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Table 3 Eighty-two protein–mRNA correlation coefficients (rho) and corresponding p values

From: A Technical Assessment of the Utility of Reverse Phase Protein Arrays for the Study of the Functional Proteome in Non-microdissected Human Breast Cancers

Protein rho (128 human breast tumors) p value (128 human breast tumors) rho (52 breast cancercell 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
  1. 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