Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis.docVIP

Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis.doc

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Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis

Wangetal.BMCPlantBiology2012,12:138 /1471-2229/12/138 RESEARCH ARTICLE OpenAccess Genome-scaleidentificationofcell-wallrelated genesinArabidopsisbasedonco-expression networkanalysis ShanWang1,3,4?,YanbinYin1,2?,QinMa1,2,XiaojiaTang1,DongyunHao3,4*andYingXu1,2,5* Abstract Background:Identificationofthenovelgenesrelevanttoplantcell-wall(PCW)synthesisrepresentsahighly importantandchallengingproblem.Althoughsubstantialeffortshavebeeninvestedintostudyingthisproblem, thevastmajorityofthePCWrelatedgenesremainunknown. Results:HerewepresentacomputationalstudyfocusedonidentificationofthenovelPCWgenesinArabidopsis basedontheco-expressionanalysesoftranscriptomicdatacollectedunder351conditions,usingabi-clustering technique.Ouranalysisidentified217highlyco-expressedgeneclusters(modules)undersomeexperimental conditions,eachcontainingatleastonegeneannotatedasPCWrelatedaccordingtothePurdueCellWallGene Familiesdatabase.Theseco-expressionmodulescover349known/annotatedPCWgenesand2,438new candidates.Foreachcandidategene,weannotatedthespecificPCWsynthesisstagesinwhichitisinvolvedand predictedthedetailedfunction.Inaddition,fortheco-expressedgenesineachmodule,wepredictedandanalyzed theircisregulatorymotifsinthepromotersusingourmotifdiscoverypipeline,providingstrongevidencethatthe genesineachco-expressionmodulearetranscriptionallyco-regulated.Fromtheallco-expressionmodules,we inferthat108modulesarerelatedtofourmajorPCWsynthesiscomponents,usingthreecomplementarymethods. Conclusions:Webelieveourapproachanddatapresentedherewillbeusefulforfurtheridentificationand characterizationofPCWgenes.AllthepredictedPCWgenes,co-expressionmodules,motifsandtheirannotations areavailableataweb-baseddatabase:/publications/materials/shanwang/CWRPdb/index. html. Keywords:Plantcellwall,Arabidopsis,Co-expressionnetworkanalysis,Bi-clustering,Cisregulatorymotifs Background to mention that it is the focal point of cellulosic biofuel Plant cell walls (PCWs)are mainly composed of polysac- studies.Itisestimatedthatge

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