Extensions to gene set enrichment

• DOI: 10.1093/bioinformatics/btl599
• Publication Date: 2006-11-25T01:13:11Z
• Authors: Zhen Jiang; Robert Gentleman
• Keywords: Expression (computer science); Data set

Abstract Motivation: Gene Set Enrichment Analysis (GSEA) has been developed recently to capture changes in the expression of pre-defined sets genes. We propose number extensions GSEA, including use different statistics describe association between genes and phenotypes interest. make dimension reduction procedures, such as principle component analysis, identify gene with correlated expression. also address issues that arise when overlap. Results: Our proposals extend range applicability GSEA allow for adjustments based on other covariates. have provided a well-defined procedure interpretation can raise substantial shown how standard methods, PCA, be used help further interpret GSEA. Contact: [e-mail] Supplementary information: data are available at Bioinformatics online.