%0 Journal Article
%T PeakidentificationforChIP-seqdatawithnocontrols
%A Yanfeng ZHANG
%A Bing SU
%J 动物学研究
%P 121-128
%D 2012
%R 10.3724/SP.J.1141.2012.E05-06E121
%X Chromatinimmunoprecipitationfollowedbysequencing(ChIP-seq)isincreasinglybeingusedforgenome-wideprofilingoftranscriptionalregulation,asthistechniqueenablesdissectionofthegeneregulatorynetworks.Withinputascontrol,avarietyofstatisticalmethodshavebeenproposedforidentifyingtheenrichedregionsinthegenome,i.e.,thetranscriptionalfactorbindingsitesandchromatinmodifications.However,whentherearenocontrols,whetherpeakcallingisstillreliableawaitssystematicevaluations.Toaddressthisquestion,weusedaBayesianframeworkapproachtoshowtheeffectivenessofpeakcallingwithoutcontrols(PCWC).UsingseveraldifferenttypesofChIP-seqdata,wedemonstratedtherelativelyhighaccuracyofPCWCwithlessthana5%falsediscoveryrate(FDR).Comparedwithpreviouslypublishedmethods,e.g.,themodel-basedanalysisofChIP-seq(MACS),PCWCisreliablewithlowerFDR.Furthermore,tointerpretthebiologicalsignificanceofthecalledpeaks,incombinationwithmicroarraygeneexpressiondata,geneontologyannotationandsubsequentmotifdiscovery,ourresultsindicatePCWCpossessesahighefficiency.Additionally,usinginsilicodata,onlyasmallnumberofpeakswereidentified,suggestingthesignificantlylowFDRforPCWC.
%K ChIP-seq
%K Bayesian
%K Peakcalling
%K Generegulation
%U http://www.zoores.ac.cn/CN/abstract/abstract3267.shtml