permutation procedure that compared differences in correlation strengths between the selected groups with differences in correlation strengths between two randomly assigned groups. This general procedure has been used to quantify network rewiring in both genomic (Gill et al. 2010) and neural imaging studies (Hosseini et al. 2012). Using this procedure, we identified the number of changed edges for each gene and then inquired as to whether some genes had a disproportionately high number of changing edges. For the latter, the binomial test was used with the following parameters. The average incidence of changing edges (the rate of the binomial test) was computed by dividing the number of changing edges (P < 0.01) by the total number of network edges. The number of trials (for each gene) was equal to the number of edges. The number of ‘successes’ was equal to the number of significantly changing edges (P < 0.01). Genes enriched in changing edges are denoted as differentially wired (DW).
