Diffusion Model Based Spectral Clustering for Protein-Protein Interaction Networks 英文参考文献.docVIP

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Diffusion Model Based Spectral Clustering for Protein-Protein Interaction Networks 英文参考文献.doc

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Diffusion Model Based Spectral Clustering for Protein-Protein Interaction Networks 英文参考文献

DiffusionModelBasedSpectralClusteringforProtein- ProteinInteractionNetworks KentaroInoue1.,WeijiangLi2.,HiroyukiKurata1* 1Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan, 2The Key Laboratory of Industrial Biotechnology, Southern Yangtze University,Wuxi,China Abstract Background: A goal of systems biology is to analyze large-scale molecular networks including gene expressions and protein-proteininteractions,revealingtherelationshipsbetweennetworkstructuresandtheirbiologicalfunctions.Dividing aprotein-proteininteraction(PPI)networkintonaturallygroupedpartsisanessentialwaytoinvestigatetherelationship between topology of networks and their functions. However, clear modular decomposition is often hard due to the heterogeneousorscale-freepropertiesofPPInetworks. Methodology/Principal Findings: To address this problem, we propose a diffusion model-based spectral clustering algorithm, which analytically solves the cluster structure of PPI networks as a problem of random walks in the diffusion processinthem.Tocopewiththeheterogeneityofthenetworks,thepowerfactorisintroducedtoadjustthediffusion matrix by weighting the transition (adjacency) matrix according to a node degree matrix. This algorithm is named adjustable diffusion matrix-based spectral clustering (ADMSC). To demonstrate the feasibility of ADMSC, we apply it to decompositionofayeastPPInetwork,identifyingbiologicallysignificantclusterswithapproximatelyequalsize.Compared withotherestablishedalgorithms,ADMSCfacilitatesclearandfastdecompositionofPPInetworks. Conclusions/Significance: ADMSC is proposed by introducing the power factor that adjusts the diffusion matrix to the heterogeneity of the PPI networks. ADMSC effectively partitions PPI networks into biologically significant clusters with almostequalsizes,whilebeingveryfast,robustandappealingsimple. Citation:InoueK,LiW,KurataH(2010)DiffusionModelBasedSpectralClusteringforProtein-ProteinInteractionNetworks.PLoSONE5(9):e1262