Table 1. 66 common significantly altered genes comparing tumour vs normal samples in the study cohort, our second cohort and the TCGA cohort.
| Transcript ID | Study cohort |
Second cohort |
TCGA |
|||
|---|---|---|---|---|---|---|
| Fold-Change(yes vs. TNBC normal) | p-value(TNBC status) | Fold-Change(IDC vs. NAT) | p-value(TvN) | Fold-Change(IDC vs. NAT) | p-value(TvN) | |
| ABCA10 | −3.07 | 3.59E–21 | −4.69 | 1.76E–09 | −2.71 | 5.51E–10 |
| ABCA6 | −8.96 | 5.42E–23 | −5.01 | 6.37E–06 | −3.83 | 4.95E–10 |
| ABCA8 | −20.18 | 5.12E–29 | −5.41 | 7.23E–05 | −2.58 | 6.91E–10 |
| ABCA9 | −15.16 | 2.85E–35 | −4.55 | 2.43E–06 | −2.54 | 4.50E–08 |
| AGR2 | −13.79 | 5.62E–49 | −20.16 | 3.97E–05 | −2.10 | 3.56E–06 |
| ANKRD30A | −31.96 | 1.48E–25 | −43.09 | 5.71E–12 | −4.91 | 9.08E–12 |
| ANKRD30B | −11.36 | 1.11E–17 | −13.74 | 0.000141 | −2.24 | 0.000458 |
| ANLN | 8.94 | 2.52E–56 | 15.88 | 2.62E–08 | 2.56 | 9.26E–06 |
| ANP32E | 3.06 | 5.47E–40 | 2.58 | 2.37E–06 | 2.05 | 0.000932 |
| APOD | −5.16 | 1.65E–16 | −4.71 | 0.002127 | −7.77 | 9.23E–09 |
| AREG | −16.35 | 1.54E–12 | −7.97 | 0.000308 | −2.06 | 2.80E–06 |
| ASPM | 19.80 | 2.17E–71 | 15.69 | 5.15E–08 | 2.97 | 4.08E–07 |
| ATAD2 | 3.95 | 3.05E–32 | 2.93 | 0.002838 | 2.63 | 2.13E–06 |
| BGN | 3.38 | 1.20E–42 | 8.53 | 1.04E–05 | 2.48 | 1.21E–05 |
| CALU | 3.26 | 1.72E–27 | 2.86 | 3.88E–08 | 2.19 | 3.88E–06 |
| CCT3 | 2.46 | 2.70E–42 | 2.39 | 1.16E–07 | 2.09 | 3.04E–06 |
| CENPF | 18.38 | 9.29E–69 | 14.06 | 1.36E–08 | 2.94 | 6.16E–08 |
| CHML | 2.58 | 1.22E–19 | 3.72 | 1.11E–05 | 2.12 | 2.98E–05 |
| CKS2 | 5.13 | 3.45E–56 | 4.93 | 2.83E–05 | 4.20 | 6.45E–08 |
| COL14A1 | −5.57 | 4.10E–14 | −3.01 | 0.000568 | −3.44 | 5.00E–09 |
| CXCL10 | 3.09 | 8.20E–33 | 24.83 | 6.19E–06 | 4.48 | 1.19E–05 |
| CXCL11 | 9.68 | 9.14E–31 | 11.91 | 0.000101 | 2.03 | 6.14E–05 |
| CXCL9 | 3.20 | 6.32E–17 | 6.31 | 0.005079 | 5.14 | 1.96E–05 |
| DSC2 | 5.31 | 1.63E–29 | 1.89 | 0.006364 | 2.38 | 0.0009 |
| ECT2 | 4.47 | 2.82E–34 | 3.38 | 0.000117 | 2.52 | 4.48E–07 |
| EGR1 | −12.87 | 8.24E–38 | −4.73 | 5.73E–05 | −3.08 | 9.70E–07 |
| FGF10 | −10.16 | 5.14E–16 | −3.04 | 3.45E–05 | −2.34 | 7.78E–11 |
| FN1 | 4.73 | 3.88E–48 | 7.90 | 2.21E–12 | 3.94 | 1.26E–06 |
| FREM1 | −13.48 | 2.05E–36 | −2.37 | 7.86E–06 | −2.18 | 9.51E–09 |
| GPI | 1.87 | 3.91E–09 | 3.66 | 0.000226 | 2.23 | 9.43E–06 |
