Figure 2.

scLinaX, a method to quantify escape from XCI using droplet-based scRNA-seq data

(A) A schematic illustration of scLinaX.

(B) A boxplot represents the estimated ratio of the expression from Xi. Genes are grouped according to the XCI status annotated in the previous study.²

(C) A plot represents the concordance of the ratio of the expression from Xi between the AIDA dataset (x axis) and the Japanese dataset (y axis). Genes that are annotated as escapee genes and the SEPTIN6 gene are included. The black line indicates x = y. Pearson’s correlation = 0.92 with a 95% confidence interval (CI) of 0.82–0.97.

(D) A plot represents the relationship between the log2 fold changes in the DEG analysis (x axis) and the ratio of the expression from Xi (y axis). Genes that are annotated as escapee genes and the SEPTIN6 gene are included. The curved line indicates the theoretical relationship under the assumption that total gene expression in males and Xa-derived gene expression in females are at the same level. Pearson’s correlation = 0.94 with a 95% CI of 0.87–0.97.

(E) A plot representing the ratio of the expression from Xa and Xi at an individual level for the DDX3X gene. The dashed black horizontal line represents the mean ratio of the expression from Xi across samples.

(F and G) Forest plots represent the log2 fold changes in the DEG analysis for each cell type (left) and plots on the right represent the ratio of the expression from Xa and Xi at an individual level. The error bars indicate 95% CI. The colors of the dots represent the log-scaled mean normalized count calculated by DEseq2 (baseMean). ∗p < 0.05. ∗∗Per-cell-type FDR <0.05. The dashed black horizontal line represents the mean ratio of the expression from Xi across samples. AIDA, Asian Immune Diversity Atlas; ALT, alternative allele; ASE, allele-specific expression; REF, reference allele; SNP, single-nucleotide polymorphism; Xa, active X chromosome; Xi, inactive X chromosome.