Identification of essential proteins based on edge clustering coefficient

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 9, Issue 4, 2012, Pages 1070-1080

  Wang, Jianxin ^a   Li, Min ^a   Wang, Huan ^a   Pan, Yi ^b  

^a CENTRAL SOUTH UNIVERSITY   (China)

^b GEORGIA STATE UNIVERSITY   (United States)

Author keywords

centrality measures; edge clustering coefficient; Essential proteins; protein interaction network; topology

Indexed keywords

BIOGRID; CENTRALITY MEASURES; CLUSTER EFFECTS; DRUG DESIGN; EDGE CLUSTERING; NETWORK LEVEL; NETWORK TOPOLOGY; PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTIONS;

ACTIVE NETWORKS; DATABASE SYSTEMS; ELECTRIC NETWORK TOPOLOGY; LARGE SCALE SYSTEMS; TOPOLOGY;

PROTEINS;

SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; BIOLOGY; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; ESSENTIAL GENE; METHODOLOGY; PHYSIOLOGY; PROTEIN PROTEIN INTERACTION; REPRODUCIBILITY;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENES, ESSENTIAL; PROTEIN INTERACTION MAPS; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84861492539     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.147     Document Type: Article

References (50)

1. M.L. Acencio and N. Lemke, "Towards the Prediction of Essential Genes by Integration of Network Topology, Cellular Localization and Biological Process Information," BMC Bioinformatics, vol. 10, article 290, 2009.
2. E.A. Winzeler et al., "Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis," Science, vol. 285, no. 5429, pp. 901-906, 1999. (Pubitemid 29381993)
3. D. Park, J. Park, S.G. Park, T. Park, and S.S. Choi, "Analysis of Human Disease Genes in the Context of Gene Essentiality," Genomics, vol. 92, no. 6, pp. 414-418, 2008.
4. W. Hu et al., "Essential Gene Identification and Drug Target Prioritization in Aspergillus fumigatus," PLoS Pathogens, vol. 3, no. 3, p. e24, 2007.
5. G. Giaever et al., "Functional Profiling of the Saccharomyces cerevisiae Genome," Nature, vol. 418, no. 6896, pp. 387-391, 2002. (Pubitemid 34826834)
6. L.M. Cullen and G.M. Arndt, "Genome-Wide Screening for Gene Function Using RNAi in Mammalian Cells," Immunology and Cell Biology, vol. 83, no. 3, pp. 217-223, 2005. (Pubitemid 40799549)
7. T. Roemer et al., "Large-Scale Essential Gene Identification in Candida albicans, and Applications to Antifungal Drug Discovery," Molecular Microbiology, vol. 50, no. 1, pp. 167-181, 2003. (Pubitemid 37222795)
8. P. Uetz et al., "A Comprehensive Analysis of Protein-protein Interactions in Saccharomyces cerevisiae," Nature, vol. 403, no. 6770, pp. 623-627, 2000. (Pubitemid 30103994)
9. T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki, "A Comprehensive Two-Hybrid Analysis to Explore the Yeast Protein Interactome," Proc. Nat'l Academy of Sciences USA, vol. 98, no. 8, pp. 4569-4574, 2001. (Pubitemid 32295017)
10. Y. Ho et al., "Systematic Identification of Protein Complexes in Saccharomyces cerevisiae by Mass Spectrometry," Nature, vol. 415, no. 6868, pp. 180-183, 2002. (Pubitemid 34059520)
11. C. von Mering, R. Krause, B. Snel, M. Cornell, S.G. Oliver, S. Fields, and P. Bork, "Comparative Assessment of Large-Scale Data Sets of Protein-Protein Interactions," Nature, vol. 417, no. 6887, pp. 399-403, 2002. (Pubitemid 34563526)
12. H. Jeong, S.P. Mason, A.-L. Barabási, and Z.N. Oltvai, "Lethality and Centrality in Protein Networks," Nature, vol. 411, no. 6833, pp. 41-42, 2001. (Pubitemid 32428180)
