Recent Advances in Clustering Methods for Protein Interaction Networks

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2010 Dec 15

PMID 21143777

Citations 52

Authors

Jianxin Wang

Min Li

Youping Deng

Yi Pan

Affiliations

Soon will be listed here.

Abstract

The increasing availability of large-scale protein-protein interaction data has made it possible to understand the basic components and organization of cell machinery from the network level. The arising challenge is how to analyze such complex interacting data to reveal the principles of cellular organization, processes and functions. Many studies have shown that clustering protein interaction network is an effective approach for identifying protein complexes or functional modules, which has become a major research topic in systems biology. In this review, recent advances in clustering methods for protein interaction networks will be presented in detail. The predictions of protein functions and interactions based on modules will be covered. Finally, the performance of different clustering methods will be compared and the directions for future research will be discussed.

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References

Zheng H, Wang H, Glass D . Integration of genomic data for inferring protein complexes from global protein-protein interaction networks. IEEE Trans Syst Man Cybern B Cybern. 2008; 38(1):5-16. DOI: 10.1109/TSMCB.2007.908912. View

Ulitsky I, Shamir R . Identification of functional modules using network topology and high-throughput data. BMC Syst Biol. 2007; 1:8. PMC: 1839897. DOI: 10.1186/1752-0509-1-8. View

Zhang C, Liu S, Zhou Y . Fast and accurate method for identifying high-quality protein-interaction modules by clique merging and its application to yeast. J Proteome Res. 2006; 5(4):801-7. DOI: 10.1021/pr050366g. View

Samanta M, Liang S . Predicting protein functions from redundancies in large-scale protein interaction networks. Proc Natl Acad Sci U S A. 2003; 100(22):12579-83. PMC: 240660. DOI: 10.1073/pnas.2132527100. View

Hartwell L, Hopfield J, Leibler S, Murray A . From molecular to modular cell biology. Nature. 1999; 402(6761 Suppl):C47-52. DOI: 10.1038/35011540. View

Friedel C, Zimmer R . Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinformatics. 2006; 7:519. PMC: 1716184. DOI: 10.1186/1471-2105-7-519. View

Spirin V, Mirny L . Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci U S A. 2003; 100(21):12123-8. PMC: 218723. DOI: 10.1073/pnas.2032324100. View

Luo F, Yang Y, Chen C, Chang R, Zhou J, Scheuermann R . Modular organization of protein interaction networks. Bioinformatics. 2006; 23(2):207-14. DOI: 10.1093/bioinformatics/btl562. View

Przulj N, Wigle D, Jurisica I . Functional topology in a network of protein interactions. Bioinformatics. 2004; 20(3):340-8. DOI: 10.1093/bioinformatics/btg415. View

10.

Hwang W, Cho Y, Zhang A, Ramanathan M . A novel functional module detection algorithm for protein-protein interaction networks. Algorithms Mol Biol. 2006; 1:24. PMC: 1764415. DOI: 10.1186/1748-7188-1-24. View

11.

Pei P, Zhang A . A "seed-refine" algorithm for detecting protein complexes from protein interaction data. IEEE Trans Nanobioscience. 2007; 6(1):43-50. DOI: 10.1109/tnb.2007.891900. View

12.

von Mering C, Krause R, Snel B, Cornell M, Oliver S, Fields S . Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 2002; 417(6887):399-403. DOI: 10.1038/nature750. View

13.

Li M, Chen J, Wang J, Hu B, Chen G . Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. BMC Bioinformatics. 2008; 9:398. PMC: 2570695. DOI: 10.1186/1471-2105-9-398. View

14.

Li S, Armstrong C, Bertin N, Ge H, Milstein S, Boxem M . A map of the interactome network of the metazoan C. elegans. Science. 2004; 303(5657):540-3. PMC: 1698949. DOI: 10.1126/science.1091403. View

15.

Zhang S, Jin G, Zhang X, Chen L . Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics. 2007; 7(16):2856-69. DOI: 10.1002/pmic.200700095. View

16.

Bu D, Zhao Y, Cai L, Xue H, Zhu X, Lu H . Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res. 2003; 31(9):2443-50. PMC: 154226. DOI: 10.1093/nar/gkg340. View

17.

Maraziotis I, Dimitrakopoulou K, Bezerianos A . Growing functional modules from a seed protein via integration of protein interaction and gene expression data. BMC Bioinformatics. 2007; 8:408. PMC: 2233647. DOI: 10.1186/1471-2105-8-408. View

18.

Yang Q, Lonardi S . A parallel edge-betweenness clustering tool for Protein-Protein Interaction networks. Int J Data Min Bioinform. 2008; 1(3):241-7. DOI: 10.1504/ijdmb.2007.011611. View

19.

Ball C, Awad I, Demeter J, Gollub J, Hebert J, Hernandez-Boussard T . The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res. 2004; 33(Database issue):D580-2. PMC: 539960. DOI: 10.1093/nar/gki006. View

20.

Mason O, Verwoerd M . Graph theory and networks in Biology. IET Syst Biol. 2007; 1(2):89-119. DOI: 10.1049/iet-syb:20060038. View