<p>Visualization of the methylation percentage at specific loci is used to zoom in on a predefined region and investigate local methylation differences between GCT subtypes. <b>(A) <i>DMRT3</i>, (B) <i>SOX2</i>, (C) <i>POU5F1</i> (<i>OCT3/4</i>), (D) <i>TEX14</i>. (Visualizations)</b> From top to bottom the following is depicted: (1) Four-color heat map indicating methylation % for each individual probe in the depicted region. For the sample groups specified on the left the median methylation % is shown. (2) Position of all probes in the region of interest (ROI) is annotated as black rectangles. (3) HMM segments are displayed as grey boxes spanning the segment’s width and grouped per state. Numbers indicate the state of each (group of) segment(s). (5) GC% was obtained from the UCSC genome browser database (gc5Base table). (6) Transcripts overlapping with the ROI are plotted at the bottom. Plot generated using the Gviz package. Abbreviations of histological subtypes are explained in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122146#pone.0122146.g001" target="_blank">Fig 1A</a>. Please note that the TE group is subdivided based on gender and localization: I = type I; II = type II/formally part of the mNS group, s = sacrum, t = testis, o = ovary, m = male, f = female. CL indicates cell lines.</p
