Dividing Protein Interaction Networks by Growing Orthologous Articulations
The increasing growth of data on protein-protein interaction (PPI) networks has boosted research on their comparative analysis. In particular, recent studies proposed models and algorithms for performing network alignment, the comparison of networks across species for discovering conserved modules. Common approaches for this task construct a merged representation of the considered networks, called alignment graph, and search the alignment graph for conserved networks of interest using greedy techniques. In this paper we propose a modular approach to this task. First, each network to be compared is divided into small subnets which are likely to contain conserved modules. To this aim, we develop an algorithm for dividing PPI networks that combines a graph theoretical property(articulation) with a biological one (orthology). Next, network alignment is performed on pairs of resulting subnets from different species. We tackle this task by means of a state-of-the-art alignment graph model for constructing alignment graphs, and an exact algorithm for searching in the alignment graph. Results of experiments show the ability of this approach to discover accurate conserved modules, and substantiate the importance of the notions of orthology and articulation for performing comparative network analysis in a modular fashion.
KeywordsProtein network dividing modular network alignment
Unable to display preview. Download preview PDF.
- 5.Srinivasan, B.S., Shah, N.H., Flannick, J., Abeliuk, E., Novak, A., Batzoglou, S.: Current Progress in Network Research: toward Reference Networks for kKey Model Organisms. Brief. in Bioinformatics (Advance access, 2007)Google Scholar
- 6.Koyutürk, M., Grama, A., Szpankowski, W.: Pairwise local alignment of protein interaction networks guided by models of evolution. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3500, pp. 48–65. Springer, Heidelberg (2005)CrossRefGoogle Scholar
- 12.Pržulj, N.: Knowledge Discovery in Proteomics: Graph Theory Analysis of Protein-Protein Interactions. CRC Press, Boca Raton (2005)Google Scholar
- 13.Singh, R., Xu, J., Berger, B.: Pairwise global alignment of protein interaction networks by matching neighborhood topology, pp. 16–31 (2007)Google Scholar
- 15.Rathod, A.J., Fukami, C.: Mathematical properties of networks of protein interactions. CS374 Fall 2005 Lecture 9, Computer Science Department, Stanford University (2005)Google Scholar
- 18.Ucar, D., Asur, S., Catalyurek, U., Parthasarathy, S.: Improving functional modularity in protein-protein interactions graphs using hub-induced subgraphs. In: Fürnkranz, J., Scheffer, T., Spiliopoulou, M. (eds.) PKDD 2006. LNCS (LNAI), vol. 4213, pp. 371–382. Springer, Heidelberg (2006)CrossRefGoogle Scholar
- 19.Bader, G.D., Lssig, M., Wagner, A.: Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications. BMC Evolutionary Biology 4(51) (2004)Google Scholar
- 22.Abou-Rjeili, A., Karypis, G.: Multilevel algorithms for partitioning power-law graphs. In: 20th International Parallel and Distributed Processing Symposium (IPDPS) (2006)Google Scholar
- 26.Wolsey, L.A.: Integer Programming, 1st edn. Wiley, Chichester (1998)Google Scholar