Yeast protein-protein interaction network model based on biological experimental data

doi:10.1007/s10483-015-1940-6

Applied Mathematics and Mechanics (English Edition) ›› 2015, Vol. 36 ›› Issue (6): 827-834.doi: https://doi.org/10.1007/s10483-015-1940-6

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Yeast protein-protein interaction network model based on biological experimental data

Chunhong WANG¹, Shuiming CAI², Zengrong LIU^1,3, Youwen CHEN¹

1. Department of Mathematics, Shanghai University, Shanghai 200444, China;
2. Faculty of Science, Jiangsu University, Zhenjiang 212013, Jiangsu Province, China;
3. Institute of Systems Biology, Shanghai University, Shanghai 200444, China

Received:2014-05-06 Revised:2014-11-24 Online:2015-06-01 Published:2015-06-01
Contact: Zengrong LIU E-mail:zrongliu@126.com
Supported by:
Project supported by the National Natural Science Foundation of China (No. 11172158)

Abstract

Abstract: Duplication and divergence have been widely recognized as the two dominant evolutionary forces in shaping biological networks, e.g., gene regulatory networks and protein-protein interaction (PPI) networks. It has been shown that the network growth models constructed on the principle of duplication and divergence can recapture the topological properties of real PPI networks. However, such network models only consider the evolution processes. How to select the model parameters with the real biological experimental data has not been presented. Therefore, based on the real PPI network statistical data, a yeast PPI network model is constructed. The simulation results indicate that the topological characteristics of the constructed network model are well consistent with those of real PPI networks, especially on sparseness, scale-free, small-world, hierarchical modularity, and disassortativity.

Key words: yeast, disassortativity, duplication-divergence, protein-protein interaction (PPI) network

2010 MSC Number:

TN711

Chunhong WANG, Shuiming CAI, Zengrong LIU, Youwen CHEN. Yeast protein-protein interaction network model based on biological experimental data. Applied Mathematics and Mechanics (English Edition), 2015, 36(6): 827-834.

