Fig. 1

DNA methylation level in the global genome and specific elements. A Flowchart of the experiment and data analysis. B Three-dimensional scatter plot of PCA showed the distribution of CVSs based on the DNA methylation pattern of all 200 bp bins (sample size: n = 22 and bin number: n = 684,403). The first three principal components of PCA were applied. C Scatter plot showed the distribution of the average DNA methylation value of each bin in both the AMA group and YMA group. The X-axis indicates the average methylation level of the AMA group, and the Y-axis denotes the average methylation level of the YMA group. Pearson correlation analysis was performed to calculate the correlation between the two groups (R = 1, P < 0.01). D Box and dot plot shows the distribution of the average DNA methylation levels of each sample. The P value between the two groups was determined using the Wilcoxon rank-sum test (P = 0.23). E Line charts presented the average DNA methylation level along the gene body, as well as 15 kilobases (kb) upstream of the transcription start site (TSS) and 15 kb downstream of the transcription end site (TES) of all genes. Each color refers to a specific sample. F Box and dot plot shows the distribution of the average DNA methylation levels of each sample for specific genome elements. P values between the two groups were determined using the Wilcoxon rank-sum test