In breast cancer, our framework identified top gene candidates such as FOXC1, PRR15, and PRKCQ, along with key epigenetic (e.g., probes in BCL9 and SFT2D2, associated with breast cancer prognosis) and miRNA features, such as miR-584–5p and let-7c-5p, that have documented roles in breast tumor progression. This evidence concerns the gene FOXC1 and breast cancer.