A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

BMC Systems Biology

Table 5 Comparison of experimental gene essentiality results with computational EcoCyc–18.0–GEM results for aerobic growth on MOPS medium with 0.4% glucose

KO growth on glucose (sim/exp)	BC	BE	NC	NE
True positive (growth/growth)	1175	1136	1204	1164
False positive (growth/no growth)	58	64	29	36
False negative (no growth/growth)	12	51	78	118
True negative (no growth/no growth)	200	194	134	127

Four comparisons are provided — gene essentiality is evaluated with regard to (B)road and (N)arrow experimental essentiality criteria, and with regard to a (C)ore biomass metabolite set that maximizes the accuracy of essentiality predictions as well as an (E)xpanded biomass metabolite set reflecting experimental measurements of healthy cells. The results of these comparisons are arranged based on correspondence between simulation and experiment: (1) true positive (simulation predicts growth, experiment shows growth), (2) false positive (simulation predicts growth, experiment shows no respiration), (3) false negative (no simulated growth, but experiment shows respiration), and (4) true negative (no simulated growth, experiment shows no respiration).

ISSN: 1752-0509