Fig. 5: The association between CpG densities and species-specific DHSs. | Nature Communications

Fig. 5: The association between CpG densities and species-specific DHSs.

From: Comparison of chromatin accessibility landscapes during early development of prefrontal cortex between rhesus macaque and human

Fig. 5

a Box and jitter plots comparing promoter CpG densities of orthologous genes, whose promoters are specifically open in the human PFC (n = 470 genes). Boxes and whiskers represent the 25th/75th percentiles and 1.5 \(\times\) the interquartile range, respectively. The center in the boxplot represents the medium value. Student’s t test with a two-sided model was used in this figure. b Box and jitter plots comparing promoter CpG densities of orthologous genes, whose promoters are specifically open in rhesus PFC (n = 430 genes). Boxes and whiskers represent the 25th/75th percentiles and 1.5 \(\times\) the interquartile range, respectively. The center in the boxplot represents the medium value. Student’s t test with a two-sided model was used in this figure. c Box plots showing DNA methylation levels of orthologous genes, whose promoters are specifically open in humans (n = 470 genes), at the human GW24 stage and the E90 stage in rhesus monkeys, respectively. Boxes and whiskers represent the 25th/75th percentiles and 1.5 \(\times\) the interquartile range, respectively. The center in the boxplot represents medium value. Student’s t test with a two-sided model was used in this figure. d Box plots showing DNA methylation levels of orthologous genes, whose promoters are specifically open in rhesus (n = 430 genes), at rhesus E90 stage and human GW24 stage, respectively. Boxes and whiskers represent the 25th/75th percentiles and 1.5 \(\times\) the interquartile range, respectively. The center in the boxplot represents the medium value. Student’s t test with two-sided model was used in this figure. e Box plots comparing promoter CpG densities of orthologous genes whose promoters are open in both human and rhesus (n = 6683 genes) PFC. Boxes and whiskers represent the 25th/75th percentiles and 1.5 \(\times\) the interquartile range, respectively. The center in the boxplot represents the medium value. Student’s t test with a two-sided model was used in this figure. f Box plots showing DNA methylation levels of orthologous genes whose promoters are conserved open in humans and rhesus monkeys (n = 6683 genes), at human GW24 stage and rhesus E90 stage, respectively. Boxes and whiskers represent the 25th/75th percentiles and 1.5 \(\times\) the interquartile range, respectively. The center in the boxplot represents the medium value. Student’s t test with a two-sided model was used in this figure. g Genome browser view of promoter DHS, RNA expression, DNA methylation level (ML) and CpG density of WDR27 in humans (top) and rhesus monkeys (bottom). The number in parenthesis indicates the promoter CpG density per 100 bp.

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