Pathway Analysis of Expression Data Deciphering Functional Building Blocks of Complex Diseases 英文参考文献.docVIP

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Pathway Analysis of Expression Data Deciphering Functional Building Blocks of Complex Diseases 英文参考文献.doc

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Pathway Analysis of Expression Data Deciphering Functional Building Blocks of Complex Diseases 英文参考文献

Education PathwayAnalysisofExpressionData:Deciphering FunctionalBuildingBlocksofComplexDiseases FrankEmmert-Streib1*,GalinaV.Glazko2 1Computational Biology and Machine Learning Lab, Center for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom, 2Division of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America This PLoS Computational Biology tuto- biology’s trend of data integration and interpretation [5–7], focusing on sets of functionally related genes (e.g., from the same signaling or metabolic pathway) ratherthanindividualgenes. mation,remainsanopenproblemaswell. Despite considerable differences between manypathway-basedapproaches[5],their common theme is to focus on a systems leveloffunctional components [10–12] of themolecularsystemcomprisingmany,as opposedtoindividual,genes. rialwaspresentedatISMB2010. Introduction Thepurposeofthispaperistoprovide abriefguidetomethodsfortheanalysisof differentially expressed pathways or gene sets, which we simply call pathway-based methods.Forthisreason,weemphasizean illustration of the methods rather than their technical description. The reader is encouraged to follow the cited literature fortechnicaldetails. Identification of differentially expressed pathways from expression data is an importantproblembecauseitallowsusto gain insights into the functional working mechanismofcellsbeyondthedetectionof differentiallyexpressedgenes.Inthispaper wepresentabriefguidetomethodsforthe pathway analysis of expression data. De- spitethevastamountofdifferentstatistical methods thathave beendeveloped sofar, there is a considerable similarity among them, allowing a systematic classification and a reduction to a few null hypotheses thatareeffectivelytested. Theanalysisofpathwaysthataresignif- icantly differentially expressed is intuitively appealing and there are several reasons in su