Figure 2

Function, network topology and disease are interrelated. (a) In each disease set, significantly enriched and under-enriched functions are shown in red and green, respectively (p<0. 05, Bonferroni-corrected hypergeometric test). The fold enrichment or depletion for each disease set and term is plotted using a red-green gradient and calculated as the ratio of the fraction of genes in the disease set that are annotated by that term to the fraction of all annotated genes that include that term. (b) For each of the three topological properties and each term, we compared the distributions of the topological property restricted to genes annotated with that term versus all annotated genes. Red (green) depicts a significant difference as determined via Wilcoxon’s rank sum test (Bonferroni-corrected p-value <0. 05); that is, genes having this functional term differ in this topological property from the set of all annotated genes. We use a red-green gradient to plot the ratio of the average of the property in the genes annotated with the term to the average of the property in all annotated genes; however, in order not to overweigh the contribution of genes with multiple annotations, when computing the average of the property across genes annotated with a particular term, we weigh the contribution of each gene inversely to the number of terms with which it is annotated.