Fig. 2: Class-specific probe usage across functional genomic regions.
From: Explainable artificial intelligence of DNA methylation-based brain tumor diagnostics
a Plot shows the overall probe usage with probes ranked from the most to least used. Vertical lines indicate the fraction of the total usage of the first 10,000 and 25,000 probes. b Plot shows the cumulative probe usage for each tumor class. The probes are ranked by their usage. The vertical line indicates the first 10,000 probes. c Heatmap indicates the average usage of probes within CpG islands, Sea, Shelf, and Shore regions for each tumor class. Number of overlapping probes is indicated above. The color code indicates if probes are predominantly hypermethylated (red) or hypomethylated (blue). d Similar heatmap indicating the mean probe usage within annotated DHS and enhancers (overlapping CpG islands). DHS DNase I hypersensitive sites. e Similar heatmap indicating the mean probe usage within large-scale LADs and heterochromatic domains. LAD lamina associated domains. f Heatmaps show the probe usage in 250 bp windows surrounding the TSS of all annotated genes (5 kb up- and downstream). Heatmaps represent the total (left) or the average (right) probe usage. Histogram on top of the left heatmap indicates the number of microarray probes overlapping each window. TSS transcription start site. Source data are provided as a Source Data file.
