Figure 3. Distribution of CpGs with differential methylation levels between ER+ and ER- breast samples. (A) Examples- CpG may have higher methylation in ER+ (cg05846044) or ER- (cg05859267). (B) Relationship between differential methylation and CpG position relative to transcription start site (from –1500 upstream to 4500 downstream of TSS). (C) Distribution of CpGs with significant (P < 1e-6) differential methylation between ER+ and ER- samples. (D) Fraction of CpGs with significant differential methylation levels at different positions. The fraction is the ratio of the number of significant CpGs to the total number of CpGs in a DNA window. CpGs with significantly higher methylation levels in ER+ (red) and in ER- (green) samples are examined separately. The relative frequency of significantly differentially methylated CpGs increases as the distance from TSS increases.