Integrating transcriptional activity in genome-scale models of metabolism

BACKGROUND: Genome-scale metabolic models provide an opportunity for rational approaches to studies of the different reactions taking place inside the cell. The integration of these models with gene regulatory networks is a hot topic in systems biology. The methods developed to date focus mostly on resolving the metabolic elements and use fairly straightforward approaches to assess the impact of genome expression on the metabolic phenotype. RESULTS: We present here a method for integrating the reverse engineering of gene regulatory networks into these metabolic models. We applied our method to a high-dimensional gene expression data set to infer a background gene regulatory network. We then compared the resulting phenotype simulations with those obtained by other relevant methods. CONCLUSIONS: Our method outperformed the other approaches tested and was more robust to noise. We also illustrate the utility of this method for studies of a complex biological phenomenon, the diauxic shift in yeast.