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Fig. 1 | Breast Cancer Research

Fig. 1

From: Accelerated aging in normal breast tissue of women with breast cancer

Fig. 1

DNA methylation changes in normal breast epithelium. a Unsupervised hierarchical clustering of 29 purified human mammary epithelial (HMEC) samples based on 45,135 CpG sites with more than 100 sequencing reads in at least 75% of the samples. DNA methylation levels are shown as the blue-red gradient. b Flowchart of steps taken to find CpG sites associated with age. Starting with all CpG sites detected, sites with greater than 1% methylation were used for a permutation test using the Spearman correlation between DNA methylation and age. Ten thousand random permutations of the age of the patient samples were used to statistically analyze age-related DNA methylation sites. The age-dependent methylation changes were selected based on a cutoff of permutation empirical p value of (p < 0.05) and based on a Spearman correlation of r ≥ 0.3 (gain of methylation with age) and r ≤ −0.3 (loss of methylation with age). The numbers in each box indicate the number of DNA methylation sites. c Summary of odds ratios of the genomic region specificity of age-related hypermethylated (red) and hypomethylated (blue) sites compared to non-age-related sites. Red and blue dots represent the point estimates of the odds ratio for hypermethylation and hypomethylation, respectively, with lines representing the 95% confidence intervals around the estimates. A chi-square test was used to test for statistical significance for each comparison; p values for all comparisons were lower than 0.0001. Genomic regions are defined as follows: CGI (CpG island), nCGI (non-CpG island), pCGI (promoter CpG island), npCGI (non-promoter CpG island), pnCGI (promoter non-CpG island), and npnCGI (non-promoter non-CpG island)

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