Identifying protein complexes from interactome based on essential proteins and local fitness method

IEEE Transactions on Nanobioscience

Volumn 11, Issue 4, 2012, Pages 324-335

  Wang, Jianxin ^a   Chen, Gang ^a   Liu, Binbin ^a   Li, Min ^a   Pan, Yi ^a,b  

^a CENTRAL SOUTH UNIVERSITY   (China)

^b GEORGIA STATE UNIVERSITY   (United States)

Author keywords

Essential protein; local fitness; protein complex; protein interactome

Indexed keywords

CELLULAR ORGANIZATION; COMPETING ALGORITHMS; COMPUTATIONAL PREDICTIONS; F-MEASURE; FITNESS VALUES; HIGH-THROUGHPUT; IDENTIFICATION OF PROTEINS; INTERACTION NETWORKS; INTERACTOME NETWORKS; LOCAL FITNESS; NOVEL PROTEINS; PROTEIN COMPLEXES; PROTEIN FUNCTIONS; S.CEREVISIAE; SUB-NETWORK; SUBGRAPHS;

ALGORITHMS; HEALTH;

PROTEINS;

SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHM; ARTICLE; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS;

ALGORITHMS; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84870926113     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2012.2197863     Document Type: Article

References (50)

1. J. I. Garrels, "Yeast genomic databases and the challenge of the postgenomic era, " Functional Integrative Genomics, vol. 2, no. 4-5, pp. 212-237, 2002. (Pubitemid 41449155)
2. A. C. Gavin and G. Superti-Furga, "Protein complexes and proteome organization from yeast to man, " Curr. Opin. Chem. Biol., vol. 7, no. 1, pp. 21-27, 2003. (Pubitemid 36126488)
3. M. Li, J. Chen, J. Wang, B. Hu, and G. Chen, "Modifying the DPClus algorithm for identifying protein complexes based on new topological structures, " BMC Bioinf., vol. 9, p. 398, 2008.
4. A. Kumar and M. Snyder, "Protein complexes take the bait, " Nature, vol. 415, pp. 123-124, 2002. (Pubitemid 34059499)
5. G. D. Bader and C. W. Hogue, "An automated method for finding molecular complexes in large protein interaction networks, " BMC Bioinf., vol. 4, no. 2, 2003 [Online]. Available: http://rd. springer. com/article/10. 1186/1471-2105-4-2
6. 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 Bioinf., vol. 7, pp. 207-219, 2006.
7. P. Jiang and M. Singh, "SPICi: A fast clustering algorithm for large biological networks, " Bioinformatics, vol. 26, no. 8, pp. 1105-1111, 2010.
8. A. D. King, N. Pržulj, and I. Jurisica, "Protein complex prediction via cost-based clustering, " Bioinformatics, vol. 20, pp. 3013-3020, 2004. (Pubitemid 39619193)
9. E. Hartuv and R. Shamir, "A clustering algorithm based graph connectivity, " Inf. Process. Lett., vol. 76, pp. 175-181, 2000. (Pubitemid 32035371)
10. M. Girvan and M. E. J. Newman, "Community structure in social and biological networks, " PNAS, vol. 99, pp. 7821-7826, 2002. (Pubitemid 34650963)
11. F. Radicchi, C. Castellano, and F. Cecconi, "Defining and identifying communities in networks, " Natl. Acad. Sci., vol. 101, no. 9, pp. 2658-2663, 2004. (Pubitemid 38327665)
12. F. Luo et al., "Modular organization of protein interaction networks, " Bioinformatics, vol. 23, no. 2, pp. 207-214, 2007. (Pubitemid 46189611)
13. M. E. J. Newman, "Fast algorithm for detecting community structure in networks, " Phys. Rev. E, vol. 69, no. 6, p. 066133, 2004.
14. M. Li, J. Wang, and J. Chen, "A fast agglomerate algorithm for mining functional modules in protein interaction networks, " in Proc. 1st Int. Conf. BioMed. Eng. Inf. (BMEI), 2008, pp. 3-7.
