Critical Nodes of Virus–Host Interaction Revealed Through an Integrated Network Analysis

Korbinian Bösl; Aleksandr Ianevski; Thoa T. Than; Petter I. Andersen; Suvi Kuivanen; Mona Teppor; Eva Zusinaite; Uga Dumpis; Astra Vitkauskiene; Rebecca J. Cox; Hannimari Kallio-Kokko; Anders Bergqvist; Tanel Tenson; Valentyn Oksenych; Magnar Bjørås; Marit W. Anthonsen; David Shum; Mari Kaarbø; Olli Vapalahti; Marc P. Windisch; Giulio Superti-Furga; Berend Snijder; Denis Kainov; Richard K. Kandasamy

Host-virus protein-protein interactions were downloaded from published studies (Pichlmair et al. 2012 , Rozenblatt-Rosen et al. 2012 , Jäger et al. 2011 , Shapira et al. 2009 , de Chassey et al. 2008 , Khadka et al. 2011 , Zhang et al. 2009 , Vidal et al. 2011 which included a total of 183 viral proteins, 2381 host proteins and 5781 host-virus interactions. Protein identifiers were mapped to UniProt IDs. Human protein-protein interaction data was imported from BioGRID database (version 3.4.139, Stark et al. 2006 ) covering 215244 interactions. The network analysis was performed using in-house programs developed in R statistical environment (version 3.4.3, www.r-project.org) with the use of the packages SparseM (version 1.77), RBGL (version 1.52.0) and graph (version 1.54.0). Network visualization was performed in Cytoscape (version 3.6.1, Shannon et al. 2003) . Network clusters/sub-networks were extracted using the Cytoscape plugin MCODE (version 1.5.1, Bader and Hogue 2003) . Data visualization was performed in R statistical environment and Cytoscape.