Figure 4: Allelic biases in gene expression in H1 lineages.
From: Chromatin architecture reorganization during stem cell differentiation
a, Proportion of genes with detectable allelic expression with statistically significant allelic bias. b, Density plot of the absolute value of the fold change in expression (log2) between alleles. c, Heat map showing k-means (k = 20) clustering of the allelic expression ratios (log2) at genes with constitutively testable expression (a minimum of 10 reads in each lineage). d, Genome browser image of variable allelic expression of the PARP9 gene. e, Fraction of imprinted genes among allele-biased genes and other genes. (P = 4.4 × 10−5, Fisher’s exact test). f, Fraction of allele-biased genes that are known imprinted genes. g, Cumulative density plot of distances from variants to the nearest allele-specific gene. Allele specific variants are defined using histone acetylation, H3K9me3, H3K27me3, DHS and H3K4me3 (n = 3,920, P < 2.2 × 10−16, KS test). h, Number of allele-biased genes showing consistent allele specific chromatin states in their promoter regions. Active variants are defined by H3K4me3, DHS or histone acetylation. Inactive promoter variants are defined by DNA methylation and H3K9me3/27me3. i, Genome browser image of mRNA-seq and chromatin features surrounding the TDG gene.
