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Open Access Research article

Characterization the regulation of herpesvirus miRNAs from the view of human protein interaction network

Zhenpeng Li, Fei Li, Ming Ni, Peng Li, Xiaochen Bo* and Shengqi Wang*

Author Affiliations

Department of Biotechnology, Beijing Institute of Radiation Medicine, No.27, Taiping Road, Haidian District, Beijing 100850, China

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BMC Systems Biology 2011, 5:93  doi:10.1186/1752-0509-5-93

Published: 13 June 2011

Abstract

Background

miRNAs are a class of non-coding RNA molecules that play crucial roles in the regulation of virus-host interactions. The ever-increasing data of known viral miRNAs and human protein interaction network (PIN) has made it possible to study the targeting characteristics of viral miRNAs in the context of these networks.

Results

We performed topological analysis to explore the targeting propensities of herpesvirus miRNAs from the view of human PIN and found that (1) herpesvirus miRNAs significantly target more hubs, moreover, compared with non-hubs (non-bottlenecks), hubs (bottlenecks) are targeted by much more virus miRNAs and virus types. (2) There are significant differences in the degree and betweenness centrality between common and specific targets, specifically we observed a significant positive correlation between virus types targeting these nodes and the proportion of hubs, and (3) K-core and ER analysis determined that common targets are closer to the global PIN center. Compared with random conditions, the giant connected component (GCC) and the density of the sub-network formed by common targets have significantly higher values, indicating the module characteristic of these targets.

Conclusions

Herpesvirus miRNAs preferentially target hubs and bottlenecks. There are significant differences between common and specific targets. Moreover, common targets are more intensely connected and occupy the central part of the network. These results will help unravel the complex mechanism of herpesvirus-host interactions and may provide insight into the development of novel anti-herpesvirus drugs.