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Fig. 1 | Genome Biology

Fig. 1

From: Distinct roles of DNMT1-dependent and DNMT1-independent methylation patterns in the genome of mouse embryonic stem cells

Fig. 1

CG density predetermines the magnitude of methylation reduction. a Methylation reduction in DNMT KO ES cells. Methylation rates were calculated as described in materials and methods and all CG sites with coverage >6 were used. b Methylation at promoter, gene body, and intergenic regions in the mouse genome. ce Correlation of DNA methylation with CG density. A two-dimensional density transformation based on kernel density estimates (KDE) was applied to reflect the relative number of CG sites that share similar methylation levels and CG density. The colors from dark blue to light blue, yellow, light red, and dark red, represent the relative number of CG sites, i.e., KDE density. The numbers of CG sites with enough coverage and Pearson correlation coefficients are shown. CG density is defined as the number of CG sites within a 600-bp window. Data in (ce) are from chromosome 3 only

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