Fig. 1.

The DNA methylation landscape of CRC samples and cell lines. A Table indicating the datasets used in this study for the identification of CRC specific DMPs. B Violin plots depicting the overall 5mC estimates from the 450 K platform in control and CRC samples. Vertical lines indicate the median value for each of the above-mentioned distributions. C Principal component analysis for 413,756 CpG sites across all samples included in the DNA methylation study. Samples are coloured according to their clinical status (control/tumour) in their corresponding dataset. D Barplot indicating the number of common (dark-grey) and specific significantly hyper- or hypomethylated CpG sites as compared with healthy controls observed in the comparisons indicated (FDR < 0.05, mean β difference > 0.25). The inset illustrates the total number of hyper- and hypomethylated CpG sites observed in each separate condition. E Stacked barplots displaying the relative frequency of significant common hyper- or hypomethylated CpGs in relation to their CpG context (top) or CpG location (bottom). The background distribution of the 450 K platform is included for interpretation purposes. F Bubble plots showing enrichment of TFBS in the context of common hyper- (top) or hypomethylated (bottom) CpG sites as determined by the information obtained from the GTRD database. Dot size denotes statistical significance (−log10 adjusted p value) of a particular TFBS dataset as compared with the background distribution of the 450 K platform. G Heatmaps illustrating histone mark enrichment analyses of common hyper- and hypomethylated CpGs. Colour scales represent the odds ratio obtained across 6 common histone modifications from the NIH Roadmap Epigenome consortium as compared with the background distribution of the 450 K platform. The legend indicates the tissue types used for these comparisons. H Same as G, but displaying chromatin state enrichment analyses across 18 chromatin states obtained from the NIH Roadmap Epigenome consortium