Extended Data Fig. 8: Distributions of asymmetric coupling.
From: Evolutionary divergence between homologous X–Y chromosome genes shapes sex-biased biology
a. Figure 4d excluding tissue-specific genes. Color indicates direction of coupling (see Fig. 4b legend). Note that although the modal number of tissues in which genes showed significant X- or Y-biased coupling was one (Fig. 4d), the current plot suggests that this pattern is driven by genes with tissue-specific expression. b. Count of genes with significant asymmetric coupling (CLIP padj < 0.05) to a given gametolog pair in a maximum of N tissues. Color indicates direction of coupling (see Fig. 4b legend). c. Extended Data Figure 8b excluding tissue-specific genes. Color indicates direction of coupling (see Fig. 4b legend). d. Count of genes with significant asymmetric coupling (CLIP padj < 0.05) with a maximum of N pairs within a given tissue. Color indicates direction of coupling (see Fig. 4b legend). Note that, while the modal number of gametolog pairs that genes were asymmetrically coupled to (across all tissues) was eight (Fig. 4d), the modal number of pairs within a given tissue was only two (shown here). e. Number of genes with significant (CLIP padj < 0.05) asymmetric coupling for each pair–tissue using the subsamples (N = 66 males, Methods; Supplementary Tables 9,10) versus the entire sample (ρ = 0.598, p < 2.2e-16). Regression lines with confidence intervals are shown. f. Number of genes with significant (CLIP padj < 0.05) asymmetric coupling for each pair using the subsamples (N = 66 males, Methods; Supplementary Tables 9,10) versus the entire sample (ρ = 0.981, p = 1.124e-10). Regression lines with confidence intervals are shown. g. Number of genes with Methods (CLIP padj < 0.05) asymmetric coupling for each tissue using the subsamples (N = 66 males, Methods; Supplementary Tables 9,10) versus the entire sample (ρ = 0.428, p = 0.005). Regression lines with confidence intervals are shown. h. Boxplots of the proportion of pair-tissue combinations in which genes are asymmetrically coupled (CLIP padj < 0.05). ANOVA p = 1.08e-05; Tukey’s HSD padj = 5.93e-05 for X > autosomal. Boxplots depict medians (horizonal lines), interquartile ranges [IQRs] (boxes), 1.5*IQRs (whiskers), and outliers (points). i. Boxplots of asymmetric coupling values among autosomal, X chromosome, and Y chromosome genes with significant asymmetric coupling (CLIP padj < 0.05). Values are shown for each gametolog pair (see Supplementary Table 8 for N genes x tissues per pair). Colored dots on the x-axis indicate significance of comparisons (see bottom legend, Supplementary Table 11; Tukey’s HSD results are only shown for pairs in which ANOVA pad < 0.05). Boxplots depict medians (horizonal lines), interquartile ranges [IQRs] (boxes), 1.5*IQRs (whiskers), and outliers (points). j. Boxplots of asymmetric coupling values among autosomal, X chromosome, and Y chromosome genes with significant asymmetric coupling (CLIP padj < 0.05). Values are shown for each tissue (see Supplementary Table 8 for N genes x pairs per tissue). Colored dots on the x-axis indicate significance of comparisons (see bottom legend, Supplementary Table 11; Tukey’s HSD results are only shown for tissues in which ANOVA padj < 0.05). Non-gametolog Y chromosome genes show strong Y-biased coupling in the testes (for example, HSFY1/2) and stomach (for example, DAZ1/2/4). Boxplots depict medians (horizonal lines), interquartile ranges [IQRs] (boxes), 1.5*IQRs (whiskers), and outliers (points).
