SEAS A System for SEED-Based Pathway Enrichment Analysis 英文参考文献.docVIP

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SEAS A System for SEED-Based Pathway Enrichment Analysis 英文参考文献.doc

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SEAS:ASystemforSEED-BasedPathwayEnrichment Analysis XizengMao1.,YuZhang3,4.,YingXu1,2,3 * 1Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United StatesofAmerica,2BioEnergyScienceCenterBESC,UniversityofGeorgia,Athens,Georgia,UnitedStatesofAmerica,3CollegeofComputerScienceandTechnology,Jilin University,Changchun,China,4KeyLaboratoryofSymbolicComputationandKnowledgeEngineeringoftheMinistryofEducation,JilinUniversity,Changchun,China Abstract Pathwayenrichmentanalysisrepresentsakeytechniqueforanalyzinghigh-throughputomicdata,anditcanhelptolink individual genes or proteins foundto be differentially expressed under specific conditions to well-understood biological pathways. We present here a computational tool, SEAS, for pathway enrichment analysis over a given set of genes in a specifiedorganismagainstthepathways(orsubsystems)intheSEEDdatabase,apopularpathwaydatabaseforbacteria. SEAS maps a given set of genes of a bacterium to pathway genes covered by SEED through gene ID and/or orthology mapping,andthencalculatesthestatisticalsignificanceoftheenrichmentofeachrelevantSEEDpathwaybythemapped genes.OurevaluationofSEASindicatesthattheprogramprovideshighlyreliablepathwaymappingresultsandidentifies moreorganism-specificpathwaysthansimilarexistingprograms.SEASispubliclyreleasedundertheGPLlicenseagreement andfreelyavailableat/,xizeng/research/seas/. Citation:MaoX,ZhangY,XuY(2011)SEAS:ASystemforSEED-BasedPathwayEnrichmentAnalysis.PLoSONE6(7):e22556.doi:10.1371/journal.pone.0022556 Editor:VladimirBrusic,Dana-FarberCancerInstitute,UnitedStatesofAmerica ReceivedMarch18,2011;AcceptedJune24,2011;PublishedJuly22,2011 Copyright:?2011Maoetal.Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense,whichpermitsunrestricted use,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:Thisworkwassupportedinpartbythe