Reordering Hierarchical Tree Based on Bilateral Symmetric Distance 英文参考文献.docVIP

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Reordering Hierarchical Tree Based on Bilateral Symmetric Distance 英文参考文献.doc

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Reordering Hierarchical Tree Based on Bilateral Symmetric Distance 英文参考文献

ReorderingHierarchicalTreeBasedonBilateral SymmetricDistance MinhoChae1,2,JamesJ.Chen1,3 * 1DivisionofPersonalizedNutritionandMedicine,NationalCenterforToxicologicalResearch,U.S.FoodandDrugAdministration,Jefferson,Arkansas,UnitedStatesof America,2CecilH.andIdaGreenCenterforReproductiveBiologySciences,UniversityofTexasSouthwesternMedicalCenteratDallas,Dallas,Texas,UnitedStatesof America,3GraduateInstituteofBiostatisticsBiostatisticsCenter,ChinaMedicalUniversity,Taichung,Taiwan Abstract Background:Inmicroarraydataanalysis,hierarchicalclustering(HC)isoftenusedtogroupsamplesorgenesaccordingto their gene expression profiles to study their associations. In a typical HC, nested clustering structures can be quickly identifiedinatree.Therelationshipbetweenobjectsislost,however,becauseclustersratherthanindividualobjectsare compared.Thisresultsinatreethatishardtointerpret. Methodology/PrincipalFindings:Thisstudyproposesanorderingmethod,HC-SYM,whichminimizesbilateralsymmetric distanceoftwoadjacentclustersinatreesothatsimilarobjectsintheclustersarelocatedintheclusterboundaries.The performanceofHC-SYMwasevaluatedbybothsupervisedandunsupervisedapproachesandcomparedfavourablywith otherorderingmethods. Conclusions/Significance: The intuitive relationship between objects and flexibility of the HC-SYM method can be very helpfulintheexploratoryanalysisofnotonlymicroarraydatabutalsosimilarhigh-dimensionaldata. Citation:ChaeM,ChenJJ(2011)ReorderingHierarchicalTreeBasedonBilateralSymmetricDistance.PLoSONE6(8):e22546.doi:10.1371/journal.pone.0022546 Editor:FrancaFraternali,King’sCollegeLondon,UnitedKingdom ReceivedDecember14,2010;AcceptedJune29,2011;PublishedAugust4,2011 Thisisanopen-accessarticle,freeofallcopyright,andmaybefreelyreproduced,distributed,transmitted,modified,builtupon,orotherwiseusedbyanyonefor anylawfulpurpose.TheworkismadeavailableundertheCreativeCommonsCC0publicdomaindedication. Funding:Dr.MinhoChaewassupportedbytheFDAResearchParticipationProgramattheNCTRadministeredbyt