Table 1.
Genes Differentially Expressed (T versus NT) in Macro and LCM Samples of NSCLC, All Three Histologies Combined
| Macro |
LCM |
||||
|---|---|---|---|---|---|
| Gene | FC∗ | Padjusted† | Gene | FC∗ | Padjusted† |
| Up-regulated (all histologies) | |||||
| SPP1 | 9.1 | 7.82 × 10−10 | SPINK1‡ | 7.0 | 1.97 × 10−2 |
| TMPRSS4 | 6 | 2.31 × 10−10 | AKR1C2‡ | 5.8 | 7.14 × 10−3 |
| MMP12 | 5.7 | 2.25 × 10−7 | CENPF | 5.0 | 2.20 × 10−4 |
| GPX2‡ | 4.7 | 6.98 × 10−6 | TOP2A‡ | 4.6 | 2.93 × 10−4 |
| MMP1 | 4.4 | 2.87 × 10−6 | CP | 4.4 | 4.42 × 10−2 |
| AFAP1 | 4.1 | 8.77 × 10−8 | DSG2 | 4.2 | 1.34 × 10−5 |
| SPINK1‡ | 3.8 | 3.24 × 10−4 | SNORA73A | 4.2 | 1.80 × 10−3 |
| AKR1B10 | 3.5 | 1.64 × 10−4 | BIRC5 | 4.0 | 1.21 × 10−3 |
| CST1 | 3.5 | 2.23 × 10−6 | TP63 | 4.0 | 1.09 × 10−2 |
| TOP2A‡ | 3.5 | 9.62 × 10−9 | ANLN‡ | 3.9 | 2.35 × 10−4 |
| AKR1C2‡ | 3.4 | 3.59 × 10−4 | DSP | 3.9 | 3.86 × 10−3 |
| CYP24A1 | 3.4 | 1.75 × 10−4 | OCIAD2 | 3.9 | 2.19 × 10−4 |
| CKMT1A | 3.3 | 3.14 × 10−7 | NQO1 | 3.8 | 3.61 × 10−3 |
| CKMT1A | 3.3 | 3.14 × 10−7 | TPX2 | 3.5 | 5.10 × 10−4 |
| MMP13 | 3.3 | 1.15 × 10−4 | CKS1B | 3.5 | 1.56 × 10−4 |
| ANLN‡ | 3.2 | 1.69 × 10−7 | DSC3 | 3.5 | 1.49 × 10−2 |
| FERMT1 | 3.2 | 2.07 × 10−9 | BAIAP2L1 | 3.4 | 2.47 × 10−5 |
| SLC2A1 | 3.1 | 2.73 × 10−7 | GPX2‡ | 3.4 | 2.70 × 10−2 |
| SLC7A11 | 3.1 | 1.72 × 10−6 | LRIG3 | 3.4 | 1.31 × 10−3 |
| ANKRD22 | 3 | 4.06 × 10−8 | DSG3 | 3.4 | 3.67 × 10−2 |
| Down-regulated (all histologies) | |||||
| FABP4‡ | 0.12 | 4.10 × 10−10 | SFTPC‡