Figure 4. CpGs in ER binding sites tend to have lower methylation levels in ER+ breast samples. (A) The fraction of CpGs with significant differential methylation levels between ER+ and ER- samples. Note that CpGs in ER binding regions tend to have higher methylation levels in ER- samples, while CpGs not in ER binding regions tend to have higher methylation levels in ER+ samples. Four different thresholds are used to determine differential methylated CpGs. (B) Distribution of t-scores (ER+ vs. ER-) of methylation levels for CpGs. Genes are divided into 3 classes based on their expression levels in ER+ vs. ER- samples: ER+ > ER- (red), ER+ < ER- (green), and ER+ = ER- (white). Distributions of CpGs associated with the three gene classes are shown separately. (C) CpGs in ER binding regions tend to have lower methylation levels in ER+ samples (lower t-scores) compared with thosenot in ER binding regions, which is the case for CpGs associated with all three gene classes.