title: Hierarchical decomposition of metabolic networks using k-modules.
abstract: The optimal solutions obtained by flux balance analysis (FBA) are typically not unique. Flux modules have recently been shown to be a very useful tool to simplify and decompose the space of FBA-optimal solutions. Since yield-maximization is sometimes not the primary objective encountered in vivo, we are also interested in understanding the space of sub-optimal solutions. Unfortunately, the flux modules are too restrictive and not suited for this task. We present a generalization, called k-module, which compensates the limited applicability of flux modules to the space of sub-optimal solutions. Intuitively, a k-module is a sub-network with low connectivity to the rest of the network. Recursive application of k-modules yields a hierarchical decomposition of the metabolic network, which is also known as branch decomposition in matroid theory. In particular, decompositions computed by existing methods, like the null-space-based approach, introduced by Poolman et al. [(2007) J. Theor. Biol. 249: , 691-705] can be interpreted as branch decompositions. With k-modules we can now compare alternative decompositions of metabolic networks to the classical sub-systems of glycolysis, tricarboxylic acid (TCA) cycle, etc. They can be used to speed up algorithmic problems [theoretically shown for elementary flux modes (EFM) enumeration] and have the potential to present computational solutions in a more intuitive way independently from the classical sub-systems.
authors.affiliation: Centre for Mathematics and Computer Science (CWI), Science Park 123, 1098 XG Amsterdam, The Netherlands arne.c.reimers@gmail.com.
authors.forename: Arne C
authors.initials: AC
authors.lastname: Reimers
mesh_terms: D000244:Adenosine Diphosphate / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli / Q000378:metabolism; D064688:Metabolic Flux Analysis; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D015203:Reproducibility of Results
chemical_list: D000244:Adenosine Diphosphate; D000255:Adenosine Triphosphate
keywords: branch decomposition; connectivity; flux module; k-module; matroid; metabolic network