SH3KBP1 and breast cancer: Protein pairs with strongly altered PQRs in basal cell lines (Supplementary Table 2) included components of the CIN85 complex, which is important for cellular invasion and associates with aggressive BC phenotypes17 and were more strongly enriched in cancer related roles when compared to significant hits from a standard protein-level comparison (KEGG ‘Pathways in cancer’ was the most significantly enriched term, Benjamini–Hochberg (BH)-adjusted P value < 3.1 × 10−5, Fisher’s exact test; Supplementary Note 1 and Supplementary Fig. 3a–c).