Huntington’s disease exerts strong effects on specific gene co-expression modules in human caudate nucleus. Analysis of human caudate nucleus (CN) sample network properties for each of 23 gene co-expression modules previously identified in CN; colors correspond to the original gene co-expression module labels from . (A) For each module sample network, the Spearman correlations cor(K C) are plotted for control (CTRL) and Huntington’s disease (HD) subjects. Each point corresponds to a module. Black line: y = x. (B) The log-transformed P–value of the difference between cor(K C) for CTRL and HD subjects is reported for each module (Methods). (C) The extent of differential expression (DE) between CTRL and HD was assessed for each module by using Student’s t-test of DE for the module eigengene (ME; i.e. the first principal component obtained by singular value decomposition of the module expression matrix) between CTRL and HD. (D) Comparison of the module significance levels reported in (B) and (C); linear least squares regression line in black. p.Diff.cor(K,C) denotes the P-value for testing the differences of cor(K C) between the CTRL and HD module sample networks. (B–D) Blue lines: P = .05; red lines: Bonferroni correction for multiple comparisons.