15. M. Li, J. Wang, J. Chen, and Y. Pan, "Hierarchical organization of functional modules in weighted protein interaction networks using clustering coefficient, " in Proc. 2009 Int. Symp. Bioinf. Res. Appl. (ISBRA), 2009, pp. 75-86.
16. S. Gregory, "An algorithm to find overlapping community structure in networks, " in Proc. 11th Eur. Conf. Principles Practice of Knowl. Disc. Databases (PKDD07), pp. 91-102.
17. J. W. Pinney and D. R. Westhead, S. Barber, P. Baxter, K. Mardia, and R. Walls, Eds., "Betweenness-based decomposition methods for social and biological networks, " in Proc. Interdisciplinary Stat. Bioinf., 2007, pp. 87-90.
18. S. Zhang, R. S. Wang, and X. S. Zhang, "Identification of overlapping community structure in complex networks using fuzzy C-means clustering, " Physica A, vol. 374, pp. 483-490, 2007.
19. A. Lancichinetti, S. Fortunato, and J. Kertesz, "Detecting the overlapping and hierarchical community structure in complex networks, " New J. Phys., vol. 11, p. 033015, 2009.
20. G. Palla, I. Dernyi, I. Farkas, and T. Vicsek, "Uncovering the overlapping community structure of complex networks in nature and society, " Nature, vol. 435, no. 7043, pp. 814-818, 2005. (Pubitemid 40839731)
21. X. L. Li, S. Tan, C. Foo, and S. Ng, "Interaction graph mining for protein complexes using local clique merging, " Genome Inf., vol. 16, pp. 260-269, 2006.
22. H. Xiong, X. He, C. Ding, Y. Zhang, V. Kumar, and S. R. Holbrook, "Identification of functional modules in protein complexes via hyperclique pattern discovery, " in Proc. Pacific Symp. Biocomput., 2005, pp. 221-232.
23. A. Bauer and B. Kuster, "Affinity purification-mass spectrometry: Powerful tools for the characterization of protein complexes, " Eur. J. Biochem., vol. 270, no. 4, pp. 570-578, 2003. (Pubitemid 36286570)
24. J. Wang, M. Li, J. Chen, and Y. Pan, "A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks, " IEEE/ACM Trans. Comput. Biol. Bioinf. (TCBB), vol. 8, no. 3, pp. 607-620, 2011.
25. 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.
26. E. A. Winzeler et al., "Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis, " Science, vol. 285, pp. 901-906, 1999. (Pubitemid 29381993)
27. R. S. Kamath et al., "Systematic functional analysis of the caenorhabditis elegans genome using RNAi, " Nature, vol. 421, pp. 231-237, 2003. (Pubitemid 36139121)
28. K. Saito, T. Yamada, and K. Kazama, "Extracting communities from complex networks by the k-dense method, " in Workshops Proc. 6th IEEE Int. Conf. Data Mining, 2006, pp. 300-304.
29. J. Reichardt and S. Bornholdt, "Detecting fuzzy community structures in complex networks with a potts model, " Phys. Rev. Lett., vol. 93, p. 218701, 2004.
30. D. Bu, Y. Zhao, L. Cai, H. Xue, X. Zhu, H. Lu, J. Zhang, S. Sun, L. Ling, N. Zhang, G. Li, and R. Chen, "Topological structure analysis of the protein-protein interaction network in budding yeast, " Nucl. Acids Res., vol. 31, pp. 2443-2450, 2003. (Pubitemid 37442113)
31. H. Yu, D. Greenbaum, H. X. Lu, Z. Zhu, and M. Gerstein, "Genomic analysis of essentiality within protein networks, " Trends Genet., vol. 20, pp. 227-231, 2004. (Pubitemid 38625679)
