Among 6 transcription factors enriched, PAX2, RFX1 and MSX1 showed stronger correlation than others, while expression profile and survival analyses revealed MSX1 significantly downregulated in breast cancer comparing to normal samples (Fig. 5b, P < 0.001) and high expression of MSX1 indicating better survival outcomes of breast cancer regarding both RFS [HR = 0 67 (0 6–0 75), logrank P = 2.1e−11] and OS [HR = 0 76 (0 58–0 99), logrank P = 0 038] (Fig. 5c). The gene discussed is MSX1; the disease is breast cancer.