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