Figure 1
From: Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity
Representation of metabolic networks as reaction-centric graphs for cyclical EFM analysis. (A) An example of a bipartite graph representing a small metabolic network. Circles and square represent metabolites and reactions, respectively. A directed edge from a metabolite node to a reaction node indicates that the reaction consumes the metabolite. A directed edge from a reaction node to a metabolite node indicates that the reaction produces the metabolite. Once cofactors and dead-end metabolites (M1, M4) are removed, EFM analysis finds two flux modes: [R1, R2, R3] and [R2, R4, R5, R6]. The latter is a substrate cycle. (B) A reaction-centric graph of the network shown in (A). Of the two elementary modes identified, only [R2, R4, R5, R6] comprises a SCC, and thus forms a cycle.