32. M. W. Hahn and A. D. Kern, "Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks, " Mol. Biol. Evol., vol. 22, no. 4, pp. 803-806, 2005. (Pubitemid 40471393)
33. S. Wuchty, "Interaction and domain networks of yeast, " Proteomics, vol. 2, pp. 1715-1723, 2002. (Pubitemid 36015507)
34. G. T. Hart, I. Lee, and E. Marcotte, "A high-accuracy consensusmap of yeast protein complexes reveals modular nature of gene essentiality, " BMC Bioinf., vol. 8, no. 1, p. 236, 2007.
35. H. Shen, X. Cheng, K. Cai, and M. B. Hu, "Detect overlapping and hierarchical community structure in networks, " Physica A, vol. 388, pp. 1706-1712, 2009.
36. S. Van Dongen, "Graph clustering by flow simulation, " Ph. D. dissertation, Centers for Mathematics and Computer Science (CWI), Univ. Utrecht, Utrecht, The Netherlands, 2000.
37. A. J. Enright, S. Van Dongen, and C. A. Ouzounis, "An efficient algorithm for large-scale detection of protein families, " Nucl. Acids Res., vol. 30, no. 7, pp. 1575-1584, 2002. (Pubitemid 34679732)
38. Liu et al., "Discovery from weighted PPI networks, " Bioinformatics, vol. 25, no. 15, pp. 1891-1897, 2009.
39. Leung et al., "Predicting protein complexes from PPI data: A coreattachment approach, " J. Comput. Biol., vol. 2, no. 16, pp. 133-144, 2009.
40. I. Xenarios et al., "DIP: The database of interaction proteins: A research tool for studying cellular networks of protien interactions, " Nucl. Acids Res., vol. 30, pp. 303-305, 2002. (Pubitemid 34679570)
41. R. Sharan et al., "Conserved patterns of protein interaction in multiple species, " Proc. Natl. Acad. Sci., vol. 102, no. 6, pp. 1974-1979, 2005. (Pubitemid 40261997)
42. T. Shlomi, D. Segal, E. Ruppin, and R. Sharan, "Qpath: A method for querying pathways in a protein-protein interaction network, " BMC Bioinf., vol. 7, p. 199, 2006.
43. H. W. Mewes et al., "MIPS: Analysis and annotation of proteins from whole genomes, " Nucl. Acids Res., vol. 32, pp. 41-44, 2004.
44. S. Pu, J. Wong, B. Turner, E. Cho, and S. J. Wodak, "Up-to-date catalogues of yeast protein complexes, " Nucl. Acids Res., vol. 37, no. 3, pp. 825-831, 2008.
45. A. Ruepp et al., "The FunCat: A functional annotation scheme for systematic classication of proteins from whole genomes, " Nucl. Acids Res., vol. 32, pp. 5539-5545, 2004. (Pubitemid 39545671)
46. Y. R. Cho et al., "Semantic integration to identify overlapping functional modules in protein interaction networks, " BMC Bioinf., vol. 8, p. 265, 2007.
47. S. P. Borgatti, "Centrality and AIDS, " Connections, vol. 18, pp. 112-115, 1995.
48. V. Spirin and L. A. Mirny, "Protein complexes and functional modules in molecular networks, " PNAS, vol. 100, pp. 12123-12128, 2003. (Pubitemid 37271525)
49. Z. Dezs, Z. N. Oltvai, and A.-L. Barabsi, "Bioinformatics analysis of experimentally determined protein complexes in the yeast saccharomyces cerevisiae, " Genome Res., vol. 13, no. 11, pp. 2450-2454, Nov. 2003. (Pubitemid 37428269)
50. G. Butland, J. M. Peregrn-Alvarez, J. Li, W. Yang, X. Yang, V. Canadien, A. Starostine, D. Richards, B. Beattie, N. Krogan, M. Davey, J. Parkinson, J. Greenblatt, and A. Emili, "Interaction network containing conserved and essential protein complexes in Escherichia coli, " Nature, vol. 433, pp. 531-537, 2005. (Pubitemid 40204311)