Discovering functional interdependence relationship in PPI networks for protein complex identification

IEEE Transactions on Biomedical Engineering

Volumn 59, Issue 4, 2012, Pages 899-908

  Lam, Winnie W M ^a   Chan, Keith C C ^a  

^a HONG KONG POLYTECHNIC UNIVERSITY   (Hong Kong)

Author keywords

Graph mining; protein complex discovery; protein protein interactions (PPIs)

Indexed keywords

COMPUTATIONAL TECHNIQUE; FALSE-ALARM RATES; GRAPH MINING; HIGH CONNECTIVITY; IDENTIFICATION OF PROTEINS; MOLECULAR FUNCTION; NETWORK DATA; NETWORK TOPOLOGY; PERFORMANCE EVALUATION; PROTEIN COMPLEX DISCOVERY; PROTEIN COMPLEXES; PROTEIN INTERACTION; PROTEIN MOLECULES; PROTEIN NETWORK; PROTEIN-PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTIONS (PPIS); SUBGRAPHS;

ELECTRIC NETWORK TOPOLOGY; IMAGE RESOLUTION; INFORMATION THEORY;

PROTEINS;

MULTIPROTEIN COMPLEX;

ALGORITHM; ARTICLE; COMPLEX FORMATION; EVALUATION; NUCLEOTIDE SEQUENCE; PERFORMANCE; PROTEIN ANALYSIS; PROTEIN COMPLEX IDENTIFICATION BY DISCOVERING FUNCTIONAL INTERDEPENDENCE; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; HUMANS; MODELS, BIOLOGICAL; PROTEIN INTERACTION MAPPING; PROTEINS; SIGNAL TRANSDUCTION;

EID: 84858991848     PISSN: 00189294     EISSN: 15582531     Source Type: Journal    
DOI: 10.1109/TBME.2010.2093524     Document Type: Article

References (33)

