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1、AnActivationForce-basedAffinityMeasureforAnalyzingComplexSUBJECTAREAS:BIOINFORMATICSNetworksCANCERMODELS121JunGuo,HanliangGuo&ZhanyiWangMODELLINGFUNCTIONALGENOMICS1SchoolofInformationandCommunicationEngineering,BeijingUniversityofPostsandTelecommunications,No.10Xitucheng2Road,HaidianDistrict,Bei
2、jing,China,DepartmentofAerospaceandMechanicalEngineering,ViterbiSchoolofEngineering,ReceivedUniversityofSouthernCalifornia,UniversityParkCampus,USC,LosAngeles,CA90089,USA.22July2011AcceptedAffinitymeasureisakeyfactorthatdeterminesthequalityoftheanalysisofacomplexnetwork.Here,we26September2011int
3、roduceatypeofstatistics,activationforces,toweightthelinksofacomplexnetworkandtherebydevelopadesiredaffinitymeasure.WeshowthattheapproachissuperiorinfacilitatingtheanalysisthroughPublishedexperimentsonalarge-scalewordnetworkandaprotein-proteininteraction(PPI)networkconsistingof12October2011,5,000
4、humanproteins.Theexperimentonthewordnetworkverifiesthatthemeasuredwordaffinitiesarehighlyconsistentwithhumanknowledge.Further,theexperimentonthePPInetworkverifiesthemeasureandpresentsageneralmethodfortheidentificationoffunctionallysimilarproteinsbasedonPPIs.Moststrikingly,wefindanaffinitynetwork
5、thatcompactlyconnectsthecancer-associatedproteinstoeachother,Correspondenceandwhichmayrevealnovelinformationforcancerstudy;thisincludeslikelyproteininteractionsandkeyrequestsformaterialsproteinsincancer-relatedsignaltransductionpathways.shouldbeaddressedtoG.J.(guojun@bupt.nalyzingacomplexnetwork
6、usuallybeginswithclusteringthenetwork,whichisfundamentalbecauseitedu.cn)canclarifythestructureofthenetworkofinterestandrevealpreviouslyunknownpropertiesorfunctionsA1–5forthemembersofeachcommunity.Forexample,clusteringprotein-proteininteraction(PPI)net-workscanpromotesignificantnewunderstandingof
7、proteinfunctions,whichiscriticalforthefieldsofbiologyandmedicine.However,clusteringincomplexnetworksisalsochallengingbecauseitisdifficulttofindaneffectiveaffinitymeasurefornodesunderconditionsthatrepresentcomplexnetworksinan