Table 3.
Protein markers with validated prognostic value in breast cancer when assessing the correlation between expression level and overall survival (A) and relapse-free survival (B). Bold: significant at p < 0.05.
| (A) Overall Survival | TCGA-RPPA | Liu 2014 | Tang 2018 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Protein marker | Symbol | Uniprot ID | n | HR | 95% CI | p value | n | HR | 95% CI | p value | n | HR | 95% CI | p value |
| Estrogen receptor | ESR1 | P03372 | 733 | 0.82 | 0.55–1.21 | 0.31 | – | – | – | – | 65 | 1.53 | 0.72–3.26 | 0.27 |
| Progesterone receptor | PGR | P06401 | 873 | 1.27 | 0.85–1.89 | 0.24 | – | – | – | – | 65 | 2.23 | 1.01–4.94 | 0.042 |
| Human epidermal growth factor receptor 2 | HER2 | P04626 | 836 | 1.32 | 0.9–1.95 | 0.16 | – | – | – | – | 65 | 1.37 | 0.64–2.92 | 0.41 |
| HER2_pY1248 | 871 | 1.63 | 1.13–2.36 | 0.0079 | ||||||||||
| Androgen receptor | AR | P10275 | 870 | 1.37 | 0.88–2.14 | 0.16 | – | – | – | – | 65 | 0.29 | 0.1–0.83 | 0.014 |
| Apoptosis Regulator, BCL2 | BCL2 | P10415 | 869 | 0.56 | 0.39–0.81 | 0.0017 | – | – | – | – | – | – | – | – |
| Basal markers, Cytokeratin-8 | KRT8 | P05787 | – | – | – | – | 125 | 1.86 | 0.99–3.49 | 0.051 | 65 | 2.16 | 1.03–4.55 | 0.038 |
| Basal markers, Cytokeratin-18 | KRT18 | P05783 | – | – | – | – | 126 | 0.35 | 0.14–0.88 | 0.02 | 65 | 2.35 | 1.11–5.00 | 0.022 |
| Basal markers, Cytokeratin-5 | KRT5 | P13647 | – | – | – | – | 126 | 0.54 | 0.29–1.01 | 0.05 | 65 | 0.41 | 0.19–0.85 | 0.014 |
| Basal markers, Cytokeratin-6A | KRT6A | P02538 | – | – | – | – | 121 | 0.63 | 0.3–1.33 | 0.22 | 65 | 2.17 | 1.02–4.61 | 0.039 |
| Basal markers, Cytokeratin-6B | KRT6B | P04259 | – | – | – | – | 115 | 0.46 | 0.23–0.9 | 0.019 | 65 | 1.89 | 0.91–3.9 | 0.081 |
| Basal markers, Cytokeratin-17 | KRT17 | Q04695 | – | – | – | – | 126 | 0.49 | 0.26–0.92 | 0.022 | 65 | 1.59 | 0.61–4.16 | 0.34 |
| Adhesion marker, E-Cadherin | CDH1 | P12830 | 668 | 1.76 | 1.07–2.89 | 0.024 | 125 | 0.21 | 0.08–0.6 | 0.0013 | 65 | 0.58 | 0.28–1.2 | 0.14 |
| Adhesion markers, Claudin-3 | CLDN3 | O15551 | – | – | – | – | 119 | 0.48 | 0.26–0.91 | 0.021 | – | – | – | – |
| Transcription factor, Y-box-binding protein 1 | YBX1 | P67809 | 872 | 0.73 | 0.5–1.07 | 0.11 | – | – | – | – | 65 | 2.07 | 0.99–4.31 | 0.047 |
| YBX1_pS102 | 873 | 1.48 | 1.0–2.17 | 0.046 | – | – | – | – | – | – | – | – | ||
| Invasion marker, Stromelysin-3 | MMP11 | P24347 | – | – | – | – | – | – | – | – | 65 | 2.09 | 1.0–4.35 | 0.044 |
| N-myc downstream-regulated gene 1 protein | NDRG1 | Q92597 | – | – | – | – | 126 | 0.66 | 0.34–1.28 | 0.216 | 65 | 2.24 | 1.07–4.72 | 0.0288 |
| Catenin beta-1 | CTNNB1 | P35222 | 873 | 1.38 | 0.84–2.29 | 0.2031 | 126 | 0.27 | 0.12–0.59 | 4E–04 | 65 | 1.73 | 0.74–4.07 | 0.2009 |
| Apolipoprotein D | APOD | P05090 | – | – | – | – | 126 | 0.56 | 0.29–1.08 | 0.081 | 65 | 0.35 | 0.12–1.0 | 0.0411 |
| Poly [ADP-ribose] polymerase 1 | PARP1 | P09874 | 873 | 1.55 | 0.77–3.09 | 0.2134 | 126 | 0.79 | 0.93–3.48 | 0.079 | 65 | 2.44 | 1.18–5.05 | 0.0131 |
| Scavenger receptor cysteine-rich type 1 protein M130 | CD163 | Q86VB7 | – | – | – | – | 126 | 0.74 | 0.35–1.53 | 0.412 | 65 | 2.43 | 1.17–5.06 | 0.0138 |
| Fascin | FSCN1 | Q16658 | – | – | – | – | 126 | 0.52 | 0.28–0.98 | 0.040 | 65 | 2.52 | 1.2–5.26 | 0.0111 |
| Asporin | ASPN | Q9BXN1 | – | – | – | – | – | – | – | – | 65 | 2.29 | 1.06–4.94 | 0.0294 |
