A dual controllability analysis of influenza virus-host protein-protein interaction networks for antiviral drug target discovery

Ackerman, Emily E.; Alcorn, John F.; Hase, Takeshi; Shoemaker, Jason E.

The host protein-protein interaction network (from Vinayagam et al. [40] ) is the combination of interactions identified in two or more repetitions of Y2H screens within the study and known, experimentally identified interactions from literature where interactions had been given direction using a naïve Bayesian predictor. After retrieving the network, a confidence level cutoff of 0.7 was used based on the correlation between confidence scores and biological relevance reported in Yu et al. [71] . This network is the HIN. Influenza A virus-host interactions detected by Co-IP RNAi assay in Watanabe et al. [41] were narrowed to interactions which contained host proteins already found within the HIN to avoid skewing degree and betweenness network metrics. All virus-host interactions are directed viral to host protein. These interactions were directly integrated into the host network, creating the VIN. All analysis was completed in R 3.4.3 using the igraph package.