基因表达模式分析及软件系统

33220033()JOURNALOFSOUTHEASTUNIVERSITY(NaturalScienceEdition)Vol133No12Mar.2003(,210096):4,.,..,,,.:;;;:Q52:A:1001-0505(2003)0220201204GeneexpressionprofileanalysisandsoftwaresystemXieJianmingSunXiaoXieXueyingLuZuhong(EducationMinistryKeyLaboratoryofMolecularandBio2molecularElectronics,SoutheastUniversity,Nanjing210096,China)Abstract:Asoftwarepackageforgeneexpressionprofileanalysishasbeenconstructed.Thekernelofthesoftwareconsistsof4clusteringalgorithmsincludingpair2wiseaveragelinkageanalysis,hierarchicalcluster2ing,self2organizationfeaturemapping,andfuzzyclusteringwhichisfirstappliedinthefield.Othertoolshavebeenintegratedintothesoftware,suchasdatapreprocessing,similaritymeasurementfunctionselectionanddatavisualization.Forthesamedatasetofgeneexpressionprofile,thissoftwarehasbeenshownasause2fulintegratedplatformtodelveintothecomplexregulatorymechanismbasedonexpressiondataoforganisms.Keywords:geneexpressionprofile;clusteringanalysis;bioinformaticssoftware;fuzzyclusteringalgo2rithm:2002209223.:863(2002AA231071)(9207031090).:(1971),,,[e-mail];(),,,,[e-mail].,,,.DNA,[1].DNA,[2][3,4].DNA,DNA[5,6],,[7].,,[7].,,[3,7].,,,,.,(geneexpressionandknowledgeexplo2ration,GEKE),,.©1995-2004TsinghuaTongfangOpticalDiscCo.,Ltd.Allrightsreserved.1,.,XGN,G,N,,.,[3],H.Ge1[8],.111XGN,(pair2wiseaveragelinkageclusteranalysis,PALCA)[3]:Xi,Xjrij,R=(rij)GG;rij=f(Xi,Xj)i,j=1,2,,G(1)R,ruv=maxi,jriji,j=1,2,,G,ij(2)X=(Xu+Xv)2(3)XGNXuXv,X,(G-1)NX,G=G-1;,G=1;2,,.PALCA.112(hierarchicalclusteringmethod,HCM)PALCA,,.,PALCA.[9].113(selforganizationfeaturemapping,SOFM)Kohonen[10,11],,,,,.SOFM2,N,,2,PP,,wij.:wij,Wj2=iwij2=1(4)Xk(k=1,2,,G),Oj=WTjXk=ni=1wijxkij=1,2,,PP(5)e,Oe=maxjOjj=1,2,,PP(6)yj=1-de(j)RdR0dR(7)wij=wij+wij=wij+(yj-Oj)xki(8),.,,i=(i+1)modG,,R;Xk(k=1,2,,G),Oj,Oe,XkCe(e[1,PP]).,wij,,,.SOFM,,,.SOFM,.114(fuzzyclusteringalgorithm,FCA),[12].FCA,:(1)Xi,Xjrij,R=(rij)GG;Rt(R)RR2R4R2k(9)R2k=(R2k)2t(R)=R2k(10),rij202()33©1995-2004TsinghuaTongfangOpticalDiscCo.,Ltd.Allrightsreserved.=maxk(min(rik,rkj))(k=1,2,,G);,t(R)rtij=1rtij0rtij(11)Rti=Rtj,RtiRtj;,.,,.2GEKEGEKE1,4:,.1211GEKE,,.,,.212.[-1,1],GEKE.,,,.GEKE,,.2133:.GEKEPearson3.10.,..,,,.GEKE..,.,,.GEKE,SOFMFCA,,Si=bi-aimax{ai,bi}(12),,bii,aii.Sii,Si.214[2,7,8,10,13].GEKE,;,,;,,.3GEKE,,,[14].[3],246718;110,3263022,:©1995-2004TsinghuaTongfangOpticalDiscCo.,Ltd.Allrightsreserved.;.FCA,SOFM,PALCA,HCM,,SOFM66.2FCA.FCA3,SOFM,PCLCAHCM.2FCA,1;3,CDC5DNA,CLB1,CLB2,BUD4,ALK1DNA;2MSH2,CDC9,CTF4,DPB2DNA.4GEKE4,,.,GEKE,,,,,,.,,.,,.,,.,,Bayesian[15,16],.(References)[1]DugganJD,BittnerM,ChenY,etal.ExpressionprofilingusingcDNAmicroarrays[J].NatureGeneticsSupplement,1999,21:1014.[2]LakhaniSR,AshworthA.Microarrayandhistopathologicalanalysisoftumours:thefutureandthepast?[J].NatureReviewsCancer,2001(1):151157.[3]EisenMB,SpellmanPT,BrownPO,etal.Clusteranaly2sisanddisplayofgenome2wideexpressionpatterns[J].ProcNatlAcadSciUSA,1998,95:1486314868.[4]TavazoieS,HughesJD,CampbellMJ,etal.Systematicdeterminationofgeneticnetworkarchitecture[J].NatureGe2netics,1999,22:281285.[5],,,.[J].(),2000,30(5):16.SunXiao,WangYe,ZhangXiaoli,etal.Asoftwaresystemforgenechipdesignanddataanalysis[J].JournalofSouth2eastUniversity(NaturalScienceEdition),2000,30(5):16.(inChinese)[6],,,.[P].,PCT/CN99100013.1998204[7]QuackenbushJ.Computationalanalysisofmicroarraydata[J].NatureReviewsGenetics,2001(2):418427.[8]GeH,ZhihuaL,ChurchGM,etal.CorrelationbetweentranscriptomeandinteractomemappingdatafromSaccha2romycescerevisiae[J].NatureGenetics,2001,29:482486.[9],.[M].:,1982.105256.[10]TamayoP,SlonimD,MesirovJ,etal.Interpretingpat2ternsofgeneexpressionwithself2organizingmaps:methodsandapplicationtohematopoieticdifferentiation[J].ProcNatlAcadSciUSA,1999,96:29072912.[11]ZuradaJM.Introductiontoartificialneuralsystems[M].Minnesota:WestPublishingCompany,1992.230245.[12],.[M].:,1993.57111.[13]PilpelY,SudarsanamP,ChurchGM.Identifyingregulato2rynetworksbycombinatorialanalysisofpromoterelements[J].NatureGenetics,2001,29:153159.[14]MewesHW,FrishmanD,GuldenerU,etal.MIPS:adatabaseforgenomesandproteinsequences[J].NucleicAcidsResearch,2002,30(1):3134.[15]HolterNS,MaritanA,CieplakM,etal.Dynamicmodel2ingofgeneexpressiondata[J].ProcNatlAcadSciUSA,2001,98:16931698.[16]SegalE,TaskarB,GaschA,etal.Richprobabilisticmod2elsforgeneexpression[J].Bioinformatics,2001(1):19.402()33©1995-2004TsinghuaTongfangOpticalDiscCo.,Ltd.Allrightsreserved.