Discovery Note Modularity of cellular networks shows general center-periphery polari- zation

The modular biology is supposed to be a bridge from the molecular to the systems biology. Using a new approach, it is shown here that the protein interaction networks of yeast S.cerevisiae and bacteria E.coli consist of two large-scale modularity layers, central and pe-ripheral, separated by a zone of depressed modularity. This finding based on the analysis of network topology is further supported by the discovery that there are many more Gene Ontology categories (terms) and KEGG biochemical pathways that are overrepresented in the central and peripheral layers than in the intermediate zone. The categories of the central layer are mostly related to nuclear information processing, regulation and cell cycle, whereas the pe-ripheral layer is dealing with various metabolic and energetic proc-esses, transport and cell communication. A similar center-periphery polarization of modularity is found in the protein domain networks ('built-in interactome') and in a powergrid (as a non-biological exam-ple). These data suggest a 'polarized modularity ' model of cellular networks where the central layer seems to be regulatory and to use information storage of the nucleus, whereas the peripheral layer seems devoted to more specialized tasks and environmental inter-actions, with a complex 'bus ' between the layers.