Figure 3.

The scLinaX-based quantification of escape from XCI across immune cell types

(A) A boxplot represents the estimated ratio of the expression from Xi for escapee genes across cell types.

(B) Scatterplots represent pairwise comparisons of the ratio of the expression from Xi for escapee genes. The dashed lines represent x = 0, x = y, and y = 0.

(C) UMAPs colored according to the ratio of the expression from Xi estimated for each cell type. Representative genes that showed a higher ratio of expression from Xi in lymphocytes than monocytes, the DDX3X and EIF2S3 genes, are indicated. Cell types whose ratio of the expression from Xi could not be estimated are colored gray.

(D) The ratio of the expression from Xa and Xi at an individual level for the DDX3X and EIF2S3 genes. The dashed horizontal line represents the mean ratio of the expression from Xi across samples for each cell type. Since the definition of alleles derived from Xa and Xi is consistent within the same individual, the ratio of expression from Xi may exceed 0.5 in some cell types.

(E) A UMAP colored according to the ratio of the expression from Xi estimated for each cell type. The PRKX gene, which shows a unique pattern of heterogeneity of escape across cell types, is indicated.

(F) The ratio of the expression from Xa and Xi at an individual level for the PRKX gene.