Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM
Figure 5
Prediction of nutrient rescue.
We curated a collection of conditions in which an auxotroph was rescued when minimal media was supplemented with a nutrient. We separated the collection into a training set, where knowledge of the rescue phenotype was used to improve the model, and a test set, where the rescue phenotype was hidden from the model. Because we only collected data on which nutrients rescued the auxotrophs, we could only measure sensitivity, not specificity. (A) Tables showing the sensitivity of limed-FBA predictions on nutrient rescue training and test sets. (B) Heatmap showing the growth phenotype of each mutant when minimal media is supplemented with each nutrient used in the training and test sets. Only mutants whose minimal media gene essentiality was correctly predicted are included. The minimal media used was Vogel's with sucrose as the carbon source except in the following cases: acu-3,5,6 genes are essential when acetate is the sole carbon source; oxD is essential when D-methionine is the sole sulfur source; nit-3 is essential when nitrate is the sole nitrogen source. Green squares indicate that the model's predictions were consistent with experiment; red squares indicate that the model failed to correctly predict growth; blue squares indicate potentially novel rescues; white squares indicate predictions of non-rescue. Striped squares show that the multi-substrate case does not contain additional information beyond the single-substrate case, e.g. methionine is predicted to rescue the cys-4 mutant, so methionine+threonine is also predicted to rescue cys-4.