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1、134DNAmicroarrays,partB[9]Troein,C.,Vallon‐Christersson,J.,andSaal,L.H.(2006).AnintroductiontoBioArraySoftwareEnvironment.MethodsEnzymol.411,99119.Tusher,V.G.,Tibshirani,R.,andChu,G.(2001).Significanceanalysisofmicroarraysappliedtotheionizingradiationresponse.Proc.Natl.Acad.Sci.U
2、SA98,51165121.Zhang,L.,Miles,M.F.,andAldape,K.D.(2004).Amodelofmolecularinteractionsonshortoligonucleotidemicroarrays:Implicationsforprobedesignanddataanalysis.NatureBiotechnol.21(7),818821.[9]TM4MicroarraySoftwareSuiteByALEXANDERI.SAEED,NIRMALK.BHAGABATI,JOHNC.BRAISTED,WEILIANG
3、,VASILYSHAROV,ELEANORA.HOWE,JIANWEILI,MATHANGITHIAGARAJAN,JOSEPHA.WHITE,andJOHNQUACKENBUSHAbstractPowerfulspecializedsoftwareisessentialformanaging,quantifying,andultimatelyderivingscientificinsightfromresultsofamicroarrayexperiment.Wehavedevelopedasuiteofsoftwareapplications,kno
4、wnasTM4,tosupportsuchgeneexpressionstudies.Thesuiteconsistsofopen‐sourcetoolsfordatamanagementandreporting,imageanalysis,normalizationandpipelinecontrol,anddataminingandvisualization.AnintegratedMIAME‐compliantMySQLdatabaseisincluded.Thischapterdescribeseachcomponentofthesuitean
5、dincludesasampleanalysiswalk‐through.IntroductionTheHumanGenomeProjectwasenvisionedasagrandendeavorthatwouldchangebiologybyprovidingacatalogofgenesinhumansandothermodelorganisms.Althoughalargenumberofgenomesequencingpro-jects,includingthatofthehumangenome,havebeendeclaredfinished
6、,thecollectionofthesequenceitselfhasnotfundamentallyalteredourap-proachtounderstandingbiologicalsystems.Rather,ithasbeenthedevel-opmentoftechniquesandtechnologiesthatallowustoanalyzepatternsofexpressionforsetsofgenes,proteins,ormetabolitesapproachingthetotalnumberthatareactivein
7、anorganismatanygivenpointintime.Sincetheirintroductionin1995(Lipshutz,1995;Schena,1995),DNAmicroarrayshavematuredsignificantlytobecomethemostwidelyusedtechniquefortheanalysisofglobalpatternsofexpressionandrepresentatechnologythatisnowusedroutinelyasameansofgeneratingtestablehypot
8、hesespriortootherstudies.DNAmicroarraysconsisto
