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Fig. 3 | Breast Cancer Research

Fig. 3

From: An integrated genomics analysis of epigenetic subtypes in human breast tumors links DNA methylation patterns to chromatin states in normal mammary cells

Fig. 3

DNA methylation patterns in breast cancer. a Distribution of average β values for all CpG sites on the platform stratified by Illumina gene location across the 188 breast tumors in the discovery cohort. TSS1500 = 1500 to 201 bp upstream of transcription start, TSS200 = 200 bp to transcription start site, Body = gene body, UTR untranslated region. b A total of 324,991 CpG sites mapped to a unique gene in the validation gene expression data (All). Of these, 35,329 CpG sites showed a Pearson correlation greater than 0.2 (Positive) and 48,593 CpG sites showed a Pearson correlation less than −0.2 (Negative) between expression and methylation levels in the validation data. For a given set of CpG sites (All/Positive/Negative), a bar indicates the fraction of CpG sites assigned to the respective annotation. c Of all CpG sites on the platform (All), 1016 were identified as methylated in breast cancer (Methylated) and 1092 as unmethylated in breast cancer (Unmethylated). For a given set of CpG sites (All/Methylated/Unmethylated), a bar indicates the fraction of CpG sites assigned to the respective Illumina CpG island annotations. d For a given set of CpG sites (All/Methylated/Unmethylated), a bar indicates the fraction of CpG sites assigned to the respective chromatin state in human embryonic stem cells (H1hESC; left) and human mammary epithelial cells (HMEC; right). CNV copy number variation

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