Table 1. Top 200 genes regulated by NKX2-3 knockdown in HIMEC.
| Gene | Fold | p-value | Gene | Fold | p-value | Gene | Fold | p-value | Gene | Fold | p-value |
| Cell growth and proliferation | Transport and structure | Inflammation and immune response | Inflammation and immune response | ||||||||
| PIM3 | 0.3 | 2.31E-06 | SYT11 | 0.35 | 3.66E-07 | TNFRSF10D | 0.31 | 3.54E-07 | SAMD9 | 7.31 | 2.01E-10 |
| TFPI2 | 0.32 | 3.94E-06 | KRT81 | 0.4 | 3.31E-07 | TNFSF18 | 0.32 | 6.43E-05 | STAT1 | 7.72 | 1.98E-09 |
| NR2F1 | 0.37 | 4.64E-07 | RPS23 | 0.4 | 2.97E-07 | CERK | 0.33 | 1.39E-06 | TAP2 | 7.83 | 7.33E-10 |
| EIF4B | 0.38 | 2.68E-07 | EXOC6 | 0.47 | 2.09E-06 | FAM172A | 0.37 | 1.94E-07 | PSMB8 | 8.22 | 1.84E-10 |
| GHR | 0.39 | 3.69E-07 | RPL23 | 0.47 | 1.33E-06 | YPEL2 | 0.39 | 0.000952 | UBE2L6 | 8.33 | 9.08E-10 |
| HMMR | 0.39 | 3.79E-06 | RPS29 | 0.48 | 2.41E-06 | PAPSS2 | 0.39 | 8.84E-06 | PTGS2 | 8.63 | 2.77E-11 |
| REEP1 | 0.4 | 2.86E-07 | ADAP1 | 3.29 | 2.36E-08 | IL8 | 0.4 | 7.63E-06 | GBP1 | 9.24 | 2.23E-08 |
| ZMAT3 | 0.41 | 3.60E-07 | SLC25A28 | 3.71 | 1.99E-07 | UACA | 0.4 | 3.05E-05 | PARP9 | 9.46 | 6.09E-10 |
| MMP7 | 0.42 | 3.43E-06 | RTP4 | 6.47 | 0.000111 | GIMAP7 | 0.41 | 9.24E-07 | SP110 | 9.83 | 1.31E-10 |
| GDF15 | 0.42 | 1.22E-05 | GJD3 | 7.95 | 0.000154 | HES2 | 0.41 | 2.05E-07 | TAP1 | 10.62 | 7.18E-11 |
| MFNG | 0.42 | 2.32E-05 | SLC40A1 | 0.41 | 2.59E-07 | USP18 | 11.2 | 9.63E-11 | |||
| AGAP3 | 0.43 | 6.31E-07 | TNFAIP8L1 | 0.43 | 3.66E-07 | DDX58 | 11.39 | 3.09E-08 | |||
| TMEM158 | 0.44 | 1.25E-05 | Cell adhesion | F2RL1 | 0.43 | 0.000121 | HLA-B | 11.89 | 8.66E-12 | ||
| UNC5A | 0.44 | 7.44E-05 | CD36 | 0.43 | 5.14E-07 | PRIC285 | 12.35 | 1.67E-10 | |||
| SHMT2 | 0.44 | 1.55E-06 | POSTN | 0.22 | 6.28E-09 | PLD1 | 0.44 | 2.12E-07 | PSMB9 | 14.18 | 1.73E-10 |
| FAM198B | 0.45 | 3.44E-06 | MMRN1 | 0.35 | 3.33E-06 | CBS | 0.46 | 3.70E-06 | |||
| HNRNPA0 | 0.46 | 6.11E-05 | CXADR | 0.36 | 7.75E-07 | CEP55 | 0.47 | 3.69E-06 | |||
| PAWR | 0.46 | 4.71E-05 | SRPX | 0.37 | 7.57E-06 | GNG12 | 0.48 | 5.21E-05 | Others | ||
| DCLK1 | 0.47 | 7.04E-07 | FLRT2 | 0.46 | 8.02E-06 | TNFSF4 | 0.48 | 1.00E-05 | |||
| TTC3 | 0.47 | 5.53E-07 | AIF1L | 3.41 | 8.77E-08 | ARHGDIB | 0.49 | 2.55E-05 | ANKRD55 | 0.18 | 1.07E-07 |
| TFF3 | 0.47 | 1.73E-05 | CLEC1A | 0.49 | 1.96E-05 | C2CD4B | 0.22 | 2.48E-08 | |||
| PTPRE | 0.47 | 4.31E-06 | CXCL16 | 3.19 | 1.04E-05 | KIAA0114 | 0.27 | 2.03E-08 | |||
| UBE4B | 0.47 | 2.02E-06 | Transcription regulation | GCH1 | 3.32 | 5.31E-05 | NT5DC2 | 0.28 | 8.23E-09 | ||
| CDKN3 | 0.48 | 0.000101 | UNC93B1 | 3.46 | 1.36E-06 | EIF4BP7 | 0.29 | 3.73E-07 | |||
| CCNB2 | 0.49 | 2.92E-05 | SDPR | 0.44 | 1.95E-06 | CD68 | 3.51 | 3.49E-07 | FLJ41200 | 0.29 | 2.64E-08 |
| ANLN | 0.49 | 3.85E-05 | HOXD1 | 0.45 | 0.000147 | TRIM21 | 3.62 | 9.21E-06 | C13orf33 | 0.34 | 7.43E-06 |
| LGMN | 3.23 | 4.42E-07 | ZNFX1 | 3.52 | 2.22E-06 | APOBEC3G | 3.67 | 5.26E-06 | EIF4BP3 | 0.38 | 1.42E-07 |
| SEMA3A | 3.25 | 2.19E-06 | BATF2 | 4.11 | 1.75E-06 | TRIM5 | 3.82 | 4.78E-05 | FBN2 | 0.39 | 5.49E-06 |
| PNPT1 | 3.44 | 2.45E-05 | KLF2 | 3.92 | 7.66E-06 | C7orf41 | 0.4 | 5.68E-07 | |||
| MAP2 | 3.57 | 4.49E-09 | PLSCR1 | 4.05 | 2.58E-08 | SNHG9 | 0.41 | 0.000156 | |||
| PMAIP1 | 3.65 | 3.66E-08 | Metabolic process | MYD88 | 4.28 | 1.98E-06 | WRB | 0.42 | 1.18E-06 | ||
| EIF2AK2 | 3.73 | 9.30E-09 | CD38 | 4.28 | 6.55E-08 | BCYRN1 | 0.42 | 0.000157 | |||
| HEY1 | 3.85 | 2.33E-07 | ACO1 | 0.2 | 8.00E-07 | CX3CL1 | 4.33 | 0.000209 | ZNF704 | 0.44 | 5.90E-07 |
| CSRNP1 | 3.87 | 1.55E-06 | HSD17B2 | 0.23 | 2.48E-06 | STAT2 | 4.34 | 1.08E-05 | ANKRD37 | 0.46 | 5.41E-06 |
| C8orf4 | 3.95 | 5.53E-06 | PHGDH | 0.29 | 1.86E-08 | PLEKHA4 | 4.37 | 1.83E-05 | HNRPA1L-2 | 0.46 | 8.27E-06 |
| XAF1 | 4.17 | 2.88E-06 | PSAT1 | 0.3 | 1.24E-07 | IFNB1 | 4.37 | 3.68E-06 | TCTEX1D2 | 0.47 | 0.000153 |
| SERPINE2 | 4.33 | 2.29E-08 | ASNS | 0.31 | 1.09E-07 | FCN3 | 4.38 | 0.000198 | CENPW | 0.48 | 7.38E-05 |
| HEY2 | 4.6 | 4.55E-08 | GALNTL2 | 0.33 | 7.00E-06 | F2RL3 | 4.44 | 2.45E-07 | NETO2 | 0.48 | 1.93E-05 |
| PARP10 | 5.54 | 5.42E-08 | PKIA | 0.34 | 7.05E-05 | ZC3HAV1 | 4.6 | 5.95E-07 | C8orf45 | 0.48 | 8.75E-05 |
| CRYAB | 6.8 | 8.25E-06 | MYO5A | 0.38 | 5.34E-05 | HCG4 | 4.61 | 2.85E-09 | MAMDC2 | 3.19 | 6.34E-07 |
| KLF4 | 6.86 | 6.09E-10 | TXNDC12 | 0.4 | 1.43E-07 | HLA-C | 4.63 | 1.63E-09 | FBXO6 | 3.26 | 7.21E-08 |
| LY6E | 7.47 | 1.94E-10 | SNCAIP | 0.41 | 0.000257 | GBP2 | 4.71 | 4.44E-08 | C1orf74 | 3.48 | 0.000186 |
| TMEM100 | 15.53 | 3.36E-07 | CHST7 | 0.44 | 7.79E-07 | SMAD7 | 4.78 | 1.31E-06 | USP41 | 3.52 | 3.72E-06 |
| MCTP1 | 0.46 | 0.000231 | NT5C3 | 4.8 | 1.92E-07 | C19orf66 | 3.92 | 2.77E-08 | |||
| FAR2 | 0.48 | 0.000238 | HLA-H | 5.39 | 4.83E-10 | HIST2H2AC | 4.18 | 5.43E-08 | |||
| Angiogenesis | PRSS12 | 0.48 | 1.43E-06 | TRIM22 | 5.49 | 9.22E-08 | GCA | 5.14 | 5.15E-06 | ||
| BCHE | 0.49 | 3.81E-06 | DHX58 | 5.58 | 1.57E-06 | HIST2H2AA3 | 5.17 | 2.92E-09 | |||
| ANGPT2 | 0.18 | 1.42E-05 | ADAMTSL2 | 3.2 | 1.26E-06 | IL18BP | 5.66 | 3.92E-09 | HIST2H2AA4 | 5.28 | 2.11E-09 |
| SRPX2 | 0.33 | 0.000284 | TIPARP | 3.28 | 1.18E-07 | HLA-F | 5.79 | 2.68E-10 | RNF213 | 6.6 | 1.03E-06 |
| TRPC6 | 0.33 | 1.08E-07 | PLA1A | 4.75 | 3.24E-08 | CASP1 | 5.82 | 5.35E-10 | DDX60L | 6.75 | 1.14E-08 |
| BTG1 | 0.43 | 3.66E-05 | GMPR | 4.8 | 5.63E-08 | PARP12 | 6.28 | 1.97E-09 | LYPD1 | 6.75 | 3.01E-05 |
| BMP4 | 0.48 | 2.53E-05 | LAP3 | 6.07 | 9.20E-09 | IDO1 | 6.93 | 1.77E-08 | DDX60 | 7.87 | 2.71E-09 |
| ANGPTL4 | 3.37 | 1.01E-08 | UBA7 | 6.64 | 9.54E-08 | HCP5 | 6.99 | 3.95E-10 | FAM46A | 8.63 | 4.81E-06 |
| TYMP | 3.38 | 1.13E-08 | CMPK2 | 10.3 | 5.63E-08 | PARP14 | 7.01 | 1.24E-08 | MT1M | 8.77 | 6.76E-11 |
| FGF2 | 4 | 5.16E-05 | ALPL | 12.12 | 0.000474 | IL7R | 7.06 | 3.94E-05 | SAMD9L | 9.07 | 1.22E-08 |