Ten simple rules to create biological network figures for communication
Fig 1
First, determine the figure purpose and assess the network.
Two representations of proteins involved in GBM. The left image (A) shows a curated cancer signaling pathway taken from the TCGA's original Mondrian plugin to Cytoscape (Cytoscape Consortium; https://cytoscape.org/). The node color represents the overall variance of expression across a set of patients, and the lines and arrows represent the function of the interactions between the proteins. In the right image (B), a PPI network was created using the Cytoscape stringApp and annotated with data downloaded from TCGA. The colors represent the fold change for subtype 3 of GBM, the node sizes vary with the number of mutations, and the edges represent functional associations. GBM, glioblastoma multiforme; PPI, protein–protein interaction.