Refining transcriptional regulatory networks using network evolutionary models and gene histories 英文参考文献.docVIP

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Refining transcriptional regulatory networks using network evolutionary models and gene histories 英文参考文献.doc

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Refining transcriptional regulatory networks using network evolutionary models and gene histories 英文参考文献

ZhangandMoretAlgorithmsforMolecularBiology2010,5:1 /content/5/1/1 RESEARCH OpenAccess Refiningtranscriptionalregulatorynetworksusing networkevolutionarymodelsandgenehistories XiuweiZhang,BernardMEMoret* Abstract Background:Computationalinferenceoftranscriptionalregulatorynetworksremainsachallengingproblem,in partduetothelackofstrongnetworkmodels.Inthispaperwepresentevolutionaryapproachestoimprovethe inferenceofregulatorynetworksforafamilyoforganismsbydevelopinganevolutionarymodelforthese networksandtakingadvantageofestablishedphylogeneticrelationshipsamongtheseorganisms.Inprevious work,weusedasimpleevolutionarymodelandprovidedextensivesimulationresultsshowingthatphylogenetic information,combinedwithsuchamodel,couldbeusedtogainsignificantimprovementsontheperformanceof currentinferencealgorithms. Results:Inthispaper,weextendtheevolutionarymodelsoastotakeintoaccountgeneduplicationsandlosses, whichareviewedasmajordriversintheevolutionofregulatorynetworks.Weshowhowtoadaptour evolutionaryapproachtothisnewmodelandprovidedetailedsimulationresults,whichshowsignificant improvementonthereferencenetworkinferencealgorithms.Differentevolutionaryhistoriesforgeneduplications andlossesarestudied,showingthatouradaptedapproachisfeasibleunderabroadrangeofconditions.Wealso provideresultsonbiologicaldata(cis-regulatorymodulesfor12speciesofDrosophila),confirmingoursimulation results. Introduction [6-8] ontheevolution ofregulatory networks in E.coli Transcriptional regulatory networks are models of the and S. cerevisiae has demonstrated the applicability of cellular regulatory system that governs transcription. such approaches to regulatory networks. They posit a Because establishing the topology of the network from simple evolutionary model for regulatory networks, benchexperimentsisverydifficultandtime-consuming, under which network edges are simply added or regulatory networksarecommonlyinferred fromgene- removed; they study how well such a model accounts expressiondata.V