Abstract
In the context of comparative analysis of protein-protein interaction graphs, we use a graph-based formalism to detect the preservation of a given protein complex (pattern graph) in the protein-protein interaction graph (target graph) of another species with respect to (w.r.t.) orthologous proteins. We give an efficient exponential-time randomized algorithm in case the occurrence of the pattern graph in the target graph is required to be exact. For approximate occurrences, we prove a tight inapproximability results and give four approximation algorithms that deal with bounded degree graphs, small ortholog numbers, linear forests and very simple yet hard instances, respectively.
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References
Crochemore, M., Hermelin, D., Landau, G., Rawitz, D., Vialette, S.: Approximating the 2-interval pattern problem, Theoretical Computer Science (special issue for Alberto Apostolico) 2006 (to appear)
Diestel, R.: Graph theory. In: Graduate texts in Mathematics, 2nd edn., vol. 173, Springer, Heidelberg (2000)
Fagnot, I., Lelandais, G., Vialette, S.: Bounded list injective homomorphism for comparative analysis of protein-protein interaction graphs. In: Proc. 1st Algorithms and Computational Methods for Biochemical and Evolutionary Networks (CompBioNets), pp. 45–70. KCL publications (2004)
Fertin, G., Rizzi, R., Vialette, S.: Finding exact and maximum occurrences of protein complexes in protein-protein interaction graphs. In: Jedrzejowicz, J., Szepietowski, A. (eds.) MFCS 2005. LNCS, vol. 3618, pp. 328–339. Springer, Heidelberg (2005)
Gavin, A.C., Boshe, M., et al.: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 414(6868), 141–147 (2002)
Ho, Y., Gruhler, A., et al.: Systematic identification of protein complexes in Saccharomyces cerevisae by mass spectrometry. Nature 415(6868), 180–183 (2002)
Kelley, B.P., Sharan, R., Karp, R.M., Sittler, T., Root, D.E., Stockwell, B.R., Ideker, T.: Conserved pathways within bacteria and yeast as revealed by global protein network alignment. PNAS 100(20), 11394–11399 (2003)
Mitzenmacher, M., Upfal, E.: Probability and computing: Randomized algorithms and probabilistic analysis. Cambridge University Press, Cambridge (2005)
Pellegrini, M., Marcotte, E.M., Thompson, M.J., Eisenberg, D., Yeates, T.O.: Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. PNAS 96(8), 4285–4288 (1999)
Pereira-Leal, J.B., Enright, A.J., Ouzounis, C.A.: Detection of functional modules from protein interaction networks. Proteins 54(1), 49–57 (2004)
Sharan, R., Ideker, T., Kelley, B., Shamir, R., Karp, R.M.: Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. In: Proc. 8th annual international conference on Computational molecular biology (RECOMB), pp. 282–289. ACM Press, New York (2004)
Sharan, R., Suthram, S., Kelley, R.M., Kuhn, T., McCuin, S., Uetz, P., Sittler, T., Karp, R., Ideker, T.: Conserved patterns of protein interaction in multiple species. PNAS 102(6), 1974–1979 (2004)
Tatusov, R.L., Koonin, E.V., Lipman, D.J.: A genomic perspective on protein families. Science 278(5338), 631–637 (1997)
Titz, B., Schlesner, M., Uetz, P.: What do we learn from high-throughput protein interaction data? Expert Review of Anticancer Therapy 1(1), 111–121 (2004)
Trotter, W.T., Harary, F.: On double and multiple interval graphs. J. Graph Theory 3, 205–211 (1979)
Uetz, P., Giot, L., et al.: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisae. Nature 403(6770), 623–627 (2000)
Vialette, S.: On the computational complexity of 2-interval pattern matching. Theoretical Computer Science 312(2-3), 223–249 (2004)
Vizing, V.G.: On an estimate of the chromatic class of a p-graph. Diskret. Analiz 3, 23–30 (1964)
Yang, Q., Sze, S.-H.: Path matching and graph matching in biological networks. JCB 14(1), 56–67 (2007)
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Brevier, G., Rizzi, R., Vialette, S. (2007). Pattern Matching in Protein-Protein Interaction Graphs . In: Csuhaj-Varjú, E., Ésik, Z. (eds) Fundamentals of Computation Theory. FCT 2007. Lecture Notes in Computer Science, vol 4639. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74240-1_13
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DOI: https://doi.org/10.1007/978-3-540-74240-1_13
Publisher Name: Springer, Berlin, Heidelberg
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