Probing the Extent of Randomness in Protein Interaction Networks 英文参考文献.docVIP

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Probing the Extent of Randomness in Protein Interaction Networks 英文参考文献.doc

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Probing the Extent of Randomness in Protein Interaction Networks 英文参考文献

ProbingtheExtentofRandomnessinProteinInteraction Networks JosephIvanic,AndersWallqvist,JaquesReifman* BiotechnologyHPCSoftwareApplicationsInstitute,TelemedicineandAdvancedTechnologyResearchCenter,U.S.ArmyMedicalResearchandMaterielCommand,Ft. Detrick,Maryland,UnitedStatesofAmerica Abstract Protein–proteininteraction(PPI)networksarecommonlyexploredfortheidentificationofdistinctivebiologicaltraits,such as pathways, modules, and functional motifs. In this respect, understanding the underlying network structure is vital to assess the significance of any discovered features. We recently demonstrated that PPI networks show degree-weighted behavior, whereby the probability of interaction between two proteins is generally proportional to the product of their numbers of interacting partners or degrees. It was surmised that degree-weighted behavior is a characteristic of randomness.Weexpanduponthesefindingsbydevelopingarandom,degree-weighted,networkmodelandshowthat eight PPI networks determined from single high-throughput (HT) experiments have global and local properties that are consistentwiththismodel.TheapparentrandomconnectivityinHTPPInetworksiscounter-intuitivewithrespecttotheir observed degreedistributions; however, we resolvethis discrepancy by introducing anon-network-based model for the evolution of protein degrees or ‘‘binding affinities.’’ This mechanism is based on duplication and random mutation, for whichthedegreedistributionconvergestoasteadystatethatisidenticaltooneobtainedbyaveragingovertheeightHT PPInetworks.TheresultsimplythatthedegreesandconnectivitiesincorporatedinHTPPInetworksarecharacteristicof unbiased interactions between proteins that have varying individual binding affinities. These findings corroborate the observationthatcuratedandhigh-confidencePPInetworksaredistinctfromHTPPInetworksandnotconsistentwitha randomconnectivity.Theseresultsprovideanavenuetodiscernindiscriminateorganizationsinbiologicalnetworksand suggestcautionintheanalysisofcuratedan