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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
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Clinical Proteomics

ISSN: 1559-0275