Figure 2.

Responses of X chromosome genes to Xi and Chr Y dosage across gene classes and cell types

(A) Scatterplots of ΔE_X versus ΔE_Y values of X chromosome genes, colored by gene class, in CD4⁺ T cells and monocytes. Pearson correlation coefficients are shown, colored by corresponding gene class. Dashed line indicates X = Y identity line.

(B) Boxplots showing median (line), interquartile range (IQR; top and bottom of box), and 1.5 × IQR (whiskers) of ΔE_X values for X chromosome genes by cell type and gene class.

(C) Boxplots showing median (line), interquartile range (IQR; top and bottom of box), and 1.5 × IQR (whiskers) of ΔE_X values for individual PAR and NPX genes with NPY homologs. Asterisks mark two genes with <3 TPM median expression in each cell type.

(D) Proportional bar plot of genes with statistically significant ΔE_X values across CD4⁺ T cells, monocytes, LCLs, and fibroblasts, parsed by the number of cell types in which a given gene’s ΔE_X FDR was less than 0.05. Bar plot coloring is as follows: PAR genes in green, NPX genes in orange, NPX genes with NPY homologs in blue.

(E) Scatterplot of ΔE_X values for all expressed X chromosome genes in CD4⁺ T cells and monocytes. Pearson correlation coefficient is shown.

(F and G) Scatterplot of ΔE_X values for genes previously annotated as expressed on Xi (“Xi-expressed”) (F) or not expressed from Xi (“Xa-only expressed”) (G) in CD4⁺ T cells and monocytes. Pearson correlation coefficients are shown.