Table 1. Survival-associated proteins and correlation with mRNA levels.
| Gene name* | Protein spot no. | Cox's P value† | Coefficient β† | Protein name | Estimated protein MW/PI | Native protein MW/PI | Identified protein isoform | Protein function | mRNA_UM Cox's P value‡ | mRNA_HV Cox's P value§ | Protein-mRNA r¶ |
|---|---|---|---|---|---|---|---|---|---|---|---|
| GRP78 | 152 | 0.020 | −0.49 | Glucose-regulated protein 78 | 72.1/5.0 | 72.3/5.1 | Native | Chaperone | 0.790 | 0.573 | −0.06 |
| PLCB3 | 1463 | <0.001 | 0.43 | Phospholipase C-β-3 | 10.9/7.9 | 138.8/5.7 | Degradation | Hydrolase | 0.426 | 0.105 | −0.15 |
| ATP5D | 1354 | 0.027 | −0.40 | FIFO-type ATP synthase subunit d | 18/5.4 | 17.5/5.4 | Native | Hydrolase | 0.403 | 0.327 | 0.09 |
| PGAM1 | 1160 | <0.001 | 0.72 | Phosphoglycerate mutase | 28.8/7.0 | 28.8/6.7 | Native | Hydrolase | 0.140 | <0.001 | 0.20 |
| EPHX1 | 891 | 0.022 | −0.46 | Microsomal epoxide hydrolase | 34.2/5.3 | 52.9/6.8 | Degradation | Hydrolase | 0.622 | 0.026 | −0.06 |
| TPI | 1204 | 0.042 | −0.38 | Triosephosphate isomerase | 26.3/6.5 | 26.7/6.5 | Native | Isomerase | 0.020 | 0.002 | 0.02 |
| ENO1B | 627 | 0.043 | 0.32 | α enolase, lung specific | 49.4/5.8 | 49.5/5.8 | Native | Lyase | 0.722 | 0.979 | 0.01 |
| SOD2 | 1328 | 0.003 | 0.59 | Superoxide dismutase(MN), mitochondria | 24.7/7.6 | 24.7/7.8 | Native | Oxidoreductase | 0.239 | 0.519 | 0.18 |
| P4HB | 320 | 0.009 | 0.42 | PDI (proly-4-OH-B) | 57.8/4.1 | 57.1/4.8 | Phosphorylation | Oxidoreductase | 0.606 | 0.132 | 0.00 |
| PDIR | 513 | 0.021 | 0.41 | Protein disulfide isomerase related A5 | 48.4/4.7 | 59.6/8.1 | Degradation | Oxidoreductase | 0.740 | 0.671 | −0.03 |
| GSTP1 | 1298 | 0.022 | 0.40 | Glutathione S-transferase π | 23.7/5.4 | 23.4/5.4 | Native | Transferase | 0.047 | 0.069 | 0.18 |
| HPRT | 1205 | 0.016 | 0.28 | HG phosphoribosyltransferase | 24.8/6.2 | 24.6/6.2 | Native | Transferase | 0.518 | <0.001 | 0.16 |
| PGK1 | 826 | 0.007 | 0.45 | Phosphoglycerate kinase 1 | 41.7/6.3 | 44.6/8.3 | Phosphorylation | Transferase | 0.018 | <0.001 | 0.37 |
| PKM2 | 468 | 0.018 | 0.35 | Pyruvate kinase, M2 | 57.8/6.5 | 57.9/7.9 | Phosphorylation | Transferase | 0.210 | 0.083 | 0.12 |
| GRK4 | 477 | 0.001 | −0.62 | G protein-coupled receptor kinase 4 | 66.9/7.9 | 66.9/7.8 | Native | Transferase | 0.451 | 0.149 | 0.19 |
| RAB14 | 1262 | 0.025 | −0.50 | Ras-associated protein RAB14 | 23.7/6.1 | 23.9/5.9 | Native | GTP-binding protein | NA | 0.176 | NA |
| FGF4 | 1331 | 0.021 | 0.39 | Fibroblast growth factor 4 (precursor) | 22/7 | 22.1/9.7 | Phosphorylation | Growth factor | 0.119 | 0.364 | 0.15 |
| MYCN | 1268 | 0.033 | −0.52 | N-myc proto-oncogene protein | 23/6.5 | 49.6/5.5 | Degradation | Transcription factor | 0.170 | 0.135 | 0.22 |
