Table 2. Top 50 DEGs, either up- or down-regulation in non-TNBC, screened between TNBC tissues and non-TNBC tissues from GSE65194, GSE43358 and GSE76275.
| Gene | Log2FC | P value |
|---|---|---|
| Up-regulated genes* | ||
| AGR3 | 5.367309395 | 2.62E−74 |
| AGR2 | 4.148029974 | 6.36E−80 |
| SCGB2A2 | 3.924608354 | 1.42E−28 |
| ANKRD30A | 3.840986534 | 3.13E−60 |
| CYP4Z1 | 3.501567014 | 5.27E−45 |
| FOXA1 | 3.479470611 | 6.43E−70 |
| SCUBE2 | 3.161262427 | 1.80E−40 |
| TFF1 | 3.082665802 | 3.93E−28 |
| TFF3 | 2.978673511 | 1.77E−36 |
| MLPH | 2.969707165 | 2.39E−48 |
| GATA3 | 2.875555464 | 5.23E−49 |
| SIDT1 | 2.854203605 | 9.62E−69 |
| C8orf4 | 2.822553566 | 1.56E−37 |
| NAT1 | 2.778675595 | 3.30E−43 |
| CYP4Z2P | 2.747967401 | 3.50E−43 |
| PRR15 | 2.660482857 | 9.26E−75 |
| MUCL1 | 2.640214101 | 6.45E−16 |
| GPR160 | 2.45896542 | 1.14E−48 |
| GUSBP9 | 2.434891966 | 5.22E−30 |
| PIP | 2.408833354 | 6.45E−17 |
| C9orf152 | 2.329344343 | 2.03E−40 |
| SCGB1D2 | 2.307943965 | 3.43E−17 |
| SLC16A6 | 2.300692779 | 7.76E−53 |
| CEACAM6 | 2.272862511 | 7.19E−17 |
| CAPN8 | 2.271306581 | 5.85E−39 |
| ACADSB | 2.231035018 | 6.09E−60 |
| ADIRF | 2.21824273 | 1.98E−57 |
| FSIP1 | 2.190739486 | 3.03E−44 |
| GALNT6 | 2.188051184 | 5.01E−52 |
| MUM1L1 | 2.15674162 | 7.76E−50 |
| VAV3 | 2.145614422 | 1.25E−57 |
| PGR | 2.115059779 | 3.46E−39 |
| DHRS2 | 2.091310833 | 5.52E−18 |
| CRIP1 | 2.084795021 | 2.80E−36 |
| DACH1 | 2.083325481 | 7.08E−42 |
| GRP | 2.07496712 | 2.94E−39 |
| DNALI1 | 2.036210855 | 2.29E−56 |
| ACOX2 | 2.035081416 | 1.51E−48 |
| SLC44A4 | 2.033853504 | 2.27E−60 |
| FAM110C | 2.017948794 | 1.74E−31 |
| GFRA1 | 2.003608609 | 1.67E−29 |
| TFAP2B | 2.001264247 | 9.83E−30 |
| AR | 1.987546306 | 5.74E−31 |
| SMIM14 | 1.980779674 | 4.99E−74 |
| CYP2B7P | 1.936882981 | 1.00E−17 |
| GUSBP3 | 1.935640297 | 9.28E−38 |
| POLI | 1.915107187 | 2.30E−57 |
| BCAS1 | 1.877903131 | 1.88E−74 |
| TMC5 | 1.87548313 | 2.39E−46 |
| TOX3 | 1.872964283 | 7.02E−29 |
| Down-regulated genes** | ||
| GABRP | −3.690068915 | 2.74E−37 |
| ROPN1B | −2.866876028 | 1.87E−46 |
| KRT5 | −2.765696183 | 1.60E−31 |
| PPP1R14C | −2.619397604 | 2.36E−44 |
| FOXC1 | −2.579072145 | 6.28E−59 |
| PGBD5 | −2.502304469 | 7.64E−38 |
| PROM1 | −2.406614771 | 3.78E−19 |
| HORMAD1 | −2.382079389 | 6.87E−28 |
| KRT6B | −2.31866403 | 1.52E−33 |
| CHI3L2 | −2.212420403 | 2.39E−29 |
| ROPN1 | −2.190087204 | 1.58E−40 |
| FDCSP | −2.179202465 | 1.93E−13 |
| ELF5 | −2.158960236 | 1.00E−30 |
| MARCO | −2.138481097 | 3.20E−41 |
| SLC34A2 | −2.131055048 | 1.00E−53 |
| FAM171A1 | −2.060415413 | 6.00E−55 |
| KIAA1804 | −2.034683723 | 1.54E−43 |
| EN1 | −2.030698626 | 2.82E−27 |
| PRAME | −1.993231048 | 1.87E−27 |
| BBOX1 | −1.983016474 | 5.10E−24 |
| KRT16 | −1.977914594 | 1.04E−36 |
| DSG3 | −1.974740056 | 1.67E−23 |
| UGT8 | −1.971689891 | 2.97E−35 |
| SOX8 | −1.970604171 | 6.10E−28 |
| TCF7L1 | −1.949027564 | 5.35E−44 |
| MMP7 | −1.926314159 | 7.91E−24 |
| MIA | −1.907102849 | 3.61E−33 |
| BCL11A | −1.87860922 | 2.91E−33 |
| FAM64A | −1.875836143 | 4.45E−58 |
| CT83 | −1.855277028 | 1.85E−26 |
| SLC7A5 | −1.846670089 | 2.41E−37 |
| SYNM | −1.839182153 | 2.06E−26 |
| LY6D | −1.828259693 | 3.05E−29 |
| SHC4 | −1.826865414 | 2.19E−24 |
| TTYH1 | −1.818126464 | 1.84E−34 |
| CRYAB | −1.815523519 | 3.18E−26 |
| PSAT1 | −1.779514025 | 3.10E−31 |
| PTX3 | −1.773838154 | 6.89E−18 |
| NRTN | −1.76293207 | 7.16E−41 |
| SFRP1 | −1.751070187 | 8.41E−26 |
| PHGDH | −1.750481413 | 1.16E−46 |
| KCNK5 | −1.749430198 | 5.77E−43 |
| MMP12 | −1.748540135 | 1.21E−13 |
| SOSTDC1 | −1.735494318 | 8.97E−21 |
| CXCL1 | −1.735027681 | 1.82E−25 |
| ADGRG2 | −1.698026849 | 4.21E−23 |
| CCL18 | −1.689598525 | 2.93E−17 |
| VANGL2 | −1.682771432 | 8.55E−30 |
| ART3 | −1.68259172 | 2.79E−16 |
| MELK | −1.670666213 | 4.47E−32 |
*, there are 95 up-regulated genes (log2FC >1.585), we list top 50 of them; **, there are 64 down-regulated genes (log2FC >1.585), we list top 50 of them. TNBC, triple negative breast cancer; DEG, differentially expressed gene.