Flux coupling analysis of genome-scale metabolic network reconstructions.
Genome Res
; 14(2): 301-12, 2004 Feb.
Article
en En
| MEDLINE
| ID: mdl-14718379
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.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Saccharomyces cerevisiae
/
Helicobacter pylori
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Genoma Fúngico
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Genoma Bacteriano
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Metabolismo Energético
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Escherichia coli
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
Genome Res
Asunto de la revista:
BIOLOGIA MOLECULAR
/
GENETICA
Año:
2004
Tipo del documento:
Article
País de afiliación:
Estados Unidos