Fig. 3

Overview of DMPs, DMRs, DEGs, and CNAs identified using the training cohort, highlighting the homogeneity of EC with respect to gene expression and DNA methylation, as well as the hypermethylation of CCC compared to the other histotypes. A DEGs/DMRs for each unique histotype contrast, B histotype-specific DEGs and histotype-specific DMRs, C DMP-site location type for unique histotype contrasts (promoter = 2000 bp upstream of TSS, 200 bp downstream of TSS), D DMP/DEG overlaps for each unique histotype contrast. Numbers above the bars represent the number of DMPs located in the gene body, non-coding regions, or promoter, while numbers below the contrast names indicate the total number of DMPs for each contrast (row 1) and DMP methylation type (Hypermethylated (δ β > 0.2)/Hypomethylated (δ β < − 0.2); row 2). E GISTIC CNA analysis results for HGSC. Red peaks represent CNA gains, blue peaks represent CNA losses (labeled with cytoband name). CCC: Clear cell carcinoma, EC: Endometrioid carcinoma, HGSC: High-grade serous carcinoma, MC: Mucinous carcinoma, G-score: Score based on the aberration amplitude relative to its frequency across samples, as used by GISTIC. DEG: Differentially expressed gene, DMP: Differentially methylated probe, DMR: Differentially methylated region, CNA: Copy number aberration, HSGs/HS-DMRs: DEGs/DMRs found in all histotype comparisons, using the same histotype as reference