Additional file 11 of Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data

Additional file 11: X chromosome regions mean and median expression values. X chromosome regions PAR1, PAR2, XTR, XDG, XAR, XCR mean and median CPM expression for male XY and female XX samples for each tissue separately when aligned to a default or sex chromosome complement informed reference genome using either HISAT and STAR. Paired t-test was used to test for significant differences in expression. XTR and XAR show a significant increase, p-value <0.05, in female expression for each tissue type. XTR and XAR additionally show a significant increase, p-value <0.05, in male expression for liver and thyroid. PAR2 shows a significant increase, p-value <0.05, in female liver expression. Additionally reported fold change in mean expression when using a sex chromosome complement informed compared to a default reference genome. The mean fold change in expression either increased or stayed the same ranging from 2.8 to 0.999 fold increase in expression. Finally, mean male over mean female expression was reported for each X chromosome region for each tissue. Mean male over mean female expression decreases for XTR when using a sex chromosome complement reference genome for each tissue.