Key genes of SOX2, KIT, PRSS56, WNT9A, SLC4A4, PRRG4, PANX2, PIR, RASSF8, MFSD4A, INS, RNF39, IL1R2, CST1, and PPP3CA might be potential prognostic markers for CCA, of which RNF39 and PRSS56 also showed significant correlation with clinical stage. This evidence concerns the gene RNF39 and cholangiocarcinoma.