Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction
General parameters described or used for simulation in this study include: number of genes included as reaction modifiers; number of included genes that are currently annotated by the Saccharomyces Genome Database as “dubious”, or unlikely to encode an expressed protein; number of metabolites; number of dead end metabolites (those metabolites that are either produced by known metabolic reactions of an organism but not consumed, or vice versa); number of reactions; and number of reactions associated with genes. Simulations were conducted for each model using the as-distributed model default biomass objective function and with the biomass objective from the iFF708 model. Reported simulation results are divided into two subcolumns to reflect the use of two different objective functions for each model. Simulation results include the number of blocked reactions for each biomass definition (those reactions which cannot carry flux due to network structural constraints); the Matthews’ Correlation Coefficient (MCC) for model predictions of single gene essentiality across all conditions simulated; and the Matthews’ Correlation Coefficient for model prediction of double gene essentiality (i.e., pairwise synthetic lethal interactions) for simulations using each models’ default biomass definition. Some parameter values differ from previously published values due to differing software implementation and annotation conventions.