Fig. 1: Characterization of the predictions of context-specific models for growth of S. cerevisiae under glucose-limited conditions. | npj Systems Biology and Applications

Fig. 1: Characterization of the predictions of context-specific models for growth of S. cerevisiae under glucose-limited conditions.

From: Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models

Fig. 1

a–c Flux predictions of metabolite exchange (glucose, oxygen, ethanol and carbon dioxide) for changing dilution rates for glucose-limited chemostats by the conventional Yeast8.4.2 a and the context-specific models, created using GIMME b and ssGSEA-GIMME c. Experimental data, triangles taken from ref. 12 and circles from ref. 22. d Comparison of experimentally determined metabolic fluxes of the central carbon metabolism (E) and predictions by the conventional GEM (M), GIMME (G) and ssGSEA-GIMME (S) model at μ = 0.30 h-1. e–g Correlation between the experimental data (X-axis) and model predictions (Y-axis) for different model implementations. Experimental data in d and on the X-axes of e–g taken from ref. 57. Flux values were normalized to that of hexokinase reaction (vHEXrel = 1). Glc glucose, Mal maltose, G6P glucose 6-phosphate, F6P fructose 6-phosphate, 6PGL 6-phosphogluconolactone, F16BP fructose 1,6-bisphosphate, DHAP dihydroxyacetone phosphate, GAP glycerol aldehyde 3-phosphate, G13BP 1,3-bisphosphoglycerate, 3PG 3-phosphoglycerate, 2PG 2-phosphoglycerate, PEP phosphoenolpyruvate, PYR pyruvate, ACALD acetaldehyde, EtOH ethanol, Ac acetate, AC-COA acetyl-CoA, OAA oxaloacetate, CIT citrate, ICIT, isocitrate; AKG, alpha-ketoglutarate; SUCC-COA, succinyl-CoA; SUCC, succinate; FUM, fumarate; MAL, malate; GLX, glyoxylate.

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