Applying modularity analysis of PPI networks to sequenced organisms.

T he interaction between proteins is one of the most important features of protein functions. In general, the protein-protein interactions (PPIs) network of an organism is very complex, consisting of huge amount of PPIs. Functional modules can be identified from the complex protein interaction networks. It follows that the investigation of functional modules will generate a better understanding of cellular organization, processes and functions. However, it is a great challenge to apply modularity analysis to under-studied organism, even though this organism has already been sequenced, as there are few or none experimental validated PPI data for them. Therefore, by integrating several bioinformatics methods, we provide a solution for modularity analysis of any sequenced organism. By this way, new information may be found for the organism in different level, such as protein-protein interaction, pathways or cellular process. For the computation part, it takes one to two weeks. The main impact factors are computer power and size of the PPI network. It takes longer time for the manually analysis of biological meanings of the modules.