Fig. 3
From: Using biological networks to integrate, visualize and analyze genomics data
Network hubs and bottlenecks. a InnateDB was used to construct a network of genes that were significantly up-regulated in the Lawless et al. [30] dataset. Interactions between the genes in the uploaded list, as well as all their interacting partners, were included in the network. The network consisted of 6259 nodes and 15,137 edges (self-loops; duplicated edges; and edges involving UBC were removed). b Hub nodes were identified using the CytoHubba plugin in Cytoscape 2.8.2. Cytoscape was used to extract and visualize the top 10 hub nodes and their interactors. Hub nodes are shown in colour with gene names. Node size is proportional to degree. c CytoHubba was also used to identify bottleneck nodes in the network. The top 10 bottleneck nodes are shown in colour with gene names. There is considerable overlap between the top 10 hub nodes and the top 10 bottleneck nodes