Abstract:

With the increase of largescale proteinprotein interaction data available, it has been possible to understand the basic components and organization of the cell mechanism from the system level. The challenge is how to analyze such complex interacting data to reveal the principles of cellular organization, processes and functions. Many studies have shown that using graphbased clustering methods is an effective approach to analyzing proteinprotein interaction data. In this review, several aspects will be presented to describe the recent advances in clustering methods for protein interaction networks, such as the graph models of the PPI network, clustering methods, evaluation methods and applications. Finally, the challenges and directions for future research will be discussed.

Key words: system biology;protein interaction network;graphbased clustering algorithms;protein complex;protein function