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. 2012 Apr 16;7(4):e34670. doi: 10.1371/journal.pone.0034670

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Hamilton, Reed.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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(A) In these two example networks, substrate (S) is utilized to produce biomass (BM) and some by-product (P). We refer to the two species as A and B, and the biomass- and product-producing reactions as and , respectively. (B) List of genes and reactions present or absent in each network. All shared reactions have orthologs present in both networks, except for the reaction associated with genes G23a and G23b, which are not orthologs. (C) A schematic view of the wildtype network behaviors in which flux through is maximized. (D) Gene deletion sets identified by CONGA for the stated CONGA objectives The first three objectives maximize in Species B over Species A. The last objective maximizes in Species A over Species B. The type of model difference (genetic, orthology, or metabolic) associated with each deletion set is also given. (E through H) Schematic views of the flux distributions associated with each gene deletion set in D. The optimal flux distributions in the example networks change as a result of the gene deletion sets in D. Differences in the optimal flux distributions are due to differences in the two networks.

Inline graphic — (A) In these two example networks, substrate (S) is utilized to produce biomass (BM) and some by-product (P). We refer to the two species as A and B, and the biomass- and product-producing reactions as and , respectively. (B) List of genes and reactions present or absent in each network. All shared reactions have orthologs present in both networks, except for the reaction associated with genes G23a and G23b, which are not orthologs. (C) A schematic view of the wildtype network behaviors in which flux through is maximized. (D) Gene deletion sets identified by CONGA for the stated CONGA objectives The first three objectives maximize in Species B over Species A. The last objective maximizes in Species A over Species B. The type of model difference (genetic, orthology, or metabolic) associated with each deletion set is also given. (E through H) Schematic views of the flux distributions associated with each gene deletion set in D. The optimal flux distributions in the example networks change as a result of the gene deletion sets in D. Differences in the optimal flux distributions are due to differences in the two networks.