Fig. 1.
CpG methylation over the promoter region ALKBH2 and ALKBH3 in breast cancers and normal breast tissue samples. a CpG methylation states obtained from GSE69914 over ALKBH2 (upper panel) and ALKBH3 (lower panel) in normal breast tissue samples and breast cancers in black and red, respectively. The y-axis represents β (beta)-values (reflecting the degree of 5-cytosine methylation) for CpG’s included on the Infinium arrays located within or proximal to the promoter region for ALKBH2 and ALKBH3 arranged on the x-axis according to nucleotide position. The dashed lines (in black) represent the upper and lower 99% confidence intervals for the distribution of β-values in normal breast tissue samples – thus displaying the “normal range” for each of the CpGs analysed. Differentially methylated CpGs between breast cancers and normal breast tissues are indicated by blue asterisk marks taking into account correction for multiple hypothesis testing including all CpGs represented on the 450 K array (Padj < 0.001). FANTOM5 regions for ALKBH2 and ALKBH3 are shown as arrows indicating transcription start sites (TSS) where p1 represents the major TSS (while p2 and p3 are less prominently used as TSS). Additionally, the location of UCSC defined CpG islands (CGI; strikethrough patterned boxes) and the 1st Exon for each of the two genes are labelled. UCSC defined CpG islands from the UCSC genome table browser. b Left panel; ALKBH3 mRNA expression levels by RNA sequencing (RNAseq) obtained from the TCGA dataset analysed with respect to normal breast tissue samples compared with breast cancers. These differences reflect generally lowered expression levels in breast cancers compared with normal breast tissue samples. The P-value indicated in the upper-left corner was derived from Wilcoxon’s hypothesis testing after adjusting for multiple hypotheses accounting for >20 thousand protein-coding genes represented in the RNAseq dataset (Padj = 0.018). The right panel displays the topmost significant CpG (ranked according to the adjusted P-value), i.e. cg12046254, illustrating the relation between ALKBH3 mRNA expression (y-axis) and CpG promoter methylation (x-axis). Again, the dashed lines (in black) represent the lower and upper 99% confidence limits for the normal breast tissue samples – reflecting the “normal range” of 5-methylcytosine levels for this particular CpG (cg12046254). The P-value indicated in the top-right corner, based on Spearman’s rho correlation analysis, was highly significant even after adjustment for multiple hypothesis testing