Figure 9

Network representing the functional associations between some of the top 250 most significant DEGs at 2 dpi. Using STRING protein query function in Cytoscape, 208 of the top 250 most significant DEGs were identified and scored based on functional association with each other. These data were used to generate a network in Cytoscape, which was then arranged based on GeneMania force directed layout. Each DEG is represented by a node, with edges (connecting lines) representing functional association. The largest contiguous network resulting from this analysis (136 nodes and 696 edges) is displayed. For visualization purposes, nodes in the peripheral regions of the network (representing DEGs LOC100006895, rnasel3, ndrg1b, pde6ha, and serpinb1l1) were omitted. This resulted in one large cluster (a), and two smaller clusters (b) and (c). STRING functional enrichment analysis indicated that most DEGs in this network were related to the immune response to infection (S6), and genes were labelled based on the main types of gene-set categories enriched in each of their respective clusters. This revealed distinct functions associated with each gene cluster, for example (a) interferon and PRR signalling, (b) antigen processing and presentation, and (c) complement response. The network was also analysed by CytoHubba, which was used to identify the potentially most important hub nodes within the network, with each node scored and coloured based on maximal clique centrality within the network, according to the CytoHubba score colour scale provided; however, this is better represented in S5, with corresponding CytoHubba scores in Table S7.