Additional file 4: Figure S3. of Epigenetic silencing of CREB3L1 by DNA methylation is associated with high-grade metastatic breast cancers with poor prognosis and is prevalent in triple negative breast cancers

Analysis of CREB3L1 DNA methylation for 40 breast cancer cell lines. a Schematic diagram of the CREB3L1 promoter region. The 5′ untranslated region (5′UTR; black box), the coding region (gray box) and CpG island (hatched box) and the exon and intron boundaries are indicated. b Sixty CpG sites were evaluated for their methylation between −429 and +259, relative to the translational start site. The frequency of methylation at each site is indicated. Samples with less methylation, invariably had the more 3′ CpG sites methylated preferentially (i.e., 259 and 238) and as more methylation was observed additional CpG sites were methylated towards the 5′ end (as evident in Additional file 5: Table S2). c Examples of the scoring system used for methylation. Predominantly methylated sites had a majority of C residues protected from sodium bisulfite conversion and were assigned a value of 2. Somewhat methylated sites had protected C nucleotides above background levels, but less than the predominant T at the same site, and were assigned a value of 1. Unmethylated CpG sites were scored as 0. (PDF 149 kb)