The blue module, which was highly correlated with breast cancer grade and metastasis (Additional file 9: Fig. S5), encompassed most key breast cancer oncogenes and TSGs, including APOBEC3B, BARD1, BRCA1, BRCA2, BRIP1, CHEK2, DNMT1, EZH2, MAP 3 K13, NF2, POLQ, PPM1D, and TRIM24. Here, PPM1D is linked to breast cancer.