Fig. 3: Differential expression analysis reveals significantly higher mRNA expression of cholangiocyte-associated genes in KRAS wildtype tumors.

a Volcano plot showing mRNA-based differential expression analysis (DEA; based on two-tailed Wald tests followed by Benjamini–Hochberg multiple test correction) results between KRAS wildtype (n = 9) and mutant (n = 54) tumors. Each point represents a gene, and genes are colored based on up (orange) and down (blue) regulation in KRAS wildtype versus mutant groups. b Bar plots demonstrating results of enrichment analysis (one-tailed hypergeometric tests; Benjamini–Hochberg multiple test correction) performed on up (orange; upper) and down (blue; lower) regulated genes. Genes upregulated in KRAS wildtype tumors are significantly enriched for genes known to be uniquely expressed in cholangiocytes. c Donut plots showing the distribution of Moffitt subtype calls across KRAS wildtype (top) and mutant (bottom) groups. Two-tailed Fisher’s exact test p value shown. d Box plots comparing median mRNA expression levels of Moffitt basal-like (left) and classical (right) genes across KRAS wildtype and mutant groups, stratified by Moffitt subtype. Left to right: KRAS mutant basal-like samples (n = 15), KRAS mutant classical samples (n = 32), KRAS wildtype classical samples (n = 9). Box plots indicate median (central line), 25–75% IQR (bounds of box), and whiskers extend from box bounds to the largest value no further than 1.5 times the IQR. Two-tailed Wilcoxon mean rank-sum p values are shown. Source data are provided as a Source Data file.