| RNA-binding protein 3 | RBM3 | P98179 | – | – | – | – | 126 | 0.42 | 0.18–1.01 | 0.045 | 65 | 2.03 | 0.97–4.26 | 0.056 |
| Glioma-associated oncogene | GLI1 | P08151 | – | – | – | – | – | – | – | – | 65 | 0.43 | 0.18–1 | 0.0427 |
| (B) Relapse-free survival | TCGA-RPPA | Liu 2014 | De Marchi 2015 | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Protein marker | Symbol | Uniprot ID | n | HR | 95% CI | p value | n | HR | 95% CI | p value | n | HR | 95% CI | p value |
| Estrogen receptor | ESR1 | P03372 | 623 | 0.64 | 0.36–1.14 | 0.13 | – | – | – | – | 112 | 0.3 | 0.19–0.49 | 1.9e − 07 |
| Progesterone receptor | PGR | P06401 | 750 | 0.42 | 0.26–0.69 | 0.0004 | – | – | – | – | 112 | 0.61 | 0.41–0.92 | 0.018 |
| Human epidermal growth factor receptor 2 | HER2 | P04626 | 719 | 1.19 | 0.73–1.96 | 0.48 | – | – | – | – | 112 | 0.75 | 0.51–1.11 | 0.15 |
| HER2_pY1248 | 748 | 0.68 | 0.39–1.21 | 0.19 | ||||||||||
| Apoptosis Regulator, BCL2 | BCL2 | P10415 | 746 | 0.51 | 0.31–0.84 | 0.0071 | – | – | – | – | 112 | 0.4 | 0.27–0.61 | 9.5e − 06 |
| Basal markers, Cytokeratin-18 | KRT18 | P05783 | – | – | – | – | 124 | 0.39 | 0.17–0.86 | 0.016 | – | – | – | – |
| Basal markers, Cytokeratin-5 | KRT5 | P13647 | – | – | – | – | 124 | 0.49 | 0.28–0.85 | 0.01 | – | – | – | – |
| Basal markers, Cytokeratin-6B | KRT6B | P04259 | – | – | – | – | 113 | 0.43 | 0.23–0.77 | 0.004 | – | – | – | – |
| Basal markers, Cytokeratin-17 | KRT17 | Q04695 | – | – | – | – | 124 | 0.51 | 0.29–0.88 | 0.014 | – | – | – | – |
| Adhesion marker, E-Cadherin | CDH1 | P12830 | 578 | 1.83 | 0.93–3.58 | 0.075 | 123 | 0.35 | 0.16–0.78 | 0.007 | 112 | 0.61 | 0.39–0.95 | 0.026 |
| Adhesion markers, Claudin-7 | CLDN7 | O95471 | 715 | 1.67 | 1–2.79 | 0.048 | – | – | – | – | 112 | 0.72 | 0.49–1.06 | 0.098 |
| Apoptotic marker, Tumorsupressor p53 | TP53 | P04637 | 727 | 1.84 | 1.12–3.02 | 0.014 | – | – | – | – | – | – | – | – |
| Bcl-2-associated athanogene 1 | BAG1 | Q99933 | – | – | – | – | – | – | – | – | 112 | 0.58 | 0.39–0.86 | 0.0061 |
| Carcinoembryonic antigen-related cell adhesion molecule 5 | CEACAM5 | P06731 | – | – | – | – | – | – | – | – | 112 | 0.66 | 0.43–1.00 | 0.049 |
| N-myc downstream-regulated gene 1 protein | NDRG1 | Q92597 | – | – | – | – | 124 | 0.58 | 0.33–1.03 | 0.059 | 112 | 0.56 | 0.37–0.87 | 0.0084 |
| Large neutral amino acids transporter small subunit 1 | SLC7A5 | Q01650 | – | – | – | – | – | – | – | – | 112 | 1.5 | 1.01–2.22 | 0.0455 |
| Catenin beta-1 | CTNNB1 | P35222 | 750 | 0.73 | 0.71–1.3 | 0.2823 | 124 | 0.36 | 0.19–0.7 | 0.002 | 112 | 0.56 | 0.36–0.85 | 0.0061 |
| Apolipoprotein D | APOD | P05090 | – | – | – | – | 124 | 0.64 | 0.35–1.15 | 0.133 | 112 | 0.59 | 0.38–0.91 | 0.0161 |
| Poly [ADP-ribose] polymerase 1 | PARP1 | P09874 | 750 | 0.46 | 0.17–1.3 | 0.1341 | 124 | 1.49 | 0.83–2.66 | 0.176 | 112 | 0.65 | 0.44–0.97 | 0.0349 |
| Carcinoembryonic antigen-related cell adhesion molecule 6 | CEACAM6 | P40199 | – | – | – | – | – | – | – | – | 112 | 0.56 | 0.38–0.84 | 0.0044 |
| Ras-related protein Rab-27B | RAB27B | O00194 | – | – | – | – | – | – | – | – | 112 | 0.59 | 0.37–0.92 | 0.0183 |
| RNA-binding protein 3 | RBM3 | P98179 | – | – | – | – | 124 | 0.40 | 0.19–0.86 | 0.016 | 112 | 0.78 | 0.51–1.18 | 0.2466 |
| GATA-binding factor 3 | GATA3 | P23771 | 750 | 0.61 | 0.37–1.01 | 0.0544 | – | – | – | – | 112 | 0.49 | 0.32–0.74 | 0.0007 |