| PBP | 1546 | 0.010 | −0.52 | Phosphatidylethanolamine-binding protein | 13/7.5 | 21.1/7.0 | Degradation | RAF kinase inhibitor | 0.514 | 0.014 | 0.18 |
| AAT | 1413 | 0.010 | 0.46 | α-1-antitrypsin (precursor) | 20/6.1 | 46.7/5.4 | Degradation | Proteinase inhibitor | 0.215 | 0.621 | 0.13 |
| KRT1 | 1888 | 0.030 | 0.35 | Cytokeratin 1 | 28/5.1 | 66.1/8.2 | Degradation | Structural protein | 0.868 | 0.148 | 0.06 |
| KRT7 | 871 | 0.005 | −0.66 | Cytokeratin 7 | 41.7/4.7 | 51.3/5.4 | Degradation | Structural protein | <0.001 | 0.234 | −0.18 |
| KRT7 | 1968 | 0.014 | 0.52 | Cytokeratin 7 | 41/4.6 | 51.3/5.4 | Degradation | Structural protein | <0.001 | 0.234 | 0.14 |
| KRT7 | 2165 | 0.019 | −0.49 | Cytokeratin 7 | 36.7/4.7 | 51.3/5.4 | Degradation | Structural protein | <0.001 | 0.234 | 0.35 |
| KRT7 | 691 | 0.025 | 0.41 | Cytokeratin 7 | 41.7/4.9 | 51.3/5.4 | Degradation | Structural protein | <0.001 | 0.234 | 0.10 |
| KRT7 | 2091 | 0.029 | 0.36 | Cytokeratin 7 | 40.4/4.6 | 51.3/5.4 | Degradation | Structural protein | <0.001 | 0.234 | 0.29 |
| KRT8 | 439 | 0.033 | 0.38 | Cytokeratin 8 | 50.7/5.4 | 53.7/5.5 | Degradation | Structural protein | 0.093 | 0.368 | 0.30 |
| KRT19 | 1955 | 0.026 | 0.43 | Cytokeratin 19 | 43.6/4.8 | 44.1/5.1 | Native | Structural protein | 0.001 | 0.130 | 0.39 |
| GFAP | 2336 | 0.041 | 0.33 | Glial fibrillary acidic protein | 28/5.5 | 49.9/5.4 | Degradation | Structural protein | 0.597 | 0.503 | −0.10 |
| ACTB/G | 634 | 0.044 | 0.39 | Actin, β/γ | 41/5.6 | 41.7/5.3 | Native | Structural protein | 0.306∥ | 0.294∥ | 0.21∥ |
| ANXA1 | 1245 | 0.026 | 0.39 | Annexin I | 26/6 | 38.7/6.6 | Degradation | Calcium binding | 0.126 | 0.571 | −0.02 |
| ANXA8 | 923 | 0.006 | −0.80 | Annexin VIII | 35.9/6.1 | 36.9/5.6 | Native | Calcium binding | 0.009 | 0.806 | −0.23 |
| CALU | 1738 | 0.004 | 0.51 | Calumenin | 38/4.1 | 37.1/4.5 | Native | Calcium binding | NA | <0.001 | NA |
MW/PI, molecular weight/isoelectric point; NA, not applicable.
*
Bold indicates proteins that were verified by 2D Western blot and immunohistochemistry; alternate gene name: GRP78, HSPA5; GRK4, GPRK2L.
†
The value of P and coefficient β were made from univariate Cox analysis based on all 90 samples.
‡
P values were made from univariate Cox analysis based on 86 samples from University of Michigan; bold values indicate P < 0.05.
§
P values were made from univariate Cox analysis based on 84 adenocarcinomas from Harvard University, bold values indicate P < 0.05.
¶
Spearman correlation coefficient based on 76 tumors, bold values indicate P < 0.05.
∥
Data from one of two ACTB mRNA probe sets were used. Thirteen unidentified protein isoforms are provided in Table 4.