Table 3.
Eighty-two protein–mRNA correlation coefficients (rho) and corresponding p values
| Protein | rho (128 human breast tumors) |
p value (128 human breast tumors) |
rho (52 breast cancer cell lines) |
p value (52 breast cancer cell lines) |
|---|---|---|---|---|
| 4EBP1 | 0.51 | 5.9E-12 | 0.688 | 0.000000875 |
| 4EBP1p37 | 0.43 | 0.000000025 | 0.736 | 0.000000141 |
| AcCoA | 0.37 | 0.0000022 | 0.6 | 0.0000302 |
| AcCoAp | 0.32 | 0.000042 | 0.594 | 0.0000385 |
| Akt | 0.33 | 0.000028 | 0.592 | 0.0000415 |
| Aktp308 | 0.15 | 0.0503 | −0.262 | 0.09 |
| Aktp473 | 0.14 | 0.07 | −0.186 | 0.231 |
| AMPK | 0.29 | 0.0002 | 0.0314 | 0.841 |
| AMPKp | 0.17 | 0.03 | −0.153 | 0.328 |
| B catenin | 0.2 | 0.03 | 0.134 | 0.389 |
| bcl2 | −0.03 | 0.72 | 0.211 | 0.174 |
| BRCA1 | 0.24 | 0.002 | 0.322 | 0.0355 |
| Caveolin 1 | 0.47 | 3.2E-10 | 0.845 | 0 |
| CCNB1 | 0.68 | 0 | 0.573 | 0.0000791 |
| CCND1 | 0.52 | 1.5E-12 | 0.84 | 1.87E-12 |
| CCNE1 | 0.59 | 2.2E-16 | N/A | |
| CD31 | N/A | N/A | 0.151 | 0.332 |
| CDK4 | 0.13 | 0.09 | 0.39 | 0.0102 |
| Cjun | 0.14 | 0.08 | 0.491 | 0.000955 |
| Ckit | 0.68 | 0 | 0.36 | 0.0182 |
| cleaved caspase 7 | 0.14 | 0.08 | 0.159 | 0.308 |
| cleaved PARP | 0.08 | 0.15 | −0.262 | 0.0896 |
| Cmyc | 0.41 | 0.000000078 | 0.52 | 0.000419 |
| Collagen VI | 0.09 | 0.28 | 0.394 | 0.00933 |
| COX2 | 0.34 | 0.000013 | N/A | N/A |
| E cadherin | 0.11 | 0.18 | 0.811 | 0 |
| EGFR | 0.42 | 0.000000038 | 0.576 | 0.0000725 |
| EGFRp1068 | 0.01 | 0.85 | 0.0107 | 0.945 |
| EGFRp922 | −0.01 | 0.9 | 0.212 | 0.173 |
| ER | 0.85 | 0 | 0.621 | 0.0000137 |
| ERK2 | −0.04 | 0.66 | 0.381 | 0.0121 |
| ERp118 | 0.35 | 0.0000084 | N/A | N/A |
| ERp167 | 0.09 | 0.24 | N/A | N/A |
| GSK3 | 0.08 | 0.34 | 0.37 | 0.0151 |
| GSK3p21.9 | −0.08 | 0.32 | 0.0474 | 0.762 |
| HER2 | 0.75 | 0 | 0.707 | 0.000000413 |
| HER2p1248 | 0.72 | 0 | N/A | N/A |
| IGF1R | 0.65 | 0 | 0.522 | 0.000403 |
| IGFRp | 0.04 | 0.65 | N/A | N/A |
| JNK | 0.04 | 0.59 | 0.0282 | 0.857 |
| JNKp | −0.08 | 0.31 | −0.0914 | 0.559 |
| MAPKp | −0.1 | 0.22 | −0.461 | 0.00187 |
| MEK1 | 0.2 | 0.01 | 0.646 | 0.00000509 |
| MEK12p | −0.08 | 0.33 | 0.301 | 0.0501 |
| mTOR | 0.04 | 0.64 | 0.486 | 0.0011 |
| p110alpha | 0.13 | 0.11 | 0.326 | 0.0336 |
| p21 | 0.07 | 0.36 | 0.156 | 0.318 |
| p27 | 0.1 | 0.22 | 0.0689 | 0.66 |
| p38 | 0.001 | 0.99 | 0.194 | 0.213 |
| p38p180_2 | −0.03 | 0.71 | −0.0741 | 0.636 |
| p53 | 0.15 | 0.06 | 0.716 | 0.00000029 |
| p7056 Kinase | 0.54 | 1.4E–13 | 0.672 | 0.00000171 |
| p70S6Kp389 | −0.1 | 0.23 | 0.291 | 0.0584 |
| PAI1 | 0.06 | 0.46 | 0.643 | 0.00000579 |
| pcmyc | 0.23 | 0.004 | 0.418 | 0.00566 |
| PDK1 | −0.13 | 0.11 | 0.0136 | 0.931 |
| PDK1p241 | −0.08 | 0.34 | −0.0637 | 0.684 |
| PKCalpha | 0.08 | 0.31 | 0.812 | 0 |
| PKCaphap657 | 0.03 | 0.73 | 0.808 | 0 |
| pmTOR | 0.04 | 0.61 | 0.357 | 0.0189 |
| PR | 0.74 | 0 | 0.634 | 0.00000841 |
| PTEN | 0.22 | 0.005 | 0.642 | 0.00000601 |
| Rab25 | 0.25 | 0.001 | 0.755 | 6.63E-08 |
| Rb | 0.15 | 0.06 | 0.56 | 0.000123 |
| Rbp | 0.05 | 0.5 | 0.648 | 0.00000469 |
| S6 | −0.08 | 0.34 | 0.286 | 0.0632 |
| S6p235–236 | −0.13 | 0.11 | 0.0521 | 0.739 |
| S6p240_4 | −0.12 | 0.13 | 0.00211 | 0.989 |
| SGK | 0.56 | 3.8E-14 | N/A | N/A |
| SGKp | 0.16 | 0.05 | N/A | N/A |
| src | −0.04 | 0.6 | 0.548 | 0.000178 |
| srcp416 | 0.13 | 0.11 | 0.361 | 0.0178 |
| srcp527 | 0.17 | 0.03 | 0.326 | 0.0333 |
| stat3 | 0.22 | 0.004 | 0.416 | 0.00581 |
| stat3p705 | 0.03 | 0.73 | 0.299 | 0.0515 |
| stat3p727 | −0.02 | 0.76 | 0.677 | 0.00000061 |
| stat6p641 | 0.09 | 0.26 | 0.0177 | 0.91 |
| stathmin | 0.13 | 0.1 | N/A | N/A |
| TSC2 | 0.11 | 0.17 | 0.317 | 0.0389 |
| TSC2p | 0.003 | 0.97 | 0.114 | 0.467 |
| VEGFR2 | 0.15 | 0.06 | 0.0375 | 0.811 |
| XIAP | N/A | N/A | N/A | N/A |
Proteins were quantified with reverse phase protein arrays (RPPA). Clearly, mRNA levels (from AB arrays) frequently do not correlate well with protein function (e.g., phosphorylation, cleavage) in cell lines or human tumors. It is also notable that protein–mRNA correlations are not consistent between human breast tumors and breast cancer cell lines for certain proteins. This may be related in part to the presence of stroma in human tumors but not in cell lines (e.g., with collagen VI and caveolin 1). In addition, the rho value for the PTEN protein–mRNA correlation is clearly poorer in human tumors than in cell lines, possibly related in part to the presence of relatively high levels of PTEN in endothelial cells in human tumors