Table 3. 113 genes with HER2-dependent POL II binding but no expression in cell lines and significant differential expression between high and low HER2-expressing breast cancer tissues (p < 0.05).
| Gene Name | HER2+/−Primary tissue LogFC | P– Value | Gene Name | HER2+/− Primary tissue LogFC | P– Value |
|---|---|---|---|---|---|
| SDC1 | 0.73 | 2.98E-18 | IGF2R | 0.19 | 0.0236 |
| C7orf24 | 0.71 | 2.13E-17 | SPECC1L | 0.19 | 0.0247 |
| CTDSP1 | 0.53 | 2.25E-10 | ALG3 | 0.19 | 0.0255 |
| CISH | 0.53 | 3.00E-10 | NUMA1 | 0.17 | 0.0383 |
| DUSP6 | 0.53 | 4.07E-10 | WDR33 | 0.17 | 0.0399 |
| SRPK3 | 0.49 | 5.78E-09 | SEC24B | 0.17 | 0.0405 |
| NDUFA3 | 0.48 | 1.02E-08 | TOR3A | 0.17 | 0.0406 |
| DDR1 | 0.46 | 4.10E-08 | SQSTM1 | 0.17 | 0.0422 |
| PPOX | 0.43 | 3.04E-07 | FABP4 | −0.17 | 0.05 |
| TACSTD2 | 0.42 | 4.52E-07 | TM4SF1 | −0.17 | 0.048 |
| NCSTN | 0.42 | 6.70E-07 | ADCY1 | −0.17 | 0.047 |
| VASP | 0.42 | 7.04E-07 | USP2 | −0.17 | 0.046 |
| SLC39A1 | 0.41 | 1.33E-06 | KIAA0999 | −0.17 | 0.042 |
| FGFR1OP | 0.37 | 8.37E-06 | STK24 | −0.17 | 0.041 |
| SGMS1 | 0.37 | 1.13E-05 | EPHA4 | −0.17 | 0.04 |
| CELSR3 | 0.35 | 3.15E-05 | BST1 | −0.18 | 0.033 |
| LAD1 | 0.35 | 3.64E-05 | RIF1 | −0.19 | 0.026 |
| SEPW1 | 0.35 | 4.06E-05 | R3HDM1 | −0.19 | 0.023 |
| FRAG1 | 0.34 | 5.09E-05 | RHOBTB3 | −0.19 | 0.021 |
| GPC1 | 0.33 | 7.12E-05 | TLX1 | −0.2 | 0.019 |
| GOLGB1 | 0.32 | 0.0001 | CCNL1 | −0.2 | 0.019 |
| XKR8 | 0.32 | 0.0001 | PDE2A | −0.2 | 0.016 |
| KCNK1 | 0.32 | 0.0001 | SPIB | −0.21 | 0.014 |
| PFDN2 | 0.32 | 0.0002 | RPL10A | −0.21 | 0.013 |
| ACOX2 | 0.32 | 0.0002 | KCNAB2 | −0.21 | 0.013 |
| PRKCZ | 0.32 | 0.0002 | ITGAE | −0.21 | 0.013 |
| DKK1 | 0.31 | 0.0002 | RBBP7 | −0.21 | 0.011 |
| MARK2 | 0.31 | 0.0003 | NUS1 | −0.22 | 0.009 |
| ATP5G1 | 0.3 | 0.0003 | CLIC4 | −0.22 | 0.008 |
| IDH2 | 0.3 | 0.0003 | CSNK2A2 | −0.22 | 0.008 |
| XRCC5 | 0.29 | 0.0005 | CHL1 | −0.24 | 0.005 |
| ACAT2 | 0.29 | 0.0005 | NEFH | −0.24 | 0.004 |
| GATA3 | 0.28 | 0.001 | RAP1A | −0.25 | 0.003 |
| BRD2 | 0.27 | 0.0011 | CBS | −0.25 | 0.003 |
| TES | 0.27 | 0.0015 | FBXO2 | −0.25 | 0.002 |
| GCNT1 | 0.26 | 0.0017 | PQLC1 | −0.26 | 0.002 |
| LRRC23 | 0.26 | 0.0018 | PTCH1 | −0.26 | 0.002 |
| ZNHIT2 | 0.26 | 0.0022 | WDR77 | −0.27 | 0.002 |
| TMEM115 | 0.25 | 0.0025 | THOC5 | −0.27 | 0.001 |
| FNBP1L | 0.25 | 0.0025 | TCP11L1 | −0.28 | 0.001 |
| STK16 | 0.25 | 0.003 | DYNLT3 | −0.29 | 0.001 |
| CTBP2 | 0.25 | 0.003 | FGL2 | −0.29 | 0 |
| ADAMTS13 | 0.25 | 0.0031 | TUBGCP3 | −0.3 | 0 |
| AP2S1 | 0.25 | 0.0035 | OTOF | −0.3 | 0 |
| KIAA0195 | 0.24 | 0.004 | HSPB2 | −0.31 | 0 |
| SNAPC5 | 0.24 | 0.0043 | VRK2 | −0.35 | 0 |
| CNN2 | 0.23 | 0.006 | RHEB | −0.35 | 0 |
| BBS1 | 0.23 | 0.0074 | RTP4 | −0.37 | 0 |
| BCAR3 | 0.22 | 0.0094 | GABRP | −0.38 | 0 |
| RNF141 | 0.22 | 0.0098 | VAMP3 | −0.39 | 0 |
| TINF2 | 0.2 | 0.0154 | CAPN6 | −0.4 | 0 |
| TETRAN | 0.2 | 0.0181 | ANKRD15 | −0.41 | 0 |
| MMP15 | 0.2 | 0.0191 | STAC | −0.45 | 0 |
| WHSC1 | 0.19 | 0.0215 | IRS2 | −0.47 | 0 |
| PMPCA | 0.19 | 0.0216 | EPB41L2 | −0.49 | 0 |
| HNRPDL | 0.19 | 0.0223 | CD320 | −0.58 | 0 |