Zhen Jiang1, Robert Gentleman. 1. Computational Biology, 1100 Fairview Avenue. N. M2-B876, PO Box 19024, Seattle, WA 98109-1024, USA. zjiang@fhcrc.org
Abstract
MOTIVATION: Gene Set Enrichment Analysis (GSEA) has been developed recently to capture changes in the expression of pre-defined sets of genes. We propose number of extensions to GSEA, including the use of different statistics to describe the association between genes and phenotypes of interest. We make use of dimension reduction procedures, such as principle component analysis, to identify gene sets with correlated expression. We also address issues that arise when gene sets overlap. RESULTS: Our proposals extend the range of applicability of GSEA and allow for adjustments based on other covariates. We have provided a well-defined procedure to address interpretation issues that can raise when gene sets have substantial overlap. We have shown how standard dimension reduction methods, such as PCA, can be used to help further interpret GSEA. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Gene Set Enrichment Analysis (GSEA) has been developed recently to capture changes in the expression of pre-defined sets of genes. We propose number of extensions to GSEA, including the use of different statistics to describe the association between genes and phenotypes of interest. We make use of dimension reduction procedures, such as principle component analysis, to identify gene sets with correlated expression. We also address issues that arise when gene sets overlap. RESULTS: Our proposals extend the range of applicability of GSEA and allow for adjustments based on other covariates. We have provided a well-defined procedure to address interpretation issues that can raise when gene sets have substantial overlap. We have shown how standard dimension reduction methods, such as PCA, can be used to help further interpret GSEA. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Lin S Chen; Carolyn M Hutter; John D Potter; Yan Liu; Ross L Prentice; Ulrike Peters; Li Hsu Journal: Am J Hum Genet Date: 2010-06-11 Impact factor: 11.025
Authors: Arna Katewa; Yugang Wang; Jason A Hackney; Tao Huang; Eric Suto; Nandhini Ramamoorthi; Cary D Austin; Meire Bremer; Jacob Zhi Chen; James J Crawford; Kevin S Currie; Peter Blomgren; Jason DeVoss; Julie A DiPaolo; Jonathan Hau; Adam Johnson; Justin Lesch; Laura E DeForge; Zhonghua Lin; Marya Liimatta; Joseph W Lubach; Sami McVay; Zora Modrusan; Allen Nguyen; Chungkee Poon; Jianyong Wang; Lichuan Liu; Wyne P Lee; Harvey Wong; Wendy B Young; Michael J Townsend; Karin Reif Journal: JCI Insight Date: 2017-04-06