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Protein quantities for the two epigenetic protein pairs with the strongest signal are shown (ranked first and third in the overall AlteredPQR scores; all significant pairs are listed in Supplementary Table 3). The two pairs include DNA (cytosine-5)-methyltransferases 3A and 1 (DNMT3A and DNMT1) with their interacting proteins sirtuin 1 (SIRT1) and zinc finger and BTB domain containing 17 (ZBTB17). For both of these pairs, altered PQR is driven by expression changes of both proteins in the complex and marked with a strong shift in the relative protein quantities. Protein quantities measured in luminal A (LumA) BC samples (left, green) and protein quantities measured in all other BC samples (right, brown) are shown.
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