Rule based classifier for the analysis of gene-gene and gene-environment interactions in genetic association studies 英文参考文献.docVIP

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Rule based classifier for the analysis of gene-gene and gene-environment interactions in genetic association studies 英文参考文献.doc

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Lehretal.BioDataMining2011,4:4 /content/4/1/4 BioData Mining RESEARCH OpenAccess Rulebasedclassifierfortheanalysisofgene-gene andgene-environmentinteractionsingenetic associationstudies ThorstenLehr1,2*,JingYuan2,DirkZeumer1,SupriyaJayadev2,3,MarylynDRitchie4 *Correspondence:thorsten. Abstract lehr@ 1BoehringerIngelheimPharma GmbHCo.KG,Departmentof Background:Severalmethodshavebeenpresentedfortheanalysisofcomplex interactionsbetweengeneticpolymorphismsand/orenvironmentalfactors.Despite DrugMetabolismand Pharmacokinetics,88397Biberach anderRiss,Germany Fulllistofauthorinformationis availableattheendofthearticle theavailablemethods,thereisstillaneedforalternativemethods,becausenosingle methodwillperformwellinallscenarios.Theaimofthisworkwastoevaluatethe performanceofthreeselectedrulebasedclassifieralgorithms,RIPPER,RIDORand PART,fortheanalysisofgeneticassociationstudies. Methods:Overall,42datasetsweresimulatedwiththreedifferentcase-control models,avaryingnumberofsubjects(300,600),SNPs(500,1500,3000)andnoise (5%,10%,20%).Thealgorithmswereappliedtoeachofthedatasetswithasetof algorithm-specificsettings.Resultswerefurtherinvestigatedwithrespecttoa)the Model,b)theRules,andc)theAttributelevel.Dataanalysiswasperformedusing WEKA,SASandPERL. Results:TheRIPPERalgorithmdiscoveredthetruecase-controlmodelatleastonce in33%ofthedatasets.TheRIDORandPARTalgorithmperformedpoorlyformodel detection.TheRIPPER,RIDORandPARTalgorithmdiscoveredthetruecase-control rulesinmorethan83%,83%and44%ofthedatasets,respectively.Allthree algorithmswereabletodetecttheattributesutilizedintherespectivecase-control modelsinmostdatasets. Conclusions:Thecurrentanalysessubstantiatetheutilityofrulebasedclassifiers suchasRIPPER,RIDORandPARTforthedetectionofgene-gene/gene-environment interactionsingeneticassociationstudies.Theseclassifierscouldprovideavaluable newmethod,complementingexistingapproaches,intheanalysisofgenetic associationstudies.Themethodsprovideanadvantageinbeingabletohandleboth categoricalandcont