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Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements

Figure 3

Exploration of alternative optimal flux distributions.

Three alternative flux distributions that maximize the number of reactions whose flux is consistent with their gene expression, for the toy pathway in Figure 1, are shown in the central column. The panels to the left and right summarize the enzyme modulations that force the MILP solver to find the flux distributions in the central column. The modulations and resulting flux distributions are organized by rows. The leftmost column summarizes the reactions whose inactivation result in the finding of the flux distribution in the central column. Note that there are multiple reactions that when forced to be inactive each give rise to the same flux distribution in the central column. Note furthermore that the flux distribution in the third row cannot be found by the inactivation of a reaction. The rightmost column summarizes the reactions that when forced to carry a flux in the indicated directions, enable finding the flux distributions in the central column. Like with the inactivation of reactions, there are multiple reactions that when forced to carry flux in the indicated direction give rise to the same flux distribution. The flux distribution in the second row of the central column cannot be found by forcing any reaction to be active.

Figure 3

doi: https://doi.org/10.1371/journal.pcbi.1002988.g003