BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
Fig 6
Comparison of phenotypic predictions and metabolite composition between the three steps of BOFdat, the original iML1515 BOF, SEED, and BOSS.
(A) Number of metabolites shared with the iML1515 wild-type (WT) biomass (positive values), and specific to each of the method (negative values). (B) Levenshtein distance calculated between the original iML1515-WT biomass and the BOF generated by each of the other methods, as well as with the iML1515-core and the yeast model iMM904 BOF. The Levenshtein distance represents the number of additions, subtractions or substitutions that need to be applied on the list of metabolites from the compared BOF to retrace the reference BOF. (C) The predicted growth rates for all Steps of BOFdat are compared to the iML1515-WT and SEED. BOSS imposes a fixed growth rate as part of the optimization problem and was hence not compared since it does not formulate a prediction. (D) Gene essentiality prediction as evaluated with a Matthews correlation coefficient when compared with experimental data generated on glucose minimal media [2].