Title: Modules in the metabolic network of E.coli with regulatory interactions

Authors: Jan Geryk; František Slanina

Addresses: Faculty of Science, Department of Philosophy and History of Sciences, Charles University, Vini?ná 7, 128 44 Prague, Czech Republic ' Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Praha 8, Czech Republic

Abstract: We examine the modular structure of the metabolic network when combined with the regulatory network representing direct regulation of enzymes by small metabolites in E.coli. We introduce novel clustering algorithm and compare it with mainstream module detection method based on simulated annealing. Both methods identify the similar modular core. Slight but significant increase in modularity is observed after regulatory interactions addition. We also identify new functional modules in the combined network, which cannot be detected in the metabolic network only. Regulatory loops in the modules are the source of their autonomy, and allow us to hypothesise about module function.

Keywords: regulation; metabolic networks; bipartite graphs; modularity; vertex similarity measure; community structure; clustering; regulatory networks; allosteric; metabolic pathways; E. coli; regulatory interactions; simulated annealing; bioinformatics; Escherichia coli.

DOI: 10.1504/IJDMB.2013.055500

International Journal of Data Mining and Bioinformatics, 2013 Vol.8 No.2, pp.188 - 202

Received: 01 Jan 2011
Accepted: 29 Dec 2011
Published online: 20 Oct 2014 *

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