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Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction

Fig 3

Change in gene essentiality predictions between model and its nearest ancestor.

When comparing the Matthews Correlation Coefficient for model gene essentiality predictions to the models’ nearest progenitors, we observe that the models may be segregated between those focusing on expanding model scope, and those focused on iterative refining an existing model by plotting the change in MCC between models. Generally, when the stated focus of a model developer is to expand the scope of the yeast metabolic network reconstruction, predictive ability suffers relative to the progenitor model. When the stated focus is to refine and curate a model, predictive ability improves relative to the progenitor model. Thus, our analysis finds that model predictive ability reflects the iterative process of model development. The asterisk near the Yeast 4 comparison indicates that it is an integrative model that not have a single nearest progenitor (we compared it to iFF708 for this analysis).

Fig 3

doi: https://doi.org/10.1371/journal.pcbi.1004530.g003