13. S. Maslov and K. Sneppen, "Specificity and Stability in Topology of Protein Networks," Science, vol. 296, no. 5569 pp. 910-913, 2002. (Pubitemid 34464896)
14. A.-L. Barabási and Z.N. Oltvai, "Network Biology: Understanding the Cell's Functional Organization," Nature Rev. Genetics, vol. 5, no. 2 pp. 101-113, 2004. (Pubitemid 38160277)
15. C.C. Lin, H.F. Juan, J.T. Hsiang, Y.C. Hwang, H. Mori, and H.C. Huang, "Essential Core of Protein-Protein Interaction Network in Escherichia coli," J. Proteome Research, vol. 8, no. 4, pp. 1925-1931, 2009.
16. M.W. Hahn and A.D. Kern, "Comparative Genomics of Centrality and Essentiality in Three Eukaryotic Protein-Interaction Networks," Molecular Biology and Evolution, vol. 22, no. 4, pp. 803-806, 2005. (Pubitemid 40471393)
17. H. Liang and W.H. Li, "Gene Essentiality, Gene Duplicability and Protein Connectivity in Human and Mouse," Trends in Genetics, vol. 23, no. 8, pp. 375-378, 2007. (Pubitemid 47088007)
18. R.R. Vallabhajosyula, D. Chakravarti, S. Lutfeali, A. Ray, and A. Raval, "Identifying Hubs in Protein Interaction Networks," PLoS ONE, vol. 4, no. 4, p. e5344, 2009.
19. K. Pang, H. Sheng, and X. Ma, "Understanding Gene Essentiality by Finely Characterizing Hubs in the Yeast Protein Interaction Network," Biochemical and Biophysical Research Comm., vol. 401, no. 1, pp. 112-116, 2010.
20. K. Ning, H.K. Ng, S. Srihari, H.W. Leong, and A.I. Nesvizhskii, "Examination of the Relationship between Essential Genes in PPI Network and Hub Proteins in Reverse Nearest Neighbor Topology," BMC Bioinformatics, vol. 11, article 505, 2010.
21. L.C. Freeman, "A Set of Measures of Centrality Based on Betweenness," Sociometry, vol. 40, no. 1, pp. 35-41, 1977.
22. M.P. Joy, A. Brock, D.E. Ingber, and S. Huang, "High-betweenness Proteins in the Yeast Protein Interaction Network," J. Biomedicine and Biotechnology, vol. 2005, no. 2, pp. 96-103, 2005. (Pubitemid 41627865)
23. S. Wuchty and P.F. Stadler, "Centers of Complex Networks," J. Theoretical Biology, vol. 223, no. 1, pp. 45-53, 2003. (Pubitemid 36627545)
24. E. Estrada and J.A. Rodríguez-Velázquez, "Subgraph Centrality in Complex Networks," Physical Rev. E, vol. 71, no. 5 p. 056103, 2005.
25. P. Bonacich, "Power and Centrality: A Family of Measures," Am. J. Sociology, vol. 92, no. 5, pp. 1170-1182, 1987.
26. K. Stevenson and M. Zelen, "Rethinking Centrality: Methods and Examples," Social Networks, vol. 11, no. 1, pp. 1-37, 1989.
27. E. Estrada, "Virtual Identification of Essential Proteins within the Protein Interaction Network of Yeast," Proteomics, vol. 6, no. 1, pp. 35-40, 2006. (Pubitemid 43142931)
28. O. Mason and M. Verwoerd, "Graph Theory and Networks in Biology," IET Systems Biology, vol. 1, no. 2, pp. 89-119, 2007. (Pubitemid 46488242)
29. M. Li, J. Wang, H. Wang, and Y. Pan, "Essential Proteins Discovery from Weighted Protein Interaction Networks," Proc. Sixth Int'l Symp. Bioinformatics Research and Applied (ISBRA), pp. 89-100, May 2010.
30. K. Park and D. Kim, "Localized Network Centrality and Essentiality in the Yeast-Protein Interaction Network," Proteomics, vol. 9, no. 22 pp. 5143-5154, 2009.
31. G. del Rio, D. Koschützki, and G. Coello, "How to Identify Essential Genes from Molecular Networks?," BMC Systems Biology, vol. 3, article 102, 2009.
32. L.C. Freeman, "Centrality in Social Networks: Conceptual Clarification," Social Networks, vol. 1, no. 3, pp. 215-239, 1979.
33. D. Gómez, E. González-Arangüena, C. Manuel, G. Owen, M. del Pozo, and J. Tejada, "Centrality and Power in Social Networks: A Game Theoretic Approach," Math. Social Sciences, vol. 46, no. 1, pp. 27-54, 2003. (Pubitemid 36614180)
