Table 1. Antibodies that were significantly differentially expressed between the 2 clusters identified by k-means and hierarchical clustering analysis of the RPPA results.
| Antibody name | Protein name | Gene symbol | Adjusted Bonferroni p-value |
|---|---|---|---|
| Higher expression in inflammation and hormonal subtype | |||
| Caveolin 1 | Caveolin 1 | CAV1 | 3.05E-10 |
| Collagen VI | Collagen VI | COL6A1 | 1.29E-09 |
| stat3pS705 | stat3 phosphorylation at S705 | STAT3 | 3.02E-08 |
| MYH11 | MYH11 | MYH11 | 3.28E-06 |
| PTCH | Patche | PTCH1 | 6.58E-06 |
| ER | Estrogen receptor alpha | ESR1 | 4.89E-05 |
| JNKpT183/Y185 | JNK phosphorylation at T183/Y185 | MAPK8 | 0.000201828 |
| BADp542 | BAD phosphorylation at 542 | BAD | 0.000212416 |
| c-JUNpS73 | cjun N terminal kinase phosphorylation at S73 | JUN | 0.000986419 |
| AR | Androgen receptor | AR | 0.001376863 |
| CCND1 | Cyclin D1 | CCND1 | 0.002897264 |
| stat6pY641 | Stat6 phosphorylation at Y641 | STAT6 | 0.006211527 |
| MAPKp | MAPK phosphorylation | MAPK3 | 0.007085294 |
| Annexin.1 | Annexin A1 | ANXA1 | 0.009194289 |
| BCLpS70 | bcl2 phosphorylation at S70 | BCL2L1 | 0.026207531 |
| Gelsolin | Gelsolin | GSN | 0.028422688 |
| EGFRpY1068 | EGFR phosphorylation at Y1068 | EGFR | 0.029595161 |
| Higher expression in DNA damage-related subtype | |||
| 4EBP1 | 4E blinding protein1 | EIF4EBP1 | 4.49E-08 |
| CCNE1 | Cyclin E1 | CCNE1 | 9.18E-08 |
| CCNB1 | Cyclin B1 | CCNB1 | 2.55E-07 |
| PCNA | Proliferating cell nuclear antigen | PCNA | 5.72E-07 |
| S6 | S6 ribosomal protein | RPS6 | 7.82E-06 |
| Cleaved PARP | Cleaved PARP | PARP1 | 8.28E-06 |
| FANCE | Fanconi anemia, complementation group E | FANCE | 8.28E-06 |
| P70 S6 Kinase | p70 S6 Kinase | RPS6KB1 | 3.17E-05 |
| MILLT10 | MILLT10 | MLLT10 | 4.16E-05 |
| 4EBP1pT70 | 4EBP1 phosphorylation at T70 | EIF4EBP1 | 0.000141 |
| YB1 | Y-box binding protein 1 | YBX1 | 0.000274 |
| cJUN | cJUN | JUN | 0.001139 |
| AlB1 | Amplified in breast cancer 1 | A1B1 | 0.001443 |
| PSAT1 | PSAT1 | PSAT1 | 0.002198 |
| BRCA1 | BRCA1 | BRCA1 | 0.002525 |
| GSK3 | Glycogen synthase kinase 3 beta | GSK3A | 0.002525 |
| IGFR1 | Insulin-like growth factor receptor 1 | IGFR1 | 0.002525 |
| FANCA | Fanconi anemia, complementation group A | FANCA | 0.002525 |
| EN1 | Engrailed-1 | EN1 | 0.002644 |
| HER2pY1248 | HER2 phosphorylation at Y1248 | ERBB2 | 0.004761 |
| βCatenin | Beta catenin | CTNNB1 | 0.007731 |
| PAI1 | Plasminogen activator inhibitor-1 | SERPINE1 | 0.013501 |
| BIM | BIM | BCL2L11 | 0.013501 |
| CXXC6 | CXXC6 | TET1 | 0.021359 |
| Src | Src | SRC | 0.047705 |
Shown are antibodies that were expressed at higher levels in the inflammation and hormonal subtype compared with the DNA damage-related subtype (top) and vice versa (bottom). A nonparametric Kruskal-Wallis test was used to identify proteins that were significantly differentially expressed. Proteins with an adjusted p-value by the Bonferroni method of less than 0.05 were considered significant.