Three faces of metabolites: Pathways, localizations and network positions

In this study, we investigate the relative organization of three (not independent) categorizations of metabolites—pathways, subcellular localizations and network clusters both qualitatively and quantitatively and further characterize the categories from topological point of view. The picture of the metabolism we obtain is that of peripheral modules, characterized both by being dense network clusters and localized to organelles, connected by a central, highly connected core. Pathways typically run through several network clusters and localizations, connecting them laterally. The significant overlap between organelles, pathways and network clusters suggest that, to some extent, the topology of metabolic networks could spell out the spatial isolations of cellular architectures and functional coherence of metabolic systems. Such systems level analysis of the correlation between different categorizations is helpful for understanding the influence of intracellular organization on the regulation of metabolic processes.