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Fig. 3 | Genome Biology

Fig. 3

From: epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data

Fig. 3

(See figure on previous page.) Epi-allelic profiling near the GNAS locus. Epi-allelic haplotypes of four samples in a 100-kb region near the GNAS locus with three known regions of ASM (R1, R2, and R3; vertical dashed lines [9]). a WA9. b Colon normal A. c Colon normal B. d Colon tumor B. e CpG site density map (red) and known genes (blue). In each of ad, the horizontal bars are inferred epi-allelic haplotypes and the bar thickness represents the average number of reads per position. The degree of methylation is shown in two ways. Firstly, the average methylation level of three consecutive CpGs in a chain is shown in color, where green is for fully methylated CpG sites, purple for fully unmethylated, and white for neither. The haplotype overall methylation level is the average methylation level of all CpGs in the whole chain. In all three regions, we clearly see ASM. The stem cell sample (WA9) shows only one (unmethylated) epi-allele in R3. To the immediate right of R3, all four samples show consistently one unmethylated epi-allele. WA9 and colon normal A are fully methylated outside the ASM regions, whereas a general loss of methylation can be seen in colon tumor B and partly in colon normal B, which is tissue adjacent to the tumor. The density of CpGs is an important determinant of the length of the haplotypes. When the density is low, haplotypes become shorter and more fragmented. ASM allele-specific methylation

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