PMC

(a) Bar chart to show the expression of NLGN4Y in men in all CNS regions. (b) Bar chart to show the expression of NLGN4X in women (red bars) and men (blue bars) in all CNS regions. (c) Bar chart to show the expression of ZFY in men in all CNS regions. (d) Bar chart to show the expression of ZFX in women (red bars) and men (blue bars) in all CNS regions. (e) Quantitative RT–PCR validation of NLGN4X and NLGN4Y expression in women (red bars) and men (blue bars) in the thalamus. The 2−ΔC_t values have been plotted to show relative gene expression levels. (f) Quantitative RT–PCR validation of NLGN4X and NLGN4Y expression in white matter (green bars) and thalamus (purple bars) in males. The 2−ΔC_t values have been plotted to show relative gene expression levels. (g) Quantitative RT–PCR validation of ZFX and ZFY expression in women (red bars) and men (blue bars) in the thalamus. The 2−ΔC_t values have been plotted to show relative gene expression levels. The error bars in all panels represent the s.e.m. (N=34).

(a) GSEA results for the Reactome complement cascade gene set demonstrated enrichment of this pathway in female as compared with male white matter (nominal P-value=0.04, enrichment P-values are estimated using an empirical permutation-based procedure). The top portion of the plot shows the running enrichment score for the gene set as the analysis walks down the ranked list and the presence of a distinct peak at the beginning suggests significant enrichment in women. The middle portion of the plot shows where members of the complement cascade gene set appear in the ranked list of genes. The bottom portion of the plot shows the value of each gene’s correlation with the phenotype, sex. (b) Box plots showing IL1RL1 expression by genotype at rs34990056 (chr2: 37453372) (GG, TG and TT) in male and female cerebellum samples demonstrate a significant association with gene expression in women only. The bottom and top of the box are the first and third quartiles, and the band inside the box is the median value. Whiskers extend from the box to 1.5 times the interquartile range.

(a) Bar chart showing the percentage of expressed genes with evidence of sex-biased expression or splicing in each brain region. FCTX, frontal cortex; TCTX, temporal cortex; OCTX, occipital cortex; WHMT, white matter; HIPP, hippocampus; THAL, thalamus; HYPO, hypothalamus; PUTM, putamen; SNIG, substantia nigra; MEDU, medulla; CRBL, cerebellum; SPCO, spinal cord. The number of samples analysed for each region is provided as additional labelling on the x axis. (b) RSPO1 expression in women (red) and men (blue) in the human CNS. Error bars represent the standard error of the mean (N=13). Hypothalamus (boxed) is the only brain region showing significant sex-biased gene expression. (c) Gene structure of NRXN3 and expression levels (y axis) plotted for each probe set (x axis) covering NRXN3 in males (blue line) and females (red line) in thalamus. All differentially expressed exons map to β-neurexins (boxed region) indicating sex-biased expression of these transcripts. Error bars represent the Standard error of the mean (s.e.m). (d) Successful quantitative RT–PCR validation of α-neurexin and β-neurexin expression in thalamus in men (blue) and women (red). The 2−ΔC_t values have been plotted to show relative gene expression levels. Error bars represent the s.e.m. (N=29).