| HIST1H2BD | 2.60 | 1.71E–32 | 2.30 | 0.004616 | 2.47 | 0.00052 |
| HIST1H3F | 2.65 | 1.06E–38 | 1.61 | 0.002149 | 4.64 | 8.42E–07 |
| IGF1 | −5.83 | 1.42E–18 | −3.65 | 0.000782 | −2.96 | 1.21E–08 |
| IL6ST | −3.20 | 1.92E–23 | −3.39 | 8.60E–08 | −2.36 | 7.53E–06 |
| INHBA | 5.23 | 3.52E–60 | 7.48 | 1.49E–06 | 2.12 | 3.42E–06 |
| JAM2 | −4.20 | 2.88E–29 | −2.47 | 0.001 | −2.08 | 6.94E–08 |
| KIF11 | 6.69 | 6.47E–60 | 8.69 | 1.39E–05 | 2.40 | 1.92E–06 |
| KPNA2 | 3.72 | 6.80E–37 | 5.28 | 4.32E–08 | 2.16 | 9.43E–05 |
| LAMA2 | −4.28 | 4.96E–14 | −2.51 | 0.001598 | −2.02 | 7.43E–07 |
| LIFR | −7.78 | 1.84E–43 | −5.28 | 0.000688 | −2.67 | 3.25E–07 |
| MEG3 | −3.39 | 3.52E–68 | −1.66 | 0.003507 | −2.53 | 6.64E–09 |
| MELK | 14.34 | 1.72E–61 | 14.49 | 1.27E–07 | 2.13 | 2.71E–05 |
| MKI67 | 14.02 | 1.35E–51 | 10.94 | 5.24E–08 | 2.18 | 9.96E–06 |
| MME | −8.64 | 6.89E–40 | −5.17 | 0.001052 | −2.08 | 6.00E–05 |
| MYBL1 | 5.34 | 8.72E–17 | 4.34 | 0.005911 | 2.24 | 0.000728 |
| NUSAP1 | 6.35 | 3.64E–46 | 8.42 | 1.55E–06 | 2.14 | 7.03E–07 |
| OGN | −58.54 | 4.14E–32 | −5.26 | 5.37E–05 | −4.13 | 7.52E–11 |
| PDK4 | −15.78 | 4.50E–36 | −3.74 | 0.006427 | −2.53 | 0.0019 |
| PRDX1 | 1.91 | 8.91E–14 | 1.92 | 0.001102 | 2.00 | 2.67E–05 |
| PRR11 | 2.52 | 2.88E–17 | 9.50 | 1.28E–08 | 2.30 | 1.58E–06 |
| RAD51AP1 | 4.44 | 1.47E–29 | 4.30 | 0.00132 | 2.20 | 7.80E–06 |
| RBMS3 | −5.25 | 2.31E–35 | −2.82 | 0.00085 | −2.17 | 3.32E–07 |
| SLC7A5 | 3.96 | 2.13E–32 | 2.25 | 0.000817 | 2.09 | 0.002088 |
| SMC4 | 3.15 | 1.08E–37 | 2.70 | 7.86E–05 | 2.01 | 1.56E–05 |
| SNRPD1 | 1.91 | 2.42E–26 | 2.39 | 0.000965 | 2.06 | 0.000118 |
| SPARCL1 | −2.16 | 2.33E–13 | −1.93 | 0.001856 | −2.65 | 9.09E–06 |
| SPP1 | 6.68 | 2.97E–12 | 11.48 | 4.91E–06 | 3.40 | 2.30E–06 |
| STIL | 9.28 | 1.33E–38 | 4.23 | 9.29E–05 | 2.14 | 7.21E–06 |
| SULF1 | 2.95 | 9.23E–24 | 5.76 | 2.21E–07 | 3.38 | 7.50E–08 |
| TAT | −3.68 | 3.73E–15 | −60.22 | 2.49E–09 | −2.27 | 6.83E–06 |
| TBC1D9 | −7.35 | 7.69E–50 | −4.12 | 2.20E–07 | −2.25 | 1.37E–07 |
| TOP2A | 8.58 | 4.63E–44 | 15.44 | 4.91E–10 | 4.13 | 6.26E–08 |
| TPX2 | 11.10 | 2.56E–63 | 11.83 | 2.71E–09 | 3.57 | 6.46E–08 |
| TSHZ2 | −3.71 | 3.89E–20 | −4.92 | 3.56E–05 | −2.28 | 2.10E–06 |
| UBE2C | 19.93 | 8.26E–57 | 2.60 | 0.000417 | 2.22 | 1.53E–07 |
| UBE2T | 6.22 | 5.05E–47 | 8.55 | 1.24E–07 | 2.18 | 2.82E–05 |
The 4 TNBC specific genes are written in bold.