Figure 3

Analysis of LINE-1 methylation by massive parallel sequencing. Summary heat maps of the massive parallel sequencing analysis of the methylation of five specific autosomal (L1C2, L1C6, L1C10, L1C11, L1C20) and six specific X-linked (L1X1, L1X3, L1X4, L1X5, L1X6, L1X8) LINE-1 loci of four selected paired tumor and neighboring non-tumor tissue samples. Each heat map corresponds to the methylation patterns of one locus from one sample. Every line in the heat map corresponds to a sequence originating from an individual sequence read; each column represents a CpG site at the promoter of the specific LINE-1. Methylated CpGs are indicated in blue, unmethylated CpGs are marked in yellow. Below each heat map average methylation across all individual sequences and all CpG sites is given followed by the average methylation entropy. The number of sequences from which the heat map was constructed is indicated at the upper left side of the heat map. Horizontal red bars in the heat maps represent the regions studied by pyrosequencing. The graphs above each heat map represent the methylation average at every CpG site of the tumor tissue (red) and the morphologically normal tissue (green); p values for differences of methylation were calculated by Wilcoxon test. The diagrams at the top show the entropy (tumor in red, normal in green) in sliding windows of four CpGs with the corresponding p values (Wilcoxon test). Entr.: entropy; Meth.: methylation.