Fig. 4

Network cartography of a nucleoporin-disrupted transcriptome. (a) The collective transcriptome inclusive of up and downregulated transcripts were analyzed by Ingenuity Pathways Analysis to identify experimentally observed interactions among the 326 genes. The network generated from this data was visualized in a circular layout that positions nodes circumferentially with their connections (edges) plotted diametrically. Singletons are network nodes with only one connection to the larger network and are arrayed on the outside of the circle plot. This layout emphasizes nodes that have high edge density, seen in this network on the right. Right panel: Magnification of network arc with high edge density. Nodes were colored properties according to degree, or number of connections, where high degree is represented by dark red and low degree in white, shown here in the colorscale above panel. b Topological analysis revealed a clustering coefficient distribution associated with hierarchical network structure. Inset: Degree distribution demonstrates a power law relationship indicative of scale-free architecture (c) Neighborhood connectivity plot identifies dissortative nature of the network, where highly connected nodes tend to connect to nodes with a lower number of edges. d Nodes with high betweenness centrality are critical to maintaining network integrity as they connect other regions of the network to one another. APP, HNF4A, TP53, NTRK1/TRKA, and CTNNB1 possessed distinct betweenness centrality scores that segregated them from other nodes in the network. Inset: Legend identifies genes with the topmost betweenness centrality scores, ranked in order from highest to lowest, and are colored to facilitate identification within the plot. e Closeness centrality scores are important for speed of informational transmission within a network. Here, nodes with the highest closeness centrality clustered together. The nodes prioritized for high betweenness centrality measures were identical to the molecules with critical closeness centrality scores. Inset: Legend depicts nodes rank ordered from high to low. Identity of nodes with discrete centrality metrics are preserved as identical, yet distinct reprioritization of those molecules is observed on comparison of closeness versus betweenness