<p>DMPs were classified according to their functional genomic location (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122146#pone.0122146.g001" target="_blank">Fig 1C</a>). Statistical over- and underrepresentation of probes in certain categories provides clues to differences between GCT subtypes in regarding function of methylation. Enrichment was assessed by comparing the number of probes in a functional category in a subset of DMPs with the that in the total dataset (Fisher’s Exact test, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122146#sec011" target="_blank">Materials & Methods</a> section). Results are shown for four pairwise (A vs B) comparisons of histological subtypes: <b>(A)</b> SE/DG versus EC/mNS; <b>(B)</b> SE/DG vs type I TE; <b>(C)</b> EC/MNS vs type I TE and <b>(D)</b> SE/DG vs SS. <b>(LEFT)</b> The number (n) of DMPs identified in either the DMP[<u><b>A</b></u>-B] (hypermethylated in A, green) or DMP[A-<u><b>B</b></u>] (hypermethylated in B, red) group. <b>(MIDDLE/RIGHT)</b> Functional enrichment in the DMP[<u><b>A</b></u>-B] and DMP[A-<u><b>B</b></u>] group respectively. X-axis: positive numbers indicate a significant overrepresentation of DMPs in a functional category compared to non-DMPs while negative numbers indicate a significant underrepresentation. Depicted is the log2 ratio of (1) the % of either DMP group assigned to a category and (2) the % of non-DMPs assigned to that category. Only significant enrichments are depicted (2-sided Fisher’s Exact test, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122146#sec011" target="_blank">Methods</a> section for Bonferroni corrected α threshold). DMPs[se/dgvs<u><b>SS</b></u>].IMPR_P1500 showed significant underrepresentation, but could not be plotted on log scale (0 probes in DMP group). Details of calculations and raw counts and percentages are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122146#pone.0122146.s008" target="_blank">S2 Table</a>. Y-axis: functional categories as specified in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122146#pone.0122146.g001" target="_blank">Fig 1C</a>.</p
