Simplivariate Models Uncovering the Underlying Biology in Functional Genomics Data 英文参考文献.docVIP

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Simplivariate Models Uncovering the Underlying Biology in Functional Genomics Data 英文参考文献.doc

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Simplivariate Models Uncovering the Underlying Biology in Functional Genomics Data 英文参考文献

SimplivariateModels:UncoveringtheUnderlying BiologyinFunctionalGenomicsData EdoardoSaccenti1,2*,JohanA.Westerhuis1,AgeK.Smilde1,Marie¨tJ.vanderWerf3,JosA.Hageman4, MargrietM.W.B.Hendriks5,6 1Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands, 2Netherlands Bioinformatics Centre, Nijmegen,TheNetherlands,3TNOQualityofLife,Zeist,TheNetherlands,4Biometris—AppliedStatistics,Wageningen,TheNetherlands,5LaboratoryofMetabolicand EndocrineDiseases,WilhelminaChildren’sHospital,UtrechtMedicalCentre,Utrecht,TheNetherlands,6NetherlandsMetabolomicCentre,Leiden,TheNetherlands Abstract Oneofthefirststepsinanalyzinghigh-dimensionalfunctionalgenomicsdataisanexploratoryanalysisofsuchdata.Cluster AnalysisandPrincipalComponentAnalysisarethenusuallythemethodofchoice.Despitetheirversatilitytheyalsohavea severe drawback: they do not always generate simple and interpretable solutions. On the basis of the observation that functionalgenomicsdataoftencontainbothinformativeandnon-informativevariation,weproposeamethodthatfinds setsofvariablescontaininginformativevariation.Thisinformativevariationissubsequentlyexpressedineasilyinterpretable simplivariate components.We present a new implementation of the recently introduced simplivariate models. In this implementation,theinformativevariationisdescribedbymultiplicativemodelsthatcanadequatelyrepresenttherelations betweenfunctionalgenomicsdata.Bothasimulatedandtworeal-lifemetabolomicsdatasetsshowgoodperformanceof themethod. Citation:SaccentiE,WesterhuisJA,SmildeAK,vanderWerfMJ,HagemanJA,etal.(2011)SimplivariateModels:UncoveringtheUnderlyingBiologyinFunctional GenomicsData.PLoSONE6(6):e20747.doi:10.1371/journal.pone.0020747 Editor:ArkadyB.Khodursky,UniversityofMinnesota,UnitedStatesofAmerica ReceivedDecember7,2010;AcceptedMay12,2011;PublishedJune16,2011 Copyright: ? 2011 Saccenti et al. This is an open-access article distributed under the terms of the Creative Commons Attribution Licen