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dc.contributor.author Barry, Bill en_US
dc.date.accessioned 2011-06-21T17:29:33Z
dc.date.available 2011-06-21T17:29:33Z
dc.date.issued 2010 en_US
dc.identifier.citation Gatti,Daniel M.;Barry,William T.;Nobel,Andrew B.;Rusyn,Ivan;Wright,Fred A.. 2010. Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets. Bmc Genomics 11( ): 574-574. en_US
dc.identifier.issn 1471-2164 en_US
dc.identifier.uri http://hdl.handle.net/10161/4348
dc.description.abstract Background: Analysis of microarray experiments often involves testing for the overrepresentation of pre-defined sets of genes among lists of genes deemed individually significant. Most popular gene set testing methods assume the independence of genes within each set, an assumption that is seriously violated, as extensive correlation between genes is a well-documented phenomenon. Results: We conducted a meta-analysis of over 200 datasets from the Gene Expression Omnibus in order to demonstrate the practical impact of strong gene correlation patterns that are highly consistent across experiments. We show that a common independence assumption-based gene set testing procedure produces very high false positive rates when applied to data sets for which treatment groups have been randomized, and that gene sets with high internal correlation are more likely to be declared significant. A reanalysis of the same datasets using an array resampling approach properly controls false positive rates, leading to more parsimonious and high-confidence gene set findings, which should facilitate pathway-based interpretation of the microarray data. Conclusions: These findings call into question many of the gene set testing results in the literature and argue strongly for the adoption of resampling based gene set testing criteria in the peer reviewed biomedical literature. en_US
dc.language.iso en_US en_US
dc.publisher BIOMED CENTRAL LTD en_US
dc.relation.isversionof doi:10.1186/1471-2164-11-574 en_US
dc.subject expression data en_US
dc.subject microarray data en_US
dc.subject functional categories en_US
dc.subject enrichment en_US
dc.subject omnibus en_US
dc.subject bioinformatics en_US
dc.subject bioconductor en_US
dc.subject carcinomas en_US
dc.subject knowledge en_US
dc.subject patterns en_US
dc.subject biotechnology & applied microbiology en_US
dc.subject genetics & heredity en_US
dc.title Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets en_US
dc.title.alternative en_US
dc.description.version Version of Record en_US
duke.date.pubdate 2010-10-18 en_US
duke.description.endpage 574 en_US
duke.description.issue en_US
duke.description.startpage 574 en_US
duke.description.volume 11 en_US
dc.relation.journal Bmc Genomics en_US

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