Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data II Analysis Beyond Single Gene英文文献资料.docVIP

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Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data II Analysis Beyond Single Gene英文文献资料.doc

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Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data II Analysis Beyond Single Gene英文文献资料

HindawiPublishingCorporation InternationalJournalofPlantGenomics Volume2008,ArticleID893941,13pages doi:10.1155/2008/893941 ReviewArticle BioinformaticToolsforInferringFunctionalInformationfrom PlantMicroarrayDataII:AnalysisBeyondSingleGene IssaCoulibalyandGrierP.Page DepartmentofBiostatistics,UniversityofAlabamaatBirmingham,1665UniversityBlvdSte327,Birmingham, AL35294-0022,USA CorrespondenceshouldbeaddressedtoGrierP.Page,gpage@ Received2November2007;Accepted5May2008 RecommendedbyGarySkuse Whileitispossibletointerpretmicroarrayexperimentsasinglegeneatatime,moststudiesgeneratelonglistsofdi?erentially expressedgeneswhoseinterpretationrequirestheintegrationofpriorbiologicalknowledge.Thispriorknowledgeisstoredin variouspublicandprivatedatabasesandcoversseveralaspectsofgenefunctionandbiologicalinformation.Inthisreview,we willdescribethetoolsandplaceswhereto?ndprioraccuratebiologicalinformationandhowtoprocessandincorporatethemto interpretmicroarraydataanalyses.Here,wehighlightselectedtoolsandresourcesforgeneclasslevelontologyanalysis(Section 2),genecoexpressionanalysis(Section3),genenetworkanalysis(Section4),biologicalpathwayanalysis(Section5),analysis oftranscriptionalregulation(Section6),andomicsdataintegration(Section7).Theoverallgoalofthisreviewistoprovide researcherswithtoolsandinformationtofacilitatetheinterpretationofmicroarraydata. Copyright?2008I.CoulibalyandGrierP.Page. This is an open access article distributed under the Creative Commons AttributionLicense,whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalworkis properlycited. 1. INTRODUCTION this review. We also address some theoretical aspects and methodologicalissuesofthealgorithmsimplementedinthe tools that have been recently developed for bioinformatic andwhatneedstobeconsideredwhenselectingatoolfor use. Microarray analysis is exploratory and very high dimen- sional, and the primary purpose is to generate a list of di?erentially regulated genes that can provide ins