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Classication of Time Series Gene Expression in Clinical Studies via Integration of Biological Network.doc

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Classication of Time Series Gene Expression in Clinical Studies via Integration of Biological Network

ClassificationofTimeSeriesGeneExpressioninClinical StudiesviaIntegrationofBiologicalNetwork LiweiQian1,HaoranZheng1,2,3*,HongZhou1,RuibinQin1,JinlongLi1 1SchoolofComputerScienceandTechnology,UniversityofScienceandTechnologyofChina,Hefei,People’sRepublicofChina, 2AnhuiKeyLaboratoryofSoftware Engineering in Computing and Communication, University of Science and Technology of China, Hefei, People’s Republic of China, 3Department of Systems Biology, UniversityofScienceandTechnologyofChina,Hefei,People’sRepublicofChina Abstract Theincreasingavailabilityoftimeseriesexpressiondatasets,althoughpromising,raisesanumberofnewcomputational challenges. Accordingly, the development of suitable classification methods to make reliable and sound predictions is becoming a pressing issue. We propose, here, a new method to classify time series gene expression via integration of biological networks. We evaluated our approach on 2 different datasets and showed that the use of a hidden Markov model/Gaussian mixture models hybrid explores the time-dependence of the expression data, thereby leading to better predictionresults.Wedemonstratedthatthebiclusteringprocedureidentifiesfunction-relatedgenesasawhole,givingrise to high accordance in prognosis prediction across independent time series datasets. In addition, we showed that integrationofbiologicalnetworksintoourmethodsignificantlyimprovespredictionperformance.Moreover,wecompared ourapproachwithseveralstate-of–the-artalgorithmsandfoundthatourmethodoutperformedpreviousapproacheswith regardtovariouscriteria.Finally,ourapproachachievedbetterpredictionresultsonearly-stagedata,implyingthepotential ofourmethodforpracticalprediction. Citation:QianL,ZhengH,ZhouH,QinR,LiJ(2013)ClassificationofTimeSeriesGeneExpressioninClinicalStudiesviaIntegrationofBiologicalNetwork.PLoS ONE8(3):e58383.doi:10.1371/journal.pone.0058383 Editor:LuonanChen,ChineseAcademyofSciences,China ReceivedSeptember18,2012;AcceptedFebruary4,2013;PublishedMarch13,2013 Co