Fig. 4: shinyMNP interface and illustrative class-specific genes.
From: Explainable artificial intelligence of DNA methylation-based brain tumor diagnostics
a Screenshot of the shinyMNP web application shows a network illustration of the top five probe-associated genes for each tumor class. Black and colored nodes represent genes and tumor classes, respectively. Width of edges indicate the total probe usage for each gene. Some genes may be associated with multiple tumor classes. b Genome plot of a 12 kb region surrounding the SHPRH promoter highlights probes that are specifically hypermethylated in ETMR. Red indicates methylated probes (beta-value of 1), blue indicates unmethylated probes (beta-value of 0) for each tumor class. Total probe usage and exact location of probes are indicated on top. SHPRH is silenced in ETMR. c Genome plot of the PWWP3A gene highlighting pronounced hypomethylation across the entire gene body specific to HGNET_MN1. PWWP3A is highly expressed in this tumor class. d Genome plot of the TBX19 gene showing hypomethylation of the promoter specific in PITAD_ACTH. e Genome plot of the RET oncogene showing hypermethylation of a small region near the fourth exon specific to HGNET_BCOR. RET is highly expressed in this tumor class.
