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Fig. 4 | BMC Bioinformatics

Fig. 4

From: Multiplex methods provide effective integration of multi-omic data in genome-scale models

Fig. 4

Validation on the phenomics dataset of growth conditions by Hui et al. [37]. The dataset includes five C-lim conditions (titrated catabolic flux through controlled inducible expression of the lacY gene), five A-lim conditions (titrated anabolic flux through controlled expression of GOGAT), and four R-lim conditions (inhibition of protein synthesis with chloramphenicol, an antibiotic). a The 14 gene expression profiles are mapped to the biomass-acetate space of flux rates. Each gene expression profile yields a condition-specific metabolic network, solved as a bilevel linear program with biomass-acetate as objectives, thus obtaining a point in the objective space. The C-lim experimental conditions allow for more acetate production while ensuring higher growth rate and greater variability in different conditions. b Measured growth rates are compared with those predicted by our method in the 14 growth conditions. c We obtain a good overall correlation between our predicted values and the measured growth rate, with Spearman’s ρ=0.678 (p-value=0.008) and Pearson’s r=0.680 (p-value=0.007). The diagonal “predicted = experimental”, representing the ideal outcome, is also shown for comparison

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