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Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements

Figure 1

Toy metabolic network.

This network enables the synthesis of a five-carbon biomass precursor from a two- or from a three-carbon substrate. The network's gene-to-reaction mapping is depicted with diamonds indicating highly (green) and lowly (red) expressed genes. Two reactions (r3 and r7) are each associated with two genes. For r3 any of the two gene-products suffices to catalyze the reaction (OR logic gate). For r7, both gene-products are needed together to bring about catalysis (AND logic gate). Highlighted in blue is a flux distribution that maximizes the number of reactions that are consistent with their gene expression. Note that the highlighted flux distribution results in four agreements between reaction fluxes and their expression (r2, r3, r5, and r6) and one disagreement (r7).

Figure 1

doi: https://doi.org/10.1371/journal.pcbi.1002988.g001