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Figure 2 | BMC Research Notes

Figure 2

From: VAN: an R package for identifying biologically perturbed networks via differential variability analysis

Figure 2

Network module visualization graph generated in R for the melanoma dataset. Network interpretation is greatly aided by visualization. Therefore, VAN provides options to visualise individual hubs of interest (in dark grey) linked to their interaction partners (in light grey) via color-coded, undirected edges that are weighted with the co-expression correlation value for a given state as shown here (see also Additional file 1, VAN User Guide Section 4: Option 1: Visualization in R). In this example, we analysed transcriptomic data in metastatic melanoma [28] in the context of a protein-protein interaction network downloaded from the Human Protein Reference Database [29] (refer to Implementation for details). The hub, CCND2, was one of 81 hubs showing significant (p-value < 0.05) differences in the average gene expression correlation with respect to its interaction partners. The graph on the left hand side of the figure displays the gene expression correlation coefficients determined for patients alive with no sign of relapse (ANSR) more than 4 years after resection of metastatic disease while the graph on the right hand side shows the same for patients who died from melanoma (DM) within 12 months. The colour scale ranges from red (strong negative correlation of expression) through yellow (no correlation) to green (strong positive correlation).

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