Temporal Expression-based Analysis of Metabolism
Figure 2
A comparison of results across different methods for a representative penalty threshold.
The media contained 36 mM L-Lactate, 13 mM D-lactate, 9 mM ammonium, and other minimally required nutrients. The oxygen concentration was set to 10 mM at each time point, mimicking the controlled 100% dissolved oxygen (DO) concentration from the experiment. The resulting usage dynamics of several metabolites of interest (including combined DL-lactate, ammonium, pyruvate, acetate, formate and glycolate) as predicted by dFBA are compared to experimental data. (A) HPLC Data, (B) dFBA, (C) TEAM with a global penalty threshold (Type 1), (D) TEAM with a gene-specific penalty threshold (Type 2), (E) TEAM with a gene-specific penalty threshold normalized by standard deviation (Type 3). Black dots represent hours when microarray measurements were taken.