We observed a widely distributed protein complex similarity index (Simpson’s Index; SI) profile among the three cell lines (Supplementary Fig. 4a–c), revealing several highly conserved complexes including the well characterized anaphase promoting complex or cyclosome (APC/C)24,25 and human PAF1 complex (hPAF1c)26,27 (SI = 0.8–1.0, Supplementary Fig. 4d, e), as well as a considerable number of differential macromolecular assemblies (SI < 0.45) relevant to breast cancer cells. This evidence concerns the gene PAF1 and breast cancer.