Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History

  • Si Li
  • Kwok Pui Choi
  • Taoyang Wu
  • Louxin Zhang
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7292)

Abstract

Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapshots of the network evolution. How to infer the whole evolution history becomes a challenging problem in computational biology. In this paper, we present a likelihood-based approach to inferring network evolution history from the topology of PPI networks and the duplication relationship among the paralogs. Simulations show that our approach outperforms the existing ones in terms of the accuracy of reconstruction. Moreover, the growth parameters of several real PPI networks estimated by our method are more consistent with the ones predicted in literature.

Keywords

Protein Interaction Network Network Evolution Anchor Node Growth History Node Sequence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Bar-Ilan, J., Mat-Hassan, M., Levene, M.: Methods for comparing rankings of search engine results. Comput. Netw. 50, 1448–1463 (2006)MATHCrossRefGoogle Scholar
  2. 2.
    Barabasi, A., Oltvai, Z.: Network biology: understanding the cell’s functional organization. Nat. Rev. Genet. 5, 101–113 (2004)CrossRefGoogle Scholar
  3. 3.
    Bhan, A., Galas, D., Dewey, T.: A duplication growth model of gene expression networks. Bioinformatics 18, 1486–1493 (2002)CrossRefGoogle Scholar
  4. 4.
    Dutkowski, J., Tiuryn, J.: Identification of functional modules from conserved ancestral protein-protein interactions. Bioinformatics 23, i149–i158 (2007)CrossRefGoogle Scholar
  5. 5.
    Farid, N., Christensen, K.: Evolving networks through deletion and duplication. New J. Phys. 8, 212–229 (2006)CrossRefGoogle Scholar
  6. 6.
    Gibson, T., Goldberg, D.: Reverse engineering the evolution of protein interaction networks. In: Pac. Symp. Biocomp., pp. 190–202 (2009)Google Scholar
  7. 7.
    Hakes, L., Pinney, J., Robertson, D., Lovell, S.: Protein-protein interaction networks and biology–what’s the connection. Nat. Biotech. 26, 69–72 (2008)CrossRefGoogle Scholar
  8. 8.
    Ispolatov, I., Krapivsky, P., Yuryev, A.: Duplication-divergence model of protein interaction network. Phys. Rev. E 71, 061911 (2005)CrossRefGoogle Scholar
  9. 9.
    Middendorf, M., Ziv, E., Wiggins, C.: Inferring network mechanisms: The drosophila melanogaster protein interaction network. Proc. Natl. Acad. Sci. 109, 3192–3197 (2005)CrossRefGoogle Scholar
  10. 10.
    Navlakha, S., Kingsford, C.: Network archaeology: Uncovering ancient networks from present-day interactions. PLoS Comput. Biol. 7, e1001119 (2011)MathSciNetCrossRefGoogle Scholar
  11. 11.
    Pastor-Satorras, R., Smith, E., Sole, R.: Evolving protein interaction networks through gene duplication. J. Theor. Biol. 222, 199–210 (2003)MathSciNetCrossRefGoogle Scholar
  12. 12.
    Patro, R., Sefer, E., Malin, J., Marcais, G., Navlakha, S., Kingsford, C.: Parsimonious Reconstruction of Network Evolution. In: Przytycka, T.M., Sagot, M.-F. (eds.) WABI 2011. LNCS, vol. 6833, pp. 237–249. Springer, Heidelberg (2011)CrossRefGoogle Scholar
  13. 13.
    Pinney, J., Amoutzias, G., Rattray, M., Robertson, D.: Reconstruction of ancestral protein interaction networks for the bZIP transcription factors. Proc. Natl. Acad. Sci. 104, 20449–20453 (2007)CrossRefGoogle Scholar
  14. 14.
    Sole, R., Smith, E., Pastor-Satorras, R., Kepler, T.: A model of large-scale proteome evolutions. Adv. Complex Syst. 5, 43–54 (2002)MATHCrossRefGoogle Scholar
  15. 15.
    Stumpf, M., Kelly, W., Thorne, T., Wiuf, C.: Evolution at the system level: the natural history of protein interaction networks. Trends Ecol. Evol. 22, 366–373 (2007)CrossRefGoogle Scholar
  16. 16.
    Vazquez, A., Flammini, A., Maritan, A., Vespignani, A.: Modeling of protein interaction networks. ComPlexUs 1, 38–44 (2003)CrossRefGoogle Scholar
  17. 17.
    Wagner, A.: The yeast protein interaction network evolves rapidly and contains few redundent duplicate genes. Mol. Biol. Evol. 18, 1283–1292 (2001)CrossRefGoogle Scholar
  18. 18.
    Yamada, T., Bork, P.: Evolution of biomolecular networks–lessons from metabolic and protein interactions. Nat. Rev. Mol. Cell Biol. 10, 791–803 (2009)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Si Li
    • 1
  • Kwok Pui Choi
    • 1
    • 2
  • Taoyang Wu
    • 1
  • Louxin Zhang
    • 1
  1. 1.Department of MathematicsNational University of SingaporeSingapore
  2. 2.Department of Statistics and Applied ProbabilityNational University of SingaporeSingapore

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