Figure 1
Flowchart and overview of DMRforPairs results of the Illumina data. (A) The subsequent steps of recoding probe classes, identifying regions, quantifying and testing methylation differences and exporting the results are described in detail in the main text. Briefly, 473,151 probes remained after quality control. Subsequently, probes not associated to any of the 11 classes or not included in any of the regions are discarded. 145,537 probes (35%) were included in 29,404 potential regions of interest. Finally, these were assessed for methylation differences. (B) Number of regions identified in the various pairwise analyses. * = relevant indicates regions with |ΔM| > 1.4, ** = significant indicates relevant + padjusted ≤ 0.05. “repl.” indicates technical replicates. (C,D) The density plots illustrate the distribution of all/the relevant/the significant regions with regard to the number of probes in each region. Only the comparisons of the two cancer cell lines (C) and the pair of lymphoblastoid cell lines (D) are depicted as the technical replicates yielded no significant DMRs.