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Fig. 3 | BMC Research Notes

Fig. 3

From: Modelling the structure of a ceRNA-theoretical, bipartite microRNA–mRNA interaction network regulating intestinal epithelial cellular pathways using R programming

Fig. 3

Network plot for visualization of high edge-weight sub-network interactions and centrality. a Network graph plot produced using miRNA–mRNA target list as an adjacency list, using the Additional file 2: R code provided in the supplement. Node size represents network Betweenness Centrality, and edge width and transparency represents edge weight as the number of shared, targeting miRNAs. b Bipartite affiliation networks such as miRNA–mRNA interaction networks can be projected as a single-mode with edge weights representing shared affiliations, as the network in a. c The 5 genes with highest number of shared, targeting miRNAs were subset and re-run in the R script with modified vertex and edge scaling (see additional comments in Additional file 2: Network_Code.R). The sub-network depicts a hypothetical ceRNA-functionality between these five genes, with edge-associated numbers equal to shared, targeting miRNAs between two genes, or nodes (See Additional file 6: Subset adjacency list). d. Genes with highest network centrality values (from the main network depicted in Fig. 3a graph where node size is scaled to network centrality), represent the most ‘central’ members of the overall miRNA–mRNA interaction network. Network centrality is a network-specific value: re-running this five-gene subnetwork in the R-script does not provide additional informative centrality information

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