Figure 3.

Diagram of possible causes and solutions for false predictions. Circles represent metabolites and arrows represent metabolic reactions A) false positive predictions B) false negative predictions. Red arrows indicate problems in the network and green arrows indicate possible solutions. Red Xs indicate knockout of the reaction and green Xs are knockouts that would reconcile the issue to achieve the correct prediction. For false negative predictions where the reaction associated with multiple genes, the gene in red indicates that the gene is knocked out or with uncertain metabolic essentiality (metabolically non-essential but essential in another capacity) and the genes in green indicate additional knockouts that can potentially resolve the false prediction.