Evaluation of Algorithm Performance in ChIP-Seq Peak Detection 英文参考文献.docVIP

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Evaluation of Algorithm Performance in ChIP-Seq Peak Detection 英文参考文献.doc

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Evaluation of Algorithm Performance in ChIP-Seq Peak Detection 英文参考文献

EvaluationofAlgorithmPerformanceinChIP-SeqPeak Detection ElizabethG.Wilbanks1,3,MarcT.Facciotti1,2,3 * 1Graduate Group in Microbiology, University of California Davis, Davis, California, United States of America, 2Department of Biomedical Engineering, University of CaliforniaDavis,Davis,California,UnitedStatesofAmerica,3GenomeCenter,UniversityofCaliforniaDavis,Davis,California,UnitedStatesofAmerica Abstract Next-generationDNAsequencingcoupledwithchromatinimmunoprecipitation(ChIP-seq)isrevolutionizingourabilityto interrogatewholegenomeprotein-DNAinteractions.IdentificationofproteinbindingsitesfromChIP-seqdatahasrequired novelcomputationaltools,distinctfromthoseusedfortheanalysisofChIP-Chipexperiments.Thegrowingpopularityof ChIP-seqspurredthedevelopmentofmanydifferentanalyticalprograms(atlastcount,wenoted31opensourcemethods), eachwithsomepurportedadvantage.Giventhattheliteratureisdenseandempiricalbenchmarkingchallenging,selecting anappropriatemethodforChIP-seqanalysishasbecomeadauntingtask.Hereinwecomparetheperformanceofeleven differentpeakcallingprogramsoncommonempirical,transcriptionfactordatasetsandmeasuretheirsensitivity,accuracy andusability.Ouranalysisprovidesanunbiasedcriticalassessmentofavailabletechnologies,andshouldassistresearchers inchoosingasuitabletoolforhandlingChIP-seqdata. Citation: Wilbanks EG, Facciotti MT (2010) Evaluation of Algorithm Performance in ChIP-Seq Peak Detection. PLoS ONE 5(7): e11471. doi:10.1371/ journal.pone.0011471 Editor:GertJanC.Veenstra,RadboudUniversityNijmegen,Netherlands ReceivedApril20,2010;AcceptedJune14,2010;PublishedJuly8,2010 Copyright:?2010Wilbanks,Facciotti.Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense,whichpermits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:ThisworkwassupportedbyaNationalScienceFoundationGraduateResearchFellowshiptoEGWandMTF’sstart-upfundsfromUCDavis.Thefunders hadnoroleinstudydesign,datacol