May 04, 2003
陳 詰 昌
For the increasing of protein-protein interactions （PPIs）data, we can now build a large network. Analyzing the topology of the network systemically, we could not only get the functional information but also predict genetic networks, protein complexes and cellular pathway. In one word, the network provide us a means for understanding the inner working of cell..
But how to achieve it ? The first step is to represent the PPI network as a graph using graph theory-based approaches. The second step is to determine graph properties of network. The third step is to generate hypothesis via iterative filtering and evaluation of the power of predictions by comparing with a random model.
After performing systematic analysis, the author got the following results. First, the lethal mutation is only the high degree nodes in the network but also the articulation points. Second, he found that there exists alternate paths without lethal mutations that bypass viable protein in the PPI networks. Third, distinct functional classes of protein have different network properties. Lats, the approach uncovers the realationships of structure and function in a PPI network.
From Bioinformatics 2004 20: 340-348
1. N. Prlj, D.A. Wigle and I. Jurisica. (2004) Functional topology in a network of protein interactions. Bioinformatics. 20, 340-348.
2. CHRISTIAN VON MERING, ROLAND KRAUSE, BEREND SNEL, MICHAEL CORNELL, STEPHEN G. OLIVER, STANLEY FIELDS & PEER BORK. (2002) Comparative assessment of large-scale data sets of protein–protein interactions. Nature. 417, 399-403.
3. Dongbo Bu, Yi Zhao, Lun Cai, Hong Xue, Xiaopeng Zhu, Hongchao Lu, Jingfen Zhang, Shiwei Sun, Lunjiang Ling, Nan Zhang, Guojie Li and Runsheng Chen. (2003) Topological structure analysis of the protein–protein interaction network in budding yeast. Nucleic Acids Research. 31, 2443-2450.