34. X. He and J. Zhang, "Why Do Hubs Tend to be Essential in Protein Networks?," PLoS Genetics, vol. 2, no. 6, p. e88, 2006.
35. E. Zotenko, J. Mestre, D.P. O'Leary, and T.M. Przytycka, "Why Do Hubs in the Yeast Protein Interaction Network Tend to be Essential: Reexamining the Connection between the Network Topology and Essentiality," PLoS Computational Biology, vol. 4, no. 8, p. e1000140, 2008.
36. J.B. Pereira-Leal, B. Audit, J.M. Peregrin-Alvarez, and C.A. Ouzounis, "An Exponential Core in the Heart of the Yeast Protein Interaction Network," Molecular Biology and Evolution, vol. 22, no. 3, pp. 421-425, 2005. (Pubitemid 40299490)
37. F. Radicchi, C. Castellano, F. Cecconi, V. Loreto, and D. Parisi, "Defining and Identifying Communities in Networks," Proc. Nat'l Academy of Sciences USA, vol. 101, no. 9, pp. 2658-2663, 2004. (Pubitemid 38327665)
38. J.X. Wang, M. Li, J.E. Chen, and Y. Pan, "A Fast Hierarchical Clustering Algorithm for Functional Modules Discovery in Protein Interaction Networks," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 8, no. 3, pp. 607-620, May/June 2011.
39. M. Girvan and M.E.J. Newman, "Community Structure in Social and Biological Networks," Proc. Nat'l Academy of Sciences USA, vol. 99, no. 12, pp. 7821-7826, 2002. (Pubitemid 34650963)
40. A.W. Rives and T. Galitski, "Modular Organization of Cellular Networks," Proc. Nat'l Academy of Sciences USA, vol. 100, no. 3, pp. 1128-1133, 2003. (Pubitemid 36183967)
41. A.-C. Gavin et al., "Functional Organization of the Yeast Proteome by Systematic Analysis of Protein Complexes," Nature, vol. 415, no. 6868, pp. 141-147, 2002. (Pubitemid 34059510)
42. G.T. Hart, I. Lee, and E.M. Marcotte, "A High-Accuracy Consensus Map of Yeast Protein Complexes Reveals Modular Nature of Gene Essentiality," BMC Bioinformatics, vol. 8, article 236, 2007.
43. I. Xenarios, D.W. Rice, L. Salwinski, M.K. Baron, E.M. Marcotte, and D. Eisenberg, "DIP: The Database of Interacting Proteins," Nucleic Acids Research, vol. 28, no. 1, pp. 289-291, 2000. (Pubitemid 30047782)
44. M.S. Livstone, J. Nixon, K. Van Auken, X. Wang, X. Shi, T. Reguly, J.M. Rust, A. Winter, K. Dolinski, and M. Tyers, "The BioGRID Interaction Database: 2011 Update," Nucleic Acids Research, vol. 39, pp. D698-D704, Nov. 2010.
45. H.W. Mewes, D. Frishman, K.F.X. Mayer, M. Münsterkötter1, O. Noubibou, P. Pagel, T. Rattei, M. Oesterheld, A. Ruepp, and V. Stümpflen, "MIPS: Analysis and Annotation of Proteins from Whole Genomes in 2005," Nucleic Acids Research, vol. 34, pp. D169-D172, 2006.
46. J.M. Cherry, C. Adler, C. Ball, S.A. Chervitz, S.S. Dwight, E.T. Hester, Y. Jia, G. Juvik, T. Roe, M. Schroeder, S. Weng, and D. Botstein, "SGD: Saccharomyces Genome Database," Nucleic Acids Research, vol. 26, no. 1, pp. 73-79, 1998. (Pubitemid 28295265)
47. R. Zhang and Y. Lin, "DEG 5.0, A Database of Essential genes in both Prokaryotes and Eukaryotes," Nucleic Acids Research, vol. 37, pp. D455-D458, 2009.
48. http://www-sequence.stanford.edu/group/yeast-deletion-project, 2011.
49. A.G. Holman et al., "Computational Prediction of Essential Genes in an Unculturable Endosymbiotic Bacterium, Wolbachia of Brugia Malayi," BMC Microbiology, vol. 9, article 243, 2009.
50. P. Shannon, A. Markiel, O. Ozier, N.S. Baliga, J.T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker, "Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks," Genome Research, vol. 13, no. 11, pp. 2498-2504, 2003. (Pubitemid 37428274).