High-throughput methylation comparison of resting B lymphocytes and matching lymphoblastoid cells. (a) Heatmaps including the data for the six RBL/LCL pairs of samples showing significant differential methylation. The left panel shows all the genes showing a FDR < 0.05. Only those genes with a FC > 2 were selected (right panel). Data from the Illumina array were normalized as xi = xi - row.mean[i])/(0.333 × row.sd[i]). A scale is shown at the bottom, whereby positive (red) and negative (blue) values correspond, respectively, to higher and lower than average methylation status. M, male; F, female. (b) Scatterplots showing methylation profiles of matching RBL/LCL pairs. Genes with significant differences (FC > 2, FDR < 0.05) in averaged results from six samples are highlighted in red. Six panels are shown: top left, mean of six experiments/pairs of samples; middle left, male samples; bottom left, female samples; right panels, three individual RBL/LCL comparisons. (c) Band patterning corresponding to the analysis of unmethylated/methylated Alu (AUMA) repeats. Four RBL/LCL (M, male; F, female) pairs are shown. To illustrate the sensitivity toward DNA methylation changes, a B cell sample is compared with the same sample following limited treatment with SssI DNA methyltransferase. (d) Comparison of the methylation levels in RBLs and LCLs for all the CpGs represented in the 27k bead array and CpGs that undergo hypomethylation in this process. Box and whisker plots are presented, where the bottom and top of the box are the 25th and 75th percentile and the bar near the middle is the 50th percentile (the median). (e) Gene Ontology (GO) analysis of hypomethylated genes during EBV-mediated RBL to LCL conversion.
Hernando et al. Genome Biology 2013 14:R3 doi:10.1186/gb-2013-14-1-r3