Fig. 2

DEG comparisons and the identification of histotype-specific biomarkers in advanced-stage EOC. (A) UpSet plot illustrating the overlap of DEGs across 21 directional histotype comparisons, each defined by selecting the histotype with the larger sample size as reference. Left-side bars indicate the total number of DEGs per comparison, while top bars (Intersection Size) represent the number of DEGs shared across one or more comparisons. Intersections are ordered by decreasing frequency, revealing that most DEGs are unique to individual comparisons, with limited transcriptomic overlap between histotypes. (B) Bar plot showing the number of upregulated and downregulated DEGs for six directional comparisons involving the four main malignant histotypes (HGSC, CCC, MC, and EC). DEG counts ranged from 321 (EC vs. HGSC) to 7,716 (MC vs. HGSC). The proportion of upregulated DEGs ranged from 40% (EC vs. CCC) to 91% (EC vs. HGSC), with most contrasts exhibiting a relatively balanced distribution (~ 40–60%). (C-F) Venn diagrams showing DEG overlap and histotype-specific candidate biomarkers for (C) HGSC, (D) CCC, (E) MC, and (F) EC. These gene sets represent subtype-enriched transcriptomic signatures with potential diagnostic and stratification value in advanced-stage EOC. Abbreviations: BOT: borderline tumor, CCC: clear cell carcinoma, DEG: differentially expressed gene/s, EC: endometrioid carcinoma, HGSC: high-grade serous carcinoma, LGSC: low-grade serous carcinoma, MC: mucinous carcinoma.