Journal
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
Volume 14, Issue 2, Pages 370-380Publisher
IEEE COMPUTER SOC
DOI: 10.1109/TCBB.2015.2394487
Keywords
United complex centrality; essential proteins; PPI network; protein complexes
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Funding
- National Natural Science Foundation of China [61370024, 61232001, 61428209]
- China Postdoctoral Science Foundation [2014T70789]
- Program for New Century Excellent Talents in University [NCET-12-0547]
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Essential proteins are indispensable for the survival or reproduction of an organism. Identification of essential proteins is not only necessary for the understanding of the minimal requirements for cellular life, but also important for the disease study and drug design. With the development of high-throughput techniques, a large number of protein-protein interaction data are available, which promotes the studies of essential proteins from the network level. Up to now, though a series of computational methods have been proposed, the prediction precision still needs to be improved. In this paper, we propose a new method, United complex Centrality (UC), to identify essential proteins by integrating the protein complexes with the topological features of protein-protein interaction (PPI) networks. By analyzing the relationship between the essential proteins and the known protein complexes of S. cerevisiae and human, we find that the proteins in complexes are more likely to be essential compared with the proteins not included in any complexes and the proteins appeared in multiple complexes are more inclined to be essential compared to those only appeared in a single complex. Considering that some protein complexes generated by computational methods are inaccurate, we also provide a modified version of UC with parameter alpha, named UC-P. The experimental results show that protein complex information can help identify the essential proteins more accurate both for the PPI network of S. cerevisiae and that of human. The proposed method UC performs obviously better than the eight previously proposed methods (DC, IC, EC, SC, BC, CC, NC, and LAC) for identifying essential proteins.
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