Functional and Transcriptional Coherency of Modules in the Human Protein Interaction Network

Summary Modularity is a major design principle in interaction networks. Various studies have shown that protein interaction networks in prokaryotes and eukaryotes display a modular structure. A majority of the studies have been performed for the yeast interaction network, for which data have become abundant. The systematic examination of the human protein interaction network, however, is still in an early phase. To assess whether the human interaction network similarly displays a modular structure, we assembled a large protein network consisting of over 30,000 interactions. More than 670 modules were subsequently identified based on the detection of cliques. Inspection showed that these modules included numerous known protein complexes. The extracted modules were scrutinized for their coherency with respect to function, localization and expression, thereby allowing us to distinguish between stable and dynamic modules. Finally, the examination of the overlap between modules identified key proteins linking distinct molecular processes.