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Finding pathway regulators: gene set approach using peak identification algorithms

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Authors
Lee, Eunjee; Woo, Jung Hoon; Park, Ji Wan; Park, Taesung
Issue Date
2007-12-18
Publisher
BioMed Central
Citation
BMC Proceedings, 1(Suppl 1):S90
Abstract
Recently, a number of different approaches have been used to examine variation in gene expression and to identify genes whose level of transcript differed greatly among unrelated individuals. Previous studies have commonly focused on identifying determinants that regulate gene expressions by targeting individual genes. However, it is difficult to detect true differences in the level of gene expression among genotypes from noise due to issues such as multiple testing and limited sample size. To increase the statistical power for detecting this difference, we consider a 'gene set' approach by focusing on subtle but coordinated changes in gene expression across multiple genes rather than individual genes. We defined a 'gene set' as a set of genes in the same biological pathway and focused on identifying common regulators based on an assumption that the genes within the same pathway are controlled by common regulators. We applied the gene set approach to the expression data of mRNA in Centre d'Etude du Polymorphisme Humain lymphoblast cells to identify regulators controlling the genes in a biological pathway. Our gene set approach successfully identified potent regulators controlling gene expression in an inflammatory response pathway.
Language
English
URI
http://hdl.handle.net/10371/109991
DOI
https://doi.org/10.1186/1753-6561-1-S1-S90
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College of Natural Sciences (자연과학대학)Program in Bioinformatics (협동과정-생물정보학전공)Journal Papers (저널논문_협동과정-생물정보학전공)
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