Methods for integration of transcriptomic data in genome-scale metabolic models

Several computational methods have been developed that integrate transcriptomic data with genome-scale metabolic reconstructions to infer condition-specific system-wide intracellular metabolic flux distributions. In this mini-review, we describe each of these methods published to date with categorizing them based on four different grouping criteria (requirement for multiple gene expression datasets as input, requirement for a threshold to define a gene's high and low expression, requirement for a priori assumption of an appropriate objective function, and validation of predicted fluxes directly against measured intracellular fluxes). Then, we recommend which group of methods would be more suitable from a practical perspective.