Analysis strategy of protein-protein interaction networks.

Protein interactions, as well as the networks they formed, play a key role in many cellular processes and the distortion of the protein interacting interfaces may lead to the development of many diseases. In this chapter, we will briefly introduce the background knowledge of the protein-protein interaction, followed by the detailed explanation of varied analysis-from basic to advanced, as well as related tools and databases. VisANT (http://visant.bu.edu)-a free Web-based software platform for the integrative visualization, mining, analysis, and modeling of the biological networks-will be used as a main tool for all examples used in this section.