenil in soils with differ...
Microbial degradation pathways of the herbicide dichlobenil in soils with different history of dichlobenil-exposure.
Environ Pollut. 2007 Jul ;148(1):343-51. Epub 2007 Jan 18 .

PubMed
Toll-like receptor-3 as a target to enhance bioactivity of cancer immunotherapy.
Toll-like receptor-3 as a target to enhance bioactivity of cancer immunotherapy.
Am J Obstet Gynecol. 2010 Jun ;202(6):608.e1-8. Epub 2010 Jan 18 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to:

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

Source

Abstract

Comment in

MeSH Terms

MeSH Terms

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Related citations

Cited by over 100 PubMed Central articles

Related information

Recent activity

Simple NCBI Directory

Getting Started

Resources

Popular

Featured

NCBI Information