Supplementary Figure 9: The protein co-regulation network satisfies scale-free topology but is difficult to visualize as an interaction network.
From: Co-regulation map of the human proteome enables identification of protein functions
(a) The “scale free plot” produced by the WGCNA R package using the treeClust-derived adjacency matrix. The log of the connectivity k is plotted against the log of the frequency of this connectivity. There is a linear relationship between these two variables, as indicated by the square of the Pearson correlation, R2, being 0.91. This shows that the protein co-regulation network derived from ProteomeHD using treeClust is at least approximately scale free. (b) Visualization of a weighted, undirected network with 5,013 nodes (proteins detected in at least 95 experiments) and 62,812 edges (top scoring 0.5% of links), based on the co-regulation score. Four common algorithms were used to create different network layouts, but with so many edges it is difficult to avoid the “hairball” problem.
