The application of MIRAGE on a toy model. Core reactions (E1, E8, E9 and E10) are marked with straight lines, while gap-filling reactions are marked with dashed lines. A weight for each reaction is computed based on the correlation of its phylogenetic and expression profiles with those of neighboring core reactions in the network. Reactions predicted for gap-filling by MIRAGE are in red. Specifically, E2 is chosen to enable the growth-associated dilution of metabolites M6 and M9. E3 and E4 are chosen (instead of E5, which has a significantly lower weight) to enable the flux activation of E8 and E9. E7 is chosen to enable flux activation of E8 and E9 under steady-state. Reaction E6 is not chosen for gap-filling as it is redundant given the above-mentioned chosen essential reactions.