Identification and evolution of structurally dominant nodes in protein-protein interaction networks

IEEE Transactions on Biomedical Circuits and Systems

Volumn 8, Issue 1, 2014, Pages 87-97

  Wang, Pei ^a,b   Yu, Xinghuo ^b   Lü, Jinhu ^c  

^a HENAN UNIVERSITY   (China)

^b RMIT UNIVERSITY   (Australia)

^c INSTITUTE OF SYSTEMS SCIENCE   (China)

Author keywords

Duplication divergence model; evolution; important node; protein protein interaction network; structurally dominant protein

Indexed keywords

ACTIVE NETWORKS;

DUPLICATION-DIVERGENCE MODEL; EIGENVECTOR CENTRALITIES; EVOLUTION; EVOLUTION CHARACTERISTICS; EVOLVING CHARACTERISTIC; IMPORTANT NODE; MULTIVARIATE STATISTICAL ANALYSIS; PROTEIN-PROTEIN INTERACTION NETWORKS;

PROTEINS;

SACCHAROMYCES CEREVISIAE PROTEIN;

BIOLOGICAL MODEL; METABOLISM; PHYSIOLOGY; PROCEDURES; PROTEIN PROTEIN INTERACTION; PROTEOMICS;

MODELS, BIOLOGICAL; PROTEIN INTERACTION MAPS; PROTEOMICS; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 84897959305     PISSN: 19324545     EISSN: None     Source Type: Journal    
DOI: 10.1109/TBCAS.2014.2303160     Document Type: Article

References (60)

