As to DMFS, we concluded that most NEK genes were significantly correlated with the prognosis of breast cancer patients: NEK1 (HR = 0.81, 95% CI = 0.69~0.96, p = 0.049), NEK2 (HR = 1.89, 95% CI = 1.61~2.23, p = 7 × 10−15), NEK4 (HR = 0.82, 95% CI = 0.69~0.97, p = 0.023), NEK6 (HR = 1.49, 95% CI = 1.13~1.98, p = 0.0048), NEK8 (HR = 1.49, 95% CI = 1.1~2, p = 0.0087), NEK9 (HR = 0.64, 95% CI = 0.55~0.75, p = 0.049), NEK10 (H = 0.45, 95% CI = 0.32~0.62, p = 7 × 10−7), and NEK11 (HR = 0.74, 95% CI = 0.56~0.99, p = 0.042). Here, NEK2 is linked to breast cancer.