Constraint-Based Modelling Of Perturbed Organisms: A ROOM for improvement

Regulatory On-Off Minimization (ROOM) is a model for predicting the behavior of metabolic networks in response to gene knockouts. It is based on minimizing the number of significant flux changes (hence, on/off) with respect to the wild-type. ROOM outperforms a previously suggested model, Minimization Of Metabolic Adjustment (MOMA), whose minimization metric is Euclidian. Furthermore, ROOM shows its ability to correctly identify alternative pathways for reactions associated with the knocked-out genes, thus strengthening its biological plausibility. ROOM outperforms MOMA in predicting intracellular fluxes and gene knockout lethality in mutated E. coli and the S. cerevisiae strains, respectively. Supplementary data: www.cns.tau.ac.il/sshlomito/room Contact: [email protected]