Figure 2

Preferential overexpression of hub genes in cancer:

(A) Boxplot showing the local entropy rate (LSR) against normal/cancerstatus, for the hub gene (BUB1) exhibiting the largest increase inthe local entropy rate. P-value is from a Wilcoxon rank sum test. (B)Scatterplot of gene expression values between a representative normal(x-axis) and cancer (y-axis) sample for the gene showing the largestincrease in the local entropy rate (gene BUB1, marked in red) andthat of its neighbours in the PPI network (over 800 neighbours, shown inblack). (C) Boxplot of the average difference in gene expression betweennormal and cancer (positive values indicate higher expression in cancer)against node-degree class. Observe how the highest-degree hubs showpreferential increased expression in cancer, whereas the largest reductionsin expression target low-degree nodes. (D) Density plot of the averagedifference in gene expression between normal and cancer for two classes ofgenes: hubs (defined as nodes of degree >316) and nodes of degree1 (k = 1). The number of each is indicated and the P-value is from aKolmogorov-Smirnov test, testing for a difference in their statisticaldistributions.