Bio‐entity network for analysis of protein–protein interaction networks

Protein–protein interactions (PPIs) are vitally important for every process in a living cell. Information about these interactions can improve our understanding of diseases and provide the basis to revolutionize therapeutic treatments. However, since PPIs are involved with extremely complicated biological processes, it is necessary to develop novel tools to deal with this kind of network systems. To realize this, a bio‐entity network approach is introduced to show the topology structure of dynamic and collective performances of PPI networks and analyze the variance of the protein node that plays an important role in the PPI network. Also, spectrum analysis is used to capture the discrete and stochastic feature of PPIs. The yeast protein interaction network is considered as a paradigm. It is demonstrated that the proposed approach can easily and clearly identify the hub‐proteins that have the most impact on the PPI system concerned. It is expected that the bio‐entity network approach as presented in this paper might become a useful tool in system biology. Copyright © 2011 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society