While in silico studies revealed CASP3 and BCL-2 among top 10 hub genes and pathway analysis demonstrated apoptosis as relevant, molecular changes in CASP3 and BCL-2 were insignificant, suggesting that paeonol’s alleviating effects against BPH progression are mainly associated with suppression of proliferation rather than enhancement of apoptosis. This evidence concerns the gene BCL2 and benign prostatic hyperplasia.