Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM
Figure 4
Minimal media gene essentiality predictions.
We curated a collection of mutant viability observations on minimal media and separated the collection into a training set, where knowledge of the viability phenotype was used to improve the model; and a test set, where the viability phenotype was hidden from the model. (A) Training and test set mutant viability observations were used to measure the sensitivity and specificity of the limed-FBA gene knockout viability predictions. While some inconsistencies were due to model error, several were resolved in the model's favor, as discussed in the text. (B) Using the same model, training and test sets, limed-FBA outperforms FBA and MD-FBA. (C) For comparison, we display the mutant viability prediction accuracies of previously published FBA models for S. cerevisiae and E. coli. Prediction accuracies of experimentally observed viability phenotypes that were used to optimize the model are displayed on the left panel [41], [42]. Prediction accuracies of viability phenotypes that were not explicitly used to construct the model are displayed on the right panel [62], [63].