Compound clustering and consensus scopes of metabolic networks

We investigate the structure of metabolic networks by identifying sets of metabolites having a similar synthesizing capacity. We measure the synthesizing capacity of a compound by determining all metabolites that can be produced from it, and call this set the scope of the compound. We then define a distance measure based on the Jaccard coefficient and apply a hierarchical clustering method. Compounds within the same cluster are chemically similar and often appear in the same metabolic pathway. For each cluster we define a consensus scope by determining a set of metabolites that is most similar to all scopes within the cluster. We find that only a few of the resulting consensus scopes are mutually disjoint while others overlap, and some consensus scopes are fully contained in others. Thus, our approach reveals a number of functional subunits of the metabolic network which are arranged into a hierarchical setting.