Figure 2.

Procedure to correct false positive (FP) gene essentiality predictions. For each predicted FP gene, we attempted to correct the prediction by (I) removing metabolites from the biomass objective function and (II) introducing new nutrient uptakes and/or changing irreversible reactions to reversible (using the optimization model developed by Kumar and Maranas [39]). When a modification was successful, as determined by the criteria shown in Figure 4, we recorded and collected it in a set of possible modifications. TN, true negative; RXN, reaction; Y, yes.