This query allows to find a set of transcription factors whose expression manipulation, in a specified medium, is predicted to optimise the production of a given metabolite.

This query requires the definition of a metabolite to be optimised, a model, a growth medium, a metric evaluating the predicted metabolite production which the list of transcription factors is ranked (metabolite exchange flux, Biomass-Product Coupled Yield (BPCY), or Product Yield with Minimum Biomass (PYMB)), and the type of regulatory associations to be considered.

The output is a table of the TFs whose expression manipulation is predicted to optimise the production of the selected metabolite, as provided by in silico simulations using the selected Genome-scale Metabolic Model and the selected growth medium.

The impact on the metabolite production of Knocking Out or Overexpressing each TF is displayed in the table, considering different effects of the TF expression manipulation on the expression of its target genes. TF KnockOut (KO) effects range from under-expressing (UE) their activated target genes (from 0 to 0.5-fold the wild-type levels) to over-expressing (OE) their repressed target genes (from 1.25-1.5-fold the wild-type levels). TF OverExpression (OE) effects range from over-expressing (OE) their activated target genes (from 0 to 0.5-fold the wild-type levels) to under-expressing (UE) their repressed target genes (from 1.25-1.5-fold the wild-type levels). The final columns highlight the highest level of the metabolite production obtained by the manipulation of expression of each TF, followed by the "View" link, which allows to obtain details on the changes imposed on reaction fluxes by said manipulations.