Skip to main content
SpringerLink
Log in

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

  • Published:
Applied Mathematics and Mechanics Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

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)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  3. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proceedings of the National Academy of Sciences, 98, 4277–4278 (2001)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  9. Barabasi, A. L. and Oltvai, Z. N. Network biology: understanding the cell’s functional organization. Nature Reviews Genetics, 5, 101–113 (2004)

    Article  Google Scholar 

  10. Sole, R. V. and Pastor-Satorra, R. Smith EA model of large-scale proteome evolution. Advances in Complex Systems, 5, 43–54 (2002)

    Article  MATH  Google Scholar 

  11. Jeong, H., Mason, S. P., BarabáRsi, A. L., and Oltvai, Z. N. Lethality and centrality in protein networks. nature, 411, 41–42 (2001)

    Article  Google Scholar 

  12. Ravasz, E. and Barabasi, A. L. Hierarchical organization in complex networks. nature, 67, 026112 (2003)

    Google Scholar 

  13. Williams, R. J., Martinez, N. D., and Berlow, E. L. Two degrees of separation in complex food webs. Science, 297, 1551–1555 (2002)

    Article  Google Scholar 

  14. Maslov, S. and Sneppen, K. Specificity and stability in topology of protein networks. Science, 296, 910–913 (2002)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

  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)

    Google Scholar 

  17. Ohno, S. Evolution by Gene Duplication, Springer, Berlin (1970)

    Book  Google Scholar 

  18. Ispolatov, I., Krapivsky, P. L., and Yuryev, A. Duplication-divergence model of protein interaction network. Physical Review E, 71, 061911 (2005)

    Article  Google Scholar 

  19. Lynch, M. and Conery, J. S. The evolutionary fate and consequences of duplicate genes. Science, 290, 1151–1155 (2000)

    Article  Google Scholar 

  20. Wagner, A. The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Molecular Biology and Evolution, 18, 1283–1292 (2003)

    Article  Google Scholar 

  21. Li, W. H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. Journal of Molecular Evolution, 36, 96–99 (1993)

    Article  Google Scholar 

  22. Prachumwat, A. and Li, W. H. Protein function, connectivity, and duplicability in yeast. Molecular Biology and Evolution, 23, 30–39 (2006)

    Article  Google Scholar 

  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)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Mathematics, Shanghai University, Shanghai, 200444, China

    Chunhong Wang, Zengrong Liu & Youwen Chen

  2. Faculty of Science, Jiangsu University, Zhenjiang, 212013, Jiangsu Province, China

    Shuiming Cai

  3. Institute of Systems Biology, Shanghai University, Shanghai, 200444, China

    Zengrong Liu

Authors
  1. Chunhong Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shuiming Cai
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zengrong Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Youwen Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Zengrong Liu.

Additional information

Project supported by the National Natural Science Foundation of China (No. 11172158)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, C., Cai, S., Liu, Z. et al. Yeast protein-protein interaction network model based on biological experimental data. Appl. Math. Mech.-Engl. Ed. 36, 827–834 (2015). https://doi.org/10.1007/s10483-015-1940-6

Download citation

  • Received:

  • Revised:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10483-015-1940-6

Key words

Chinese Library Classification

2010 Mathematics Subject Classification

Search

Navigation