A Graph Modification Approach for Finding Core–Periphery Structures in Protein Interaction Networks
The core–periphery model for protein interaction (PPI) networks assumes that protein complexes in these networks consist of a dense core and a possibly sparse periphery that is adjacent to vertices in the core of the complex. In this work, we aim at uncovering a global core–periphery structure for a given PPI network. We propose two exact graph-theoretic formulations for this task, which aim to fit the input network to a hypothetical ground truth network by a minimum number of edge modifications. In one model each cluster has its own periphery, and in the other the periphery is shared. We first analyze both models from a theoretical point of view, showing their NP-hardness. Then, we devise efficient exact and heuristic algorithms for both models and finally perform an evaluation on subnetworks of the S. cerevisiae PPI network.
KeywordsInteger Linear Programming Genetic Interaction Cluster Graph Split Graph Induce Subgraph
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- 6.Chatr-aryamontri, A., et al.: The BioGRID interaction database: 2013 update. Nucleic Acids Research 41(D1), D816–D823 (2013)Google Scholar
- 8.Du, Z., Li, L., Chen, C.-F., Yu, P.S., Wang, J.Z.: G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery. Nucleic Acids Research 37(suppl. 2), W345–W349 (2009)Google Scholar
- 9.Farrugia, A.: Vertex-partitioning into fixed additive induced-hereditary properties is NP-hard. The Electronic Journal of Combinatorics 11(1), R46 (2004)Google Scholar
- 11.Fomin, F.V., Kratsch, S., Pilipczuk, M., Pilipczuk, M., Villanger, Y.: Subexponential fixed-parameter tractability of cluster editing. CoRR, abs/1112.4419 (2011)Google Scholar
- 19.Luo, F., Li, B., Wan, X.-F., Scheuermann, R.: Core and periphery structures in protein interaction networks. BMC Bioinformatics (Suppl. 4), S8 (2009)Google Scholar
- 24.Xu, X., Yuruk, N., Feng, Z., Schweiger, T.A.J.: SCAN: a structural clustering algorithm for networks. In: Proc. 13th KDD, pp. 824–833. ACM (2007)Google Scholar
- 25.Zotenko, E., Guimarães, K.S., Jothi, R., Przytycka, T.M.: Decomposition of overlapping protein complexes: a graph theoretical method for analyzing static and dynamic protein associations. Algorithms for Molecular Biology 1(7) (2006)Google Scholar