VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus–host interaction networks

Navratil, Vincent; de Chassey, Benoît; Meyniel, Laurène; Delmotte, Stéphane; Gautier, Christian; André, Patrice; Lotteau, Vincent; Rabourdin-Combe, Chantal

Public access to the VirHostNet knowledge base is available at http://pbildb1.univ-lyon1.fr/virhostnet. Access can be made either anonymously (by default) or by creating a personal account (register in the account menu). On simple request, this personal account allows users to participate to the literature-curation effort. Literaturecurated and Database-curated protein-protein interactions flat files are available in a tabulated format on request. Contact V.N. ([e-mail]) for more information. Figure 5 . VirHostNet Visualisator. Graph representation of the mTOR-infection network is drawn (right of the applet). Only interacting proteins of the mTOR pathway are represented (cellular proteins = blue nodes; host-host protein-protein interactions = blue edges). Viral interacting proteins are also added to define the infection network (viral proteins = coloured nodes according to viral taxonomy; virus-host protein-protein interactions = red edges). Cellular proteins of the network targeted by at least one viral protein (red stroke) are highlighted. The width of the edges is roughly proportional to the number of PMIDs used to describe the interaction. The width of the nodes is roughly proportional to the cellular degree, i.e. the number of cellular partners in the whole network. The taxonomical classification of viral proteins interacting with the mTOR network is given (left panel of the applet). The menu of the applet (top of the applet) allows users to define nodes and edges preferences (width, colour, labelling), interaction filtering (according to the number of methods, number of PMIDs or both), network navigation (expand viral or host neighbours) and graph layout. To obtain this figure, from the list of the 89 selected protein-protein interactions obtained in Figure 4E , users have to click on 'visualize' button. Then from the applet, in picking mode, they have to select all proteins and ask for viral proteins neighbours (in expand menu).