1. L. Freeman, "A set of measures of centrality based on betweenness," Sociometry, vol. 40, no. 1, pp. 35-41, 1977.
2. L. Freeman, "Centrality in social networks: Conceptual clarification," Social Netw., vol. 1, no. 3, pp. 215-239, 1979.
3. D. J. Watts and S. H. Strogatz, "Collective dynamics of 'small-world' networks," Nature, vol. 393, pp. 440-442, 1998. (Pubitemid 28292183)
4. M. E. J. Newman, "The structure and function of complex networks," SIAM Rev., vol. 45, no. 2, pp. 167-256, 2003.
5. M. E. J. Newman, "A measure of betweenness centrality based on random walks," Social Netw., vol. 27, pp. 39-54, 2005. (Pubitemid 40272648)
6. S. Carmi, S. Havlin, S. Kirkpatrick, Y. Shavitt, and E. Shir, "A model of Internet topology using k-shell decomposition," Proc. Nat. Acad. Sci. USA, vol. 104, pp. 11150-11154, 2007. (Pubitemid 47175109)
7. P. Bonacich and P. Lloyd, "Eigenvector-like measures of centrality for asymmetric relations," Social Netw., vol. 23, no. 3, pp. 191-201, 2001. (Pubitemid 33633649)
8. C. Canali and R. Lancellotti, "A quantitative methodology based on component analysis to identify key users in social networks," Int. J. Social Netw. Mining, vol. 1, no. 1, pp. 27-50, 2012.
9. D. Chen, L. Lü, M. Shang, and T. Zhou, "Identifying influential nodes in complex networks," Physica A, vol. 391, pp. 1777-1787, 2012.
10. S. Brin and L. Page, "The anatomy of a largescale hypertextual web search engine," Comput. Netw. ISDN Syst., vol. 30, pp. 107-117, 1998.
11. L. Lü, Y. Zhang, C. Yeung, and T. Zhou, "Leaders in social networks, the delicious case," PLoS One, vol. 6, no. art. e21202, 2011.
12. F. Probst, D. K. L. Grosswiele, and D. K. R. Pfleger, "Who will lead and who will follow: Identifying influential users in online social networks," Bus. Inform. Syst. Eng., vol. 5, pp. 179-193, 2013.
13. O. Sporns, C. J. Honey, and R. Kötter, "Identification and classification of hubs in brain networks," PLoS One, vol. 2, no. 10, art. e1049, 2007.
14. P. Bertolazzi, M. E. Bock, and C. Guerra, "On the functional and structural characterization of hubs in protein-protein interaction networks," Biotechnol. Adv., vol. 31, no. 2, pp. 274-286, 2013.
15. M. Kitsak, L. K. Gallos, S. Havlin, F. Liljeros, L. Muchnik, H. E. Stanley, and H. A. Makse, "Identification of influential spreaders in complex networks," Nat. Phys., vol. 6, pp. 888-893, 2010.
16. P. Wang, C. Tian, and J. Lu, "Identifying influential spreaders in artificial complex networks," J. Syst. Sci. Complex., 2013, to be published.
17. P. Wang, J. Lü, and X. Yu, "Identification of important nodes in directed biological networks: A method based on network motifs," PLoS One, 2014, revised version, currently under review, submitted for publication.
18. E. Wang, A. Lenferink, and M. O'Connor-McCourt, "Cancer systems biology: Exploring cancer-associated genes on cellular networks," Cell Mol. Life Sci., vol. 64, pp. 1752-1762, 2007. (Pubitemid 47093012)
19. G. Östlund, M. Lindskog, and E. L. Sonnhammer, "Network-based identification of novel cancer genes," Mol. Cell Proteom., vol. 9, pp. 648-655, 2010.
20. X. Wang, N. Gulbahce, and H. Yu, "Network-based methods for human disease gene prediction," Brief Funct. Genom., vol. 10, pp. 280-293, 2011.
21. A. Wagner, "The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes," Mol. Biol. Evol., vol. 18, no. 7, pp. 1283-1292, 2001. (Pubitemid 32660673)
22. S. Wuchty, "Interaction and domain networks of yeast," Proteom., vol. 2, no. 12, pp. 1715-1723, 2002. (Pubitemid 36015507)
23. B. Schwikowski, P. Uetz, and S. Fields, "A network of protein-protein interactions in yeast," Nat. Biotechnol., vol. 18, no. 12, pp. 1257-1261, 2000.
24. H. Yu et al., "High-quality binary protein interaction map of the Yeast interactome network," Science, vol. 322, no. 5898, pp. 104-110, 2008.
25. Y. Jin, D. Turaev, T. Weinmaier, T. Rattei, and H. A. Makse, "The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks," PLoS One, vol. 8, no. 3, art. e58134, 2013.
26. 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.
27. W. E. Payne and J. I. Garrels, "Yeast Protein database (YPD): A database for the complete proteome of Saccharomyces cerevisiae," Nucleic Acids Res., vol. 25, no. 1, pp. 57-62, 1997. (Pubitemid 27303150)
28. H. W. Mewes et al., "MIPS: Analysis and annotation of proteins from whole genomes in 2005," Nucleic Acids Res., vol. 34, pp. D169-D172, 2006.
29. I. Xenarios, D. W. Rice, L. Salwinski, M. K. Baron, E. M. Marcotte, and D. Eisenberg, "DIP: The database of interacting proteins," Nucleic Acids Res., vol. 28, no. 1, pp. 289-291, 2000. (Pubitemid 30047782)
30. 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)
31. T. Ito et al., "Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins," Proc. Nat. Acad. Sci. USA, vol. 97, pp. 1143-1147, 2000. (Pubitemid 30080826)
32. R. V. Solé, R. Pastor-Satorras, E. Smith, and T. B. Kepler, "A model of large-scale proteome evolution," Adv. Complex Syst., vol. 5, pp. 43-54, 2002.
33. A. Vázquez, A. Flammini, A. Maritan, and A. Vespignani, "Modeling of protein interaction networks," Complexus, vol. 1, pp. 38-44, 2003.
34. I. Ispolatov, P. L. Krapivsky, and A. Yuryev, "Duplication- divergence model of protein interaction network," Phys. Rev. E, vol. 71, no. art. 061911, 2005.
35. X. Wan, S. Cai, J. Zhou, and Z. Liu, "Emergence of modularity and disassortativity in protein-protein interaction networks," Chaos, vol. 20, no. art. 045113, 2010.
36. C. Xu, Z. Liu, and R. Wang, "How divergence mechanisms influence disassortative mixing property in biology," Physica A, vol. 389, no. 3, pp. 643-650, 2010.
37. D. Zhao, Z. Liu, and J. Wang, "Duplication: A mechanism producing disassortative mixing networks in biology," Chin. Phys. Lett., vol. 24, pp. 2766-2768, 2007.
38. S. N. Dorogovtsev and J. F. F. Mendes, "Evolution of networks," Adv. Phys., vol. 51, pp. 1079-1187, 2002. (Pubitemid 34759032)
39. P. Wang, X. Yu, and J. Lü, "Identification of important nodes in artificial bio-molecular networks," in Proc. IEEE Int. Symp. Circuits Syst., Jun. 2014.
40. R. Pastor-Satorras, E. Smith, and R. V. Solé, "Evolving protein interaction networks through gene duplication," J. Theor. Biol., vol. 222, no. 2, pp. 199-210, 2003. (Pubitemid 36506752)
41. R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon, "Network motifs: Simple building blocks of complex networks," Science, vol. 298, pp. 824-827, 2002. (Pubitemid 35231534)
42. S. S. Shen-Orr, R. Milo, S. Mangan, and U. Alon, "Network motifs in the transcriptional regulation network of Escherichia coli," Nat. Genet., vol. 31, pp. 64-68, 2002.
43. K. Pearson, "On lines and planes of closest fit to systems of points in space," Philosoph. Mag., vol. 2, pp. 559-572, 1901.
44. W. K. Härdle and L. Simar, Applied Multivariate Statistical Analysis. Berlin, Germany: Springer-Verlag, 2012.
45. U. Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits. London, U.K.: Chapman & Hall/CRC, 2007.
46. P. Wang, J. Lü, and M. Ogorzalek, "Global relative parameter sensitivities of the feed-forward loops in genetic networks," Neurocomput., vol. 78, pp. 55-165, 2012.
47. P. Wang, J. Lü, Y. Zhang, and M. Ogorzalek, "Global relative inputoutput sensitivities of the feed-forward loops in genetic networks," in Proc. 31th Chin. Control Conf., Jul. 25-27, 2012, pp. 7376-7381.
48. P. Wang and J. Lü, "Control of genetic regulatory networks: Opportunities and challenges," Acta. Automat. Sinica, vol. 39, no. 12, pp. 1969-1979, 2013.
49. P. Wang, J. Lü, Y. Zhang, and M. Ogorzalek, "Intrinsic noise induced state transition in coupled positive and negative feedback genetic circuit," in Proc. IEEE Int. Conf. Syst. Biol., Sep. 2-4, 2011, pp. 356-361.
50. M. Ashburner et al., "Gene ontology: Tool for the unification of biology. The Gene Otology Consortium," Nat. Genet., vol. 25, no. 1, pp. 25-29, 2000. (Pubitemid 30257031)
51. D. E. Sterner et al., "Functional organization of the yeast SAGA complex: Distinct components involved in structural integrity, nucleosome acetylation, and TATA-binding protein interaction," Mol. Cell Biol., vol. 19, no. 1, pp. 86-98, 1999. (Pubitemid 29018412)
52. E. Koutelou, C. L. Hirsch, and S. Y. R. Dent, "Multiple faces of the SAGA complex," Curr. Opin. Cell Biol., vol. 22, pp. 374-382, 2010.
53. P. Jancura and E. Marchiori, "A survey on evolutionary analysis in PPI networks," InTech, Protein interaction/book 2, 2011.
54. R. Albert, H. Jeong, and A. L. Barabási, "Error and attack tolerance of complex networks," Nature, vol. 406, no. 6794, pp. 378-82, 2000. (Pubitemid 30625551)
55. 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)
56. B. Chen, W. Wu, Y. Wang, and W. Li, "On the robust circuit design schemes of biochemical networks: Steady-state approach," IEEE Trans. Biomed. Circuits Syst., vol. 1, no. 2, pp. 91-104, 2007. (Pubitemid 350141710)
57. B. Chen and P. Chen, "Robust engineered circuit design principles for stochastic biochemical networks with parameter uncertainties and disturbances," IEEE Trans. Biomed. Circuits Syst., vol. 2, no. 2, pp. 114-132, 2008.
58. M. Gu and S. Chakrabartty, "FAST: A framework for simulation and analysis of large-scale protein-silicon biosensor circuits," IEEE Trans. Biomed. Circuits Syst., vol. 7, no. 4, pp. 451-459, Aug. 2013.
59. F. Wu, "Global and robust stability analysis of genetic regulatory networks with time-varying delays and parameter uncertainties," IEEE Trans. Biomed. Circuits Syst., vol. 5, no. 4, pp. 391-398, Aug. 2011.
60. S. Roy, "Systems biology beyond degree, hubs and scale-free networks: The case for multiple metrics in complex networks," Syst. Synth. Biol., vol. 6, pp. 31-34, 2012.