Abstract
The classic view of metabolism as a collection of metabolic pathways is being questioned with the currently available possibility of studying whole networks. Novel ways of decomposing the network into modules and motifs that could be considered as the building blocks of a network are being suggested. In this work, we introduce a new definition of motif in the context of metabolic networks. Unlike in previous works on (other) biochemical networks, this definition is not based only on topological features. We propose instead to use an alternative definition based on the functional nature of the components that form the motif. After introducing a formal framework motivated by biological considerations, we present complexity results on the problem of searching for all occurrences of a reaction motif in a network, and introduce an algorithm that is fast in practice in most situations. We then show an initial application to the study of pathway evolution.
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References
Recommendations of the Nomenclature Commitee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classificationof Enzymes. Oxford University Press, Oxford (1992)
Alm, E., Arkin, A.: Biological networks. Current opinion in Structural Biology 13, 193–202 (2003)
Arita, M.: The metabolic world of escherichia coli is not small. PNAS 101(6), 1543–1547 (2004)
Garey, M.R., Johnson, D.S.: Computers and Intractability. A Guide to the Theory of NP-Completeness. Freeman, New York (1979)
Guimerà, R., Nunes Amaral, L.A.: Functional cartography of complex metabolic networks. Nature 433(7028), 895–900 (2005)
Hartwell, L., Hopfield, J., Leibler, A., Murray, A.: From molecular to modular cell biology. Nature 402, c47–c52 (1999)
Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N., Barabasi, A.L.: The large-scale organization of metabolic networks. Nature 407, 651–654 (2000)
Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M.: The KEGG resource for deciphering the genome. Nucleic Acids Research 32, 277–280 (2004)
Kitano, H.: Systems biology: A brief overview. Science 295, 1662–1664 (2002)
Ma, H.W., Zhao, X.M., Yuan, Y.J., Zeng, A.P.: Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. Bioinformatics 20(12), 1870–1876 (2004)
Papin, J.A., Reed, J.L., Palsson, B.O.: Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends Biochem Sci. 29(12), 641–647 (2004)
Papin, J.A., Stelling, J., Price, N.D., Klamt, S., Schuster, S., Palsson, B.O.: Comparison of network-based pathway analysis methods. Trends Biotechnol 22(8), 400–405 (2004)
Pinter, R.Y., Rokhlenko, O., Tsur, D., Ziv-Ukelson, M.: Approximate labelled subtree homeomorphism. In: Sahinalp, S.C., Muthukrishnan, S.M., Dogrusoz, U. (eds.) CPM 2004. LNCS, vol. 3109, pp. 59–73. Springer, Heidelberg (2004)
Schuster, S., Pfeiffer, T., Moldenhauer, F., Koch, I., Dandekar, T.: Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 18(2), 351–361 (2002)
Segrè, D.: The regulatory software of cellular metabolism. Trends Biotechnol. 22(6), 261–265 (2004)
Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., Ideker, T.: Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 13(11), 2498–2504 (2003)
Shen-Orr, S., Milo, R., Mangan, S., Alon, U.: Network motifs in the transcriptional regulation network of escherichia coli. Nat. Genet. 31(1), 64–68 (2002)
Stelling, J.: Mathematical models in microbial systems biology. Curr Opin Microbiol. 7(5), 513–518 (2004)
Tohsato, Y., Matsuda, H., Hashimoto, A.: A multiple alignment algorithm for metabolic pathway analysis using enzyme hierarchy. In: Proc. Int. Conf. Intell. Syst. Mol. Biol., pp. 376–383 (2000)
Velasco, A.M., Leguina, J.I., Lazcano, A.: Molecular evolution of the lysine biosynthetic pathways. J. Mol. Evol. 55, 445–459 (2002)
Voss, K., Heiner, M., Koch, I.: Steady state analysis of metabolic pathways using Petri nets. Silico Biol. 3(3), 367–387 (2003)
Wolf, D., Arkin, A.: Motifs, modules and games in bacteria. Curr. Opin. Microbiol. 6(2), 125–134 (2003)
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Lacroix, V., Fernandes, C.G., Sagot, MF. (2005). Reaction Motifs in Metabolic Networks. In: Casadio, R., Myers, G. (eds) Algorithms in Bioinformatics. WABI 2005. Lecture Notes in Computer Science(), vol 3692. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11557067_15
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DOI: https://doi.org/10.1007/11557067_15
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-29008-7
Online ISBN: 978-3-540-31812-5
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