1. B. Adamcsek, G. Palla, I. J. Farkas, I. Derenyi, and T. Vicsek, "CFinder: locating cliques and overlapping modules in biological networks," Bioinformatics, vol. 22, no. 8, pp. 1021-1023, 2006.
2. M. Altaf-Ul-Amin, Y. Shinbo, K. Mihara, K. Kurokawa, and S. Kanaya, "Development and implementation of an algorithm for detection of protein complexes in large interaction networks,"BMC Bioinformatics, vol. 7, p. 207, 2006. Available: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1473204/.
3. M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J.M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G.M. Rubin, and G. Sherlock, "Gene ontology: Tool for the unification of biology," Nature Genet., vol. 25, no. 1, pp. 25-29, 2000. (Pubitemid 30257031)
4. G. D. Bader and C. W. Hogue, "Analyzing yeast protein-protein interaction data obtained from different sources," Nature Biotechnol., vol. 10, pp. 991-997, 2002.
5. G. D. Bader and C. W. Hogue, "An automated method for finding molecular complex in large protein interaction networks,"BMC Bioinformatics, vol. 4, p. 2, 2003. Available: http://www.ncbi.nlm.nih.gov/pmc/ articles/PMC149346/.
6. A. K. Bjorklund, S. Light, L. Hedin, and A. Elofsson, "Quantitative assessment of the structural bias in protein-protein interaction assays," Proteomics, vol. 8, no. 22, pp. 4657-4667, 2008.
7. B. J. Breitkreutz, C. Stark, T. Reguly, L. Boucher, A. Breitkreutz, M. Livstone, R. Oughtred, D. H. Lackner, J. Bahler, V. Wood, K. Dolinski, and M. Tyers, "The BioGRID interaction database: 2008 update," Nucleic Acids Res, vol. 36, pp. D637-640, 2008. (Pubitemid 351149798)
8. S. Brohee and J. van Helden, "Evaluation of clustering algorithms for protein-protein interaction networks," BMCBioinformatics, vol. 7, p. 488, 2006. Available: http://www.biomedcentral.com/1471-2105/7/488.
9. K. C. C. Chan and A. K. C. Wong, "A statistical technique for extracting classificatory knowledge from databases, in Knowledge Discovery in Databases, G. Piatetsky-Shapiro and W. J. Frawley, Eds. Cambridge:MA: MIT Press, 1991, pp. 107-123.
10. P. C. H. Ma and K. C. C. Chan, "A novel approach for discovering overlapping clusters in gene expression data," IEEE Trans. Biomed. Eng., vol. 56, no. 7, pp. 1803-1809, Jul. 2009.
11. W. H. Au, K. C. C. Chan, A. K. C. Wong, and W. Yang, "Attribute clustering for grouping, selection and classification of gene expression data," IEEE/ACM Trans. Comput. Biol. Bioinformatics, vol. 2, no. 2, pp. 83-101, Apr./Jun. 2005.
12. I. Derenyi, G. Palla, and T. Vicsek, "Clique percolation in random networks,"Phys. Rev. Lett., vol. 94, pp. 160202-1-160202-4, 2005.
13. S. Dongen, "A cluster algorithm for graphs," National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam, The Netherlands, Tech. Rep. INS-R0010, 2000.
14. A. J. Enright, S. Van Dongen, and C. A. Ouzounis, "An efficient algorithm for large-scale detection of protein families," Nucleic Acids Res., vol. 30, no. 7, pp. 1575-1584, 2002. (Pubitemid 34679732)
15. A. C. Gavin, M. Bösche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J. M. Rick, A.-M. Michon, C.-M. Cruciat, M. Remor, C. Höfert, M. Schelder, M. Brajenovic, H. Ruffner, A. Merino, K. Klein, M. Hudak, D. Dickson, T. Rudi, V. Gnau, A. Bauch, S. Bastuck, B. Huhse, C. Leutwein, M.-A. Heurtier, R. R. Copley, A. Edelmann, E. Querfurth, V. Rybin, G. Drewes, M. Raida, T. Bouwmeester, P. Bork, B. Seraphin, B.Kuster,G.Neubauer, andG. Superti-Furga, "Functional organization of the yeast proteome by systematic analysis of protein complexes," Nature, vol. 415, pp. 141-147, 2002. (Pubitemid 34059510)
16. A. C. Gavin, P. Aloy, P. Grandi, R. Krause, M. Boesche, M. Marzioch, C. Rau, L. J. Jensen, S. Bastuck, B. Dumpelfeld, A. Edelmann, M. A. Heurtier, V. Hoffman, C. Hoefert, K. Klein, M. Hudak, A. M. Michon, M. Schelder, M. Schirle, M. Remor, T. Rudi, S. Hooper, A. Bauer, T. Bouwmeester,G.Casari, G. Drewes,G.Neubauer, J. M. Rick,B.Kuster, P. Bork, R. B. Russell, and G. Superti-Furga, "Proteome survey reveals modularity of the yeast cell machinery," Nature, vol. 440, pp. 631-636, 2006.
