a new essential protein discovery method based on the integration of protein-protein interaction and gene expression data一种新的重要蛋白质的发现方法基于蛋白质相互作用和基因表达数据的集成.pdfVIP

Li et al. BMC Systems Biology 2012, 6:15 /1752-0509/6/15 METHODOLOGY ARTICLE Open Access A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data 1,2* 1 1* 1,2* Min Li , Hanhui Zhang , Jian-xin Wang and Yi Pan Abstract Background: Identification of essential proteins is always a challenging task since it requires experimental approaches that are time-consuming and laborious. With the advances in high throughput technologies, a large number of protein-protein interactions are available, which have produced unprecedented opportunities for detecting proteins’ essentialities from the network level. There have been a series of computational approaches proposed for predicting essential proteins based on network topologies. However, the network topology-based centrality measures are very sensitive to the robustness of network. Therefore, a new robust essential protein discovery method would be of great value. Results: In this paper, we propose a new centrality measure, named PeC, based on the integration of protein- protein interaction and gene expression data. The performance of PeC is validated based on the protein-protein interaction network of Saccharomyces cerevisiae. The experimental results show that the predicted precision of PeC clearly exceeds that of the other fifteen previously proposed centrality measures: Degree Centrality (DC), Betweenness Centrality (BC), Closeness Centrality (CC), Subgraph Centrality (SC), Eigenvector Centrality (EC), Information Centrality (IC), Bottle Neck (BN), Density of Maximum Neighborhood Component (DMNC), Local Average Connectivity-based method (LAC), Sum of ECC (SoECC), Range-Limited Centrality (RL), L-index (LI), Leader Rank (LR), Normalized a