## 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.

Original language | English (US) |
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Pages (from-to) | 301-312 |

Number of pages | 12 |

Journal | Genome research |

Volume | 14 |

Issue number | 2 |

DOIs | |

State | Published - Feb 2004 |

## All Science Journal Classification (ASJC) codes

- Genetics
- Genetics(clinical)