It is well understood that cellular functions are carried out using various specialized groups of molecules interacting via intricate networks. No approach to complex systems can succeed without exploiting network topology . In this study, we investigated characteristics associated with the targeting of herpesvirus miRNAs to proteins in the human PIN. Virus-encoded miRNAs have unique advantages: they can function at the RNA level, affecting the expression of many genes rapidly and extensively. The results of this study will contribute to a better understanding of the complex herpesvirus-host interactions at the miRNA level.
We found that herpesvirus miRNAs preferentially target PIN hubs and bottlenecks, a process similar to that of human-encoded miRNAs. The biological networks displayed scale-free characteristics, i.e. most of the nodes have a relatively low degree, making them resistant to attacks on random nodes . It seems that the vulnerability of human protein networks (only a few nodes have a high degree) is successfully exploited by herpesviruses, suggesting that these viruses must have evolved to target key nodes preferentially, allowing them to take maximum control of the human protein network during infection. Although the various roles carried out by virus-encoded proteins have been extensively studied over the past few decades, it is only recently that viral protein-regulated PIN have been studied in detail. Matthew D. Dyer et al.  examined some human-pathogen protein-protein interactions and found that both viral and bacterial pathogens interacted with human PIN hubs and bottlenecks.
The results of our comparison between common and specific targets suggested that some topological differences existed between nodes related to processes associated with common and specific virus pathogenesis mechanisms. Furthermore, the significant hub and bottleneck proportions for common targets validated the preference of viral miRNAs for hubs and bottlenecks. These results provided valuable information that will help unravel mechanisms associated with herpesvirus pathogenesis.
We also characterized the modularity of common PIN targets. We found that common targets tend to form a larger module and have a higher density than randomly chosen nodes and that they are located in the global central core of PIN. During virus-host interactions, viruses use their limited resources to exploit fundamental cellular processes for finishing their life cycles. From that perspective, targeting nodes located in the central part of PIN seems a reasonable strategy designed to affect nodes in other parts of the network efficiently and rapidly. The nodes in the central part represent fundamental components of the cell, the control over which might be necessary for the virus to infect successfully. As our GO analysis confirmed, these nodes are related to processes associated with fundamental cellular regulation and development indispensable to viral survival.
To test the robustness of our results, two additional algorithms, miRanda  and TargetScan , were used to predict the herpesvirus miRNAs targets; meanwhile, a high confidence protein-protein interaction data set, HPRD (Human Protein Reference Database)-filtered, was also used to construct the PIN. Most results are in agreement with those obtained using PITA algorithm  and HPRD dataset . The detailed results are described in additional files (see additional files 1, 2 and 3).
In this paper, we focused on the description of statistically significant, functional characteristics of herpesvirus miRNAs involved in the process of regulation of the human PIN. Some limitations to the analysis described in this report are, first, the PIN used was incomplete and therefore subject to considerable error rates; second, the large number of predicted miRNA targets makes experimental validation rather difficult. Moreover, we know that the results of different types of predictions do not fully agree with each other . Our predicted herpesvirus miRNAs collection might not be complete; that is, the use of improved miRNA prediction algorithms and a wider implementation of high-throughput techniques might identify new miRNAs. Third, the herpesvirus miRNA mediated human protein interaction network, in the context of herpesvirus protein and human protein interactions, was not analyzed due to the disequilibrium and lack of herpesvirus protein and human protein interaction data. Despite these limitations, our analysis of herpesvirus miRNA interactions with the human PIN should help to reveal a broader picture of their functional mechanisms at the systems level and add to our knowledge of the viral pathogenesis process.