Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions
Fig 6
CANYUNs reaction Certainty Values accurately identify reactions found in iML1515.
The manually curated metabolic network, iML1515, provides a point of comparison to determine if CANYUNs accurately identifies reactions for inclusion in the network. (A) By comparing the CANYUNs model with iML1515, we were able to place reactions into four categories. FCRs with genetic evidence and in iML1515 (confirmed), FCRs without genetic evidence in iML1515 (true discovered), FCRs with genetic evidence not in iML1515 (likely additions), and FCRs without genetic evidence and not in iML1515 (false discovered). The total amount of genetic evidence that is used to generate a CANYUNs model influences the accuracy of the FCRs. (B) When we use pFBA instead of dgFBA in the CANYUNs pipeline, there are far more reactions that lack genetic evidence and are not in iML1515. (C) The percent overlap of FCRs with reactions present in iML1515 increases from 62% when no genetic evidence is used (pFBA) to 76% overlap when all of the available genetic evidence is used.