PMID:14718379
| Citation |
Burgard, AP, Nikolaev, EV, Schilling, CH and Maranas, CD (2004) Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 14:301-12 |
|---|---|
| Abstract |
In this paper, we introduce the Flux Coupling Finder (FCF) framework for elucidating the topological and flux connectivity features of genome-scale metabolic networks. The framework is demonstrated on genome-scale metabolic reconstructions of Helicobacter pylori, Escherichia coli, and Saccharomyces cerevisiae. The analysis allows one to determine whether any two metabolic fluxes, v(1) and v(2), are (1) directionally coupled, if a non-zero flux for v(1) implies a non-zero flux for v(2) but not necessarily the reverse; (2) partially coupled, if a non-zero flux for v(1) implies a non-zero, though variable, flux for v(2) and vice versa; or (3) fully coupled, if a non-zero flux for v(1) implies not only a non-zero but also a fixed flux for v(2) and vice versa. Flux coupling analysis also enables the global identification of blocked reactions, which are all reactions incapable of carrying flux under a certain condition; equivalent knockouts, defined as the set of all possible reactions whose deletion forces the flux through a particular reaction to zero; and sets of affected reactions denoting all reactions whose fluxes are forced to zero if a particular reaction is deleted. The FCF approach thus provides a novel and versatile tool for aiding metabolic reconstructions and guiding genetic manipulations. |
| Links |
PubMed PMC327106 Online version:10.1101/gr.1926504 |
| Keywords |
Aerobiosis/genetics; Anaerobiosis/genetics; Biomass; Computational Biology/methods; DNA, Bacterial; DNA, Fungal; Energy Metabolism/genetics; Escherichia coli/genetics; Escherichia coli/growth & development; Escherichia coli/metabolism; Genome, Bacterial; Genome, Fungal; Glucose/metabolism; Helicobacter pylori/genetics; Helicobacter pylori/growth & development; Helicobacter pylori/metabolism; Models, Biological; Purines/biosynthesis; Saccharomyces cerevisiae/genetics; Saccharomyces cerevisiae/growth & development; Saccharomyces cerevisiae/metabolism |
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