Table 2

Comparison of experimental with predicted exometabolome fluxes, at 85% maximal biomass level
Experiment Predicted: Gene expression Predicted: Standard FBA Predicted: Fitted FBA Predicted: GIMME Predicted: iMAT
Ethanol 13.0 16.2 0 0 0 0
CO2 21.0 20.1 25.0 21.0 16.0 32.2
Glycerol 2.17 0.126 0 0 0 0
Acetate 0.239 0.00911 0 0 0 0
Trehalose 0.0215 0.0220 0 0 0 0
Lactate 0.00609 0.0176 0 0 0 0
R2 0.96 0.54 0.58 0.52 0.28

Fluxes are reported in units of mmoles/hr/g dry weight (DW), and are scaled by measured glucose uptake flux [see additional file – exometabolomics.xls].

Predicted fluxes are given for the gene expression constrained approach, introduced here, and the standard FBA method that relies upon maximisation of biomass. As standard FBA generates a number of feasible solutions, the “best” solution (the one which minimises the taxicab distance between prediction and data) is reported as “Fitted FBA”. Additionally, the existing algorithms GIMME [18] and iMAT [14] are applied, using the same model and gene expression data as was used to generate the gene expression constrained results.

Lee et al.

Lee et al. BMC Systems Biology 2012 6:73   doi:10.1186/1752-0509-6-73

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