Regulatory on/off minimization of metabolic flux changes after genetic perturbations.

ABSTRACT: Predicting the metabolic state of an organism after a gene knockout is a challenging task, because the regulatory system governs a series of transient metabolic changes that converge to a steady-state condition. Regulatory on/off minimization (ROOM) is a constraint-based algorithm for predicting the metabolic steady state after gene knockouts. It aims to minimize the number of significant flux changes (hence on/off) with respect to the wild type. ROOM is shown to accurately predict steady-state metabolic fluxes that maintain flux linearity, in agreement with experimental flux measurements, and to correctly identify short alternative pathways used for rerouting metabolic flux in response to gene knockouts. ROOM's growth rate and flux predictions are compared with previously suggested algori

SUBMITTER: Shlomi T 

PROVIDER: S-EPMC1140402 | biostudies-literature | 2005 May

REPOSITORIES: biostudies-literature