Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions
Fig 4
E. coli K-12 CANYUNs model generation and draft processing.
(A) Ranked scatter plot of forward reaction Certainty Values. (B) Reverse reaction Certainty Values. (C) Certainty values for reversible reactions that carry flux in both directions. (D) Initial accuracy of CANYUNs model before curation of the universal biochemical network is 80% with a Matthews Correlation Coefficient of 0.45. (E) Simulation of conditionally essential reactions allow for the user to identify reactions that can be selectively removed from the resulting model that improve the overall predictive accuracy. The net benefit refers to the number of false positives that will be corrected minus the number of true positives lost due to removing a given reaction. RuBisCO is the forward reaction in the top left corner of the plot with maximum net benefit and minimum genetic evidence.