Fig. 3
Directionality and community structure of graphs for Escherichia coli metabolism. a Reactions of the core model of E. coli metabolism grouped into eleven biochemical pathways, b, c Graphs A and \({\cal D}\) from Fig. 2b–c partitioned into communities computed with the Markov Stability method; for clarity, the graph edges are not shown. The Sankey diagrams68,69 show the correspondence between biochemical pathways and the communities found in each graph. The word clouds contain the metabolites that participate in the reactions each community, and the word size is proportional to the number of reactions in which each metabolite participates
