Often, common driver genes were identified by both versions of the pipeline, e.g., GATA3 for breast cancer (BRCA), but in many cases the knowledge-guided version reported known drivers that were missed by the standard pipeline, e.g., FOXA1 for BRCA, NRAS and KRAS for acute myeloid leukemia (AML), and CDH1, CTNNB1, and EGFR for HNSCC. Here, FOXA1 is linked to breast cancer.