Abstract
Recent studies of complex networks offer new methods for characterizing large scale of networks and provide new insights on how such networks are developed. In particular, researchers focused on biological networks such as gene regulatory systems, protein interactions and metabolic pathways in order to understand how these elemental reactions are integrated as an organism. Although various statistical features of network structures, such as scale-free or small-world, have been studied to approach underlying principles of network organization, more detailed analysis on network properties is required to understand their functions.
The community finding algorithm proposed by Girvan and Newman provides another useful technique for investigating topological structures of large networks. Applying this method to metabolic networks, we found that behavior like that of Zipf’s law of the distribution of community size is shared very generally among a wide range of organisms. With the aim of realizing how this property is achieved, we present a new evolutionary model of metabolic reactions based on artificial chemistry.
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References
Agrawal, H.: Extreme self-organization in networks constructed from gene expression data. Phys. Rev. Lett. 89(26), 268702 (2002)
Arenas, A., Danon, L., Díaz-Guilera, A., Gleiser, P.M., Guimerà, R.: Community analysis in social networks. Eur. Phys. J. B 38, 373–380 (2004)
Arita, M.: The metabolic world of Escherichia Coli is not small. Proc. Natl. Acad. Sci. USA 101(6), 1543–1547 (2004)
Barabási, A.L., Albert, R.: Emergence of scaling in random networks. Science 286, 509–512 (1999)
Clauset, A., Newman, M.E.J., Moore, C.: Finding community structure in very large networks. Phys. Rev. E 70, 66111 (2004)
Featherstone, D.E., Broadie, K.: Wrestling with pleiotropy: genomic and topological analysis of the yeast gene expression network. BioEssays 24(3), 267–274 (2002)
Girvan, M., Newman, M.E.J.: Community structure in social and biological networks. Proc. Natl. Acad. Sci. USA 99(12), 7821–7826 (2002)
Holme, P., Huss, M., Jeong, H.: Subnetwork hierarchies of biochemical pathways. Bioinformatics 19(4), 532–538 (2003)
Horowitz, N.H.: On the evolution of biochemical syntheses. Proc. Natl. Acad. Sci. USA 31, 153–157 (1945)
Jensen, R.A.: Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30, 409–425 (1976)
Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N., Barabási, A.L.: The large-scale organization of metabolic networks. Nature 407(6804), 651–654 (2000)
Light, S., Kraulis, P.: Network analysis of metabolic enzyme evolution in Escherichia Coli. BMC Bioinformatics 5(1), 15 (2004)
Pastor-Satorras, R., Smith, E., Sole, R.: Evolving protein interaction networks through gene duplication. J. Theor. Biol. 222, 199–210 (2003)
di Fenizio, P.S., Dittrich, P., Banzhaf, W.: Spontaneous formation of proto-cells in an universal artificial chemistry on a planar graph. In: Kelemen, J., Sosík, P. (eds.) ECAL 2001. LNCS (LNAI), vol. 2159, pp. 206–215. Springer, Heidelberg (2001)
Strogatz, S.H.: Exploring complex networks. Nature 410(6825), 268–276 (2001)
Teichmann, S.A., Rison, S.C., Thornton, J.M., Riley, M., Gough, J., Chothia, C.: The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia Coli. J. Mol. Biol. 311(4), 693–708 (2001)
Vázquez, A.: Growing network with local rules: preferential attachment, clustering hierarchy, and degree correlations. Phys. Rev. E 67, 56104 (2003)
Wagner, A.: The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol. Biol. Evol. 18(7), 1283–1292 (2001)
Wagner, A., Fell, D.A.: The small world inside large metabolic networks. Proc. Roy. Soc. Lond Ser. B 268(1478), 1803–1810 (2001)
Watts, D.J., Strogatz, S.H.: Collective dynamics of ’small-world’ networks. Nature 393(6684), 440–442 (1998)
Wuchty, S.: Scale-free behavior in protein domain networks. Mol. Biol. Evol. 18(9), 1694–1702 (2001)
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Ono, N., Fujiwara, Y., Yuta, K. (2005). Artificial Metabolic System: An Evolutionary Model for Community Organization in Metabolic Networks. In: Capcarrère, M.S., Freitas, A.A., Bentley, P.J., Johnson, C.G., Timmis, J. (eds) Advances in Artificial Life. ECAL 2005. Lecture Notes in Computer Science(), vol 3630. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11553090_72
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DOI: https://doi.org/10.1007/11553090_72
Publisher Name: Springer, Berlin, Heidelberg
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