17. G. T. Hart, I. Lee, and E. R. Marcotte, "A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality," BMC Bioinformatics, vol. 8, p. 236, 2007. Available: http://www.biomedcentral.com/1471-2105/8/236.
18. S. Jones and J. M. Thornton, "Principles of protein-protein interactions,"Proc. Nat. Acad. Sci. USA, vol. 93, pp. 13-20, 1996.
19. P. M. Kim, L. J. Lu, Y. Xia, and M. B. Gerstein, "Relating three-dimensional structures to protein networks provides evolutionary insights,"Science, vol. 314, pp. 1938-1941, 2006. (Pubitemid 46026118)
20. N. J. Krogan, G. Cagney, H. Yu, G. Zhong, X. Guo, A. Ignatchenko, J. Li, S. Pu, N. Datta, A. P. Tikuisis, T. Punna, J. M. Peregrín-Alvarez, M. Shales,X. Zhang, M. Davey, M. D. Robinson, A. Paccanaro, J. E. Bray, A. Sheung, B. Beattie, D. P. Richards, V. Canadien, A. Lalev, F. Mena, P. Wong, A. Starostine, M. M. Canete, J. Vlasblom, S. Wu, C. Orsi, S. R. Collins, S. Chandran, R. Haw, J. J. Rilstone, K. Gandi, N. J. Thompson, G. Musso, P. St Onge, S. Ghanny, M. H. Y. Lam, G. Butland, A. M. Altaf-Ul, S. Kanaya, A. Shilatifard, E. O'Shea, J. S. Weissman, C. J. Ingles, T. R. Hughes, J. Parkinson, M. Gerstein, S. J. Wodak, A. Emili, and J. F. Greenblatt, "Global landscape of protein complexes in the yeast Saccharomyces cerevisiae," Nature, vol. 440, pp. 637-643, 2006.
21. A. Kumar and M. Snyder, "Protein complexes take the bait," Nature, vol. 415, pp. 123-124, 2002.
22. M. Li, J.-E. Chen, J.-X.Wang, B. Hu, and G. Chen, "Modifying the DPclus algorithm for identifying protein complexes based on new topological structures," BMC Bioinformatics, vol. 9, pp. 345-352, 2008.
23. G. Liu, L. Wong, and H. N. Chua, "Complex discovery from weight PPI networks," Bioinformatics, vol. 25, no. 15, pp. 1891-1897, 2009.
24. D. J. C. MacKay, Information Theory, Inference, and Learning Algorithms. Cambridge, U.K.: Cambridge Univ. Press, 2003.
25. P. Pagel, S. Kovac, M. Oesterheld, B. Brauner, I. Dunger-Kaltenbach, G. Frishman, C.Montrone, P.Mark,V. Stumpflen,H.W.Mewes,ARuepp, and D. Frishman, "The MIPS mammalian protein-protein interaction database," Bioinformatics, vol. 21, no. 6, pp. 832-834, 2005. (Pubitemid 40439425)
26. K. Pearson, "The problem of the random walk," Nature, vol. 72, pp. 139-144, 1905.
27. A. Ruepp, B. Brauner, I. Dunger-Kaltenbach, G. Frishman, C. Montrone, M. Stransky, B. Waegele, T. Schmidt, O. N. Doudieu, V. Stumpflen, and H. W. Mewes, "CORUM: The comprehensive resource of mammalian protein complexes - 2009," Nucleic Acids Res., vol. 36, pp. D646-D650, 2009. (Pubitemid 351149800)
28. L. Salwinski, C. S. Miller, A. J. Smith, F. K. Pettit, J. U. Bowie, and D. Eisenberg, "The database of interacting proteins: 2004 update," Nucleic Acid Res., vol. 32, pp. D449-D451, 2004. (Pubitemid 38081696)
29. C. Stark, B. J. Breitkreutz, T. Reguly, L. Boucher, A. Breitkreutz, and M. Tyers, "BioGRID: A general repository for interaction datasets," Nucleic Acids Res., vol. 34, pp. D535-D539, 2006.
30. The UniProt Consortium "The universal protein resource (UniProt)," Nucleic Acids Res., vol. 36, pp. D190-D195, 2008.
31. A. H. Tong, B. Drees,G.Nardelli, G. D. Bader, B. Brannetti, L. Castagnoli, M. Evangelista, S. Ferracuti, B. Nelson, S. Paoluzi, M. Quondam, A. Zucconi, C. W. Hoque, S. Fields, C. Boone, and G. Cesareni, "A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules," Science, vol. 295, pp. 321-324, 2002. (Pubitemid 34074361)
32. H. Xiong, X. He, C. Ding, Y. Zhang, V. Kumar, and S. R. Holbrook, "Identification of functionalmodules in protein complexes via hyperclique pattern discovery," in Proc. Pacific Symp. Biocomput., 2005, pp. 221-232.
33. S. J. Haberman, "The analysis of residuals in cross-classificed tables,"Biometrics, vol. 29, pp. 205-220, 1973.