Pathway enrichment revealed that there were 11 significant pathways were enriched in Ph + B-ALLIKZF1+/DDX41dm compared to Ph + B-ALLIKZF1+/DDX41−, and one of the most significant pathways was transcriptional misregulation in cancer (hs05202) genes (p < 0.001), which contained common cancer-related genes, such as HIST1H3G, SUPT3H, HIST1H3I, BCL2L1, WT1, HIST1H3A, CD86, CDK14, CSF1R, and PROM1. Detailed analysis of the dysregulated genes revealed several candidates linked to relevant signaling pathways in Ph + B-ALLIKZF1+/DDX41dm, which may represent pathogenetically relevant genes. Here, SUPT3H is linked to cancer.