Figure 4.
The UBI effects on gene expression patterns in the hypothalamus and pituitary gland. Analysis of the left (LdN) and right (RdN) dominant gene co-expression networks in the hypothalamus. (A–D) Gene expression levels in the left hypothalamus (HPT) and the pituitary gland (Pit) collected 3 h after left sham surgery (Sh: n = 11 rats) or left UBI (n = 12 rats) that were performed in the spinalized rats. The expression levels in the log2 scale and the Bonferroni adjusted P-values determined by Mann–Whitney test are shown. (E) The asymmetry index AIL/R = log2[L/R], where L and R are the median expression levels in the left and right hypothalamus, is shown for each gene analyzed. There were no differences in the AIL/R between sham surgery and UBI groups; therefore, they were combined (n = 22) for statistical analysis. Wilcoxon signed-rank test followed by Bonferroni multiple testing correction: *, P-adj < .05; **, P-adj < .01; #, P ≤ .05 (not adjusted). Boxes denote genes with AIL/R > 0 or AIL/R < 0 that were defined as the LdN and RdN genes. In (A–E), data are presented as boxplots with median and hinges representing the first and third quartiles, and whiskers extending from the hinge to the highest/lowest value that lies within the 1.5 interquartile range of the hinge. (F and G) Patterns of intra-modular correlations internal for each the LdN (LdN–LdN) and RdN (RdN–RdN), and between the networks (LdN–RdN) are shown for the left and right modules of sham surgery and left UBI groups. In (F), correlation strengths |Rho| (absolute value of each pairwise correlation) are presented as violin plots with white line indicating mean coordination strength. The proportion of positive correlations is shown as horizontal lines in (G). The 3 correlation patterns were compared within each (ie, left and right) module. Each pattern was compared between the modules and between UBI and sham surgery groups (for details, see Figure 4—figure supplement S10A). P-values were determined by permutation testing with Benjamini–Hochberg family wise multiple test correction. Significance for contrasts was determined by analysis of 3 AIL/R categorization variants (Figure 4—figure supplement S9); P-values are shown for the categorization variant with the median AIL/R of the combined sham surgery and UBI group. (H and I) Heatmaps for Spearman’s rank coefficients for pairwise gene–gene correlations in the left- (lm) and right- (rm) modules of sham surgery and UBI groups. Source data: the EXCEL source data files “Hypoth_SO_UBI.xlsx; RD Hypophis_ Master file.xlsx; Table III-S6 23 05 10.xlsx; raw_groups.xlsx.”