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Figure 3 | BMC Research Notes

Figure 3

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

Figure 3

Network module visualization graphs generated in Cytoscape for the melanoma dataset. For a global impression of network modules of interest, VAN generates output files that are directly importable into Cytoscape [26], together with a 'color-blind safe’ edge palette file (ExampleVisualStyle.props) and suggested layout protocol (see also Additional file 1, VAN User Guide Section 4: Option 2: Visualization in Cytoscape). As described in Figure 2, we used VAN to analyse gene expression data in metastatic melanoma from Mann et al.[28] in the context of a protein-protein interaction network downloaded from the Human Protein Reference Database [29]. The coordination of gene expression among patients with a survival time greater than four years (Figure 3A) and patients not surviving beyond 12 months (Figure 3B) is affected as indicated by the changes in edge colour. Figures 3C and 3D zoom in on the same subsets of 3A and 3B, respectively and show in more detail the significant (p-value < 0.05) disruption in the coordination of gene co-expression for the hub TRAF1 and its interaction partners. Our example visualisation protocol can be applied to two or more conditions (not shown here) and the Cytoscape platform provides dynamic zooming to allow focus on one, or a few, hubs of interest (C and D).

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