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References

[1] Yook, S. H., Oltvai, Z. N., and Barabasi, A. L. Functional and topological characterization of protein interaction networks. Proteomics, 4, 928-942 (2004)
[2] Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S., and Rothberg, J. M. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. nature, 403, 623-627 (2000)
[3] Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. A comprehensive twohybrid analysis to explore the yeast protein interactome. Proceedings of the National Academy of Sciences, 98, 4277-4278 (2001)
[4] Güldener, U., Münsterkötter, M., Oesterheld, M., Pagel, P., Ruepp, A., Mewes, H. W., and Stümpflen, V. The MIPS protein interaction resource on yeast. Nucleic Acids Research, 34, 436-441 (2006)
[5] Li, S. M., Armstrong, C. M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P. O., Han, J. D. J., Chesneau, A., Hao, T., Goldberg, D. S., Li, N., Martinez, M., Rual, J. F., Lamesch, P., Xu, L., Tewari, M., Wong, S. L., Zhang, L. V., Berriz, G. F., Jacotot, L., Vaglio, P., Reboul, J., Hirozane-Kishikawa, T., Li, Q. R., Gabel, H. W., Elewa, A., Baumgartner, B., Rose, D. J., Yu, H. Y., Bosak, S., Sequerra, R., Fraser, A., Mango, S. E., Saxton, W. M., Strome, S., van den Heuvel, S., Piano, F., Vandenhaute, J., Sardet, C., Gerstein, M., Doucette-Stamm, L., Gunsalus, K. C., Harper, J. W., Cusick, M. E., Roth, F. P., Hill, D. E., and Vidal, M. A map of the interactome network of the Metazoan C. elegans. Science, 303, 540-543 (2004)
[6] Giot, L., Bader, J. S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y. L., Ooi, C. E., Godwin, B., Vitols, E., Vijayadamodar, G., Pochart, P., Machineni, H., Welsh, M., Kong, Y., Zerhusen, B., Malcolm, R., Varrone, Z., Collis, A., Minto, M., Burgess, S., McDaniel, L., Stimpson, E., Spriggs, F., Williams, J., Neurath, K., Ioime, N., Agee, M., Voss, E., Furtak, K., Renzulli, R., Aanensen, N., Carrolla, S., Bickelhaupt, E., Lazovatsky, Y., DaSilva, A., Zhong, J., Stanyon, C. A., Finley, R. L., Jr, White, K. P., Braverman, M., Jarvie, T., Gold, S., Leach, M., Knight, J., Shimkets, R. A., McKenna, M. P., Chant, J., and Rothberg, J. M. A protein interaction map of Drosophila melanogaster. Science, 302, 1727-1736 (2003)
[7] Stelzl, U., Worm, U., Lalowski, M., Haenig, C., Brembeck, F. H., Goehler, H., Stroedicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., Timm, J., Mintzlaff, S., Abraham, C., Bock, N., Kietzmann, S., Goedde, A., Toksöz, E., Droege, A., Krobitsch, S., Korn, B., Birchmeier, W., Lehrach, H., and Wanker, E. E. A human protein-protein interaction network: a resource for annotating the proteome. Cell, 122, 957-968 (2005)
[8] Rual, J. F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi-Guedehoussou, N., Klitgord, N., Simon, C., Boxem, M., Milstein, S., Rosenberg, J., Goldberg, D. S., Zhang, L. V., Wong, S. L., Franklin, G., Li, S., Albala, J. S., Lim, J., Fraughton, C., Llamosas, E., Cevik, S., Bex, C., Lamesch, P., Sikorski, R. S., Vandenhaute, J., Zoghbi, H. Y., Smolyar, A., Bosak, S., Sequerra, R., Doucette-Stamm, L., Cusick, M. E., Hill, D. E., Roth, F. P., and Vidal, M. Towards a proteome-scale map of the human protein-protein interaction network. nature, 437, 1173-1178 (2005)
[9] Barabasi, A. L. and Oltvai, Z. N. Network biology: understanding the cell's functional organization. Nature Reviews Genetics, 5, 101-113 (2004)
[10] Sole, R. V. and Pastor-Satorra, R. Smith EA model of large-scale proteome evolution. Advances in Complex Systems, 5, 43-54 (2002)
[11] Jeong, H., Mason, S. P., BarabáRsi, A. L., and Oltvai, Z. N. Lethality and centrality in protein networks. nature, 411, 41-42 (2001)
[12] Ravasz, E. and Barabasi, A. L. Hierarchical organization in complex networks. nature, 67, 026112 (2003)
[13] Williams, R. J., Martinez, N. D., and Berlow, E. L. Two degrees of separation in complex food webs. Science, 297, 1551-1555 (2002)
[14] Maslov, S. and Sneppen, K. Specificity and stability in topology of protein networks. Science, 296, 910-913 (2002)
[15] Hase, T., Niimura, Y., Kaminuma, T., and Tanaka, H. Non-uniform survival rate of heterodimerization links in the evolution of the yeast protein-protein interaction network. PloS One, 3, e1667 (2008)
[16] Cai, S. M. Construction and Analysis of Batch Control and Biological Network Chaotic Systems and Complex Dynamical Networks (in Chinese), Ph.D. dissertation, Shanghai University, Shanghai (2012)
[17] Ohno, S. Evolution by Gene Duplication, Springer, Berlin (1970)
[18] Ispolatov, I., Krapivsky, P. L., and Yuryev, A. Duplication-divergence model of protein interaction network. Physical Review E, 71, 061911 (2005)
[19] Lynch, M. and Conery, J. S. The evolutionary fate and consequences of duplicate genes. Science, 290, 1151-1155 (2000)
[20] Wagner, A. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Molecular Biology and Evolution, 18, 1283-1292 (2003)
[21] Li, W. H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. Journal of Molecular Evolution, 36, 96-99 (1993)
[22] Prachumwat, A. and Li, W. H. Protein function, connectivity, and duplicability in yeast. Molecular Biology and Evolution, 23, 30-39 (2006)
[23] Costa, L. F., Rodrigues, F. A., Vieso, G. T., and Boas, P. R. V. Characterization of complex networks: a survey of measurements. Advances in Physics, 56, 167-242 (2007)

Yeast protein-protein interaction network model based on biological experimental data

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