Complex tree: the basic framework of protein-protein interaction networks

In living cells, proteins are dynamically connected through biochemical reactions, so its functional features are properly encoded into proteinprotein interaction networks (PINs). Up to present, many efforts have been devoted to exploring the basic feature of PINs. However, it is still a challenging problem to explore a universal property of PINs. Here we employed the complex networks theory to analyze the protein-protein interactions from Database of Interacting Protein. Complex tree: the unique framework of PINs was revealed by three topological properties of the giant component of PINs (GCOP), including right-skewed degree distributions, relatively small clustering coefficients and short characteristic path lengths. Furthermore, we proposed a nonlinearly growth model: complex tree model to reflect the tree framework, the simulation results of this model showed that GCOPs were well represented by our model, which could be helpful for understanding the tree-structure: basic framework of PINs. Source code and binaries freely available for download at http://cic.scu. edu.cn/bioinformatics/STM/STM_code.rar.