Figure 1.

Differing representations of metabolic networks. Showing a bipartite representation of two pathways (abc and def) linked by a highly connected metabolite (I), as used in ambient and a reaction-only representation (II), such as that used in GiGA. In representation A, penalising metabolite 5 allows for pathways including only abc, or only def, as well as pathway crossover if there is sufficient evidence for it. Representation B shows how the network would be construed if metabolites were used to link reactions together; the original pathways are lost in this case. Representation C shows the network if metabolite 5 were deemed to be a currency metabolite. This retains the two original pathways, but would never link the two pathways even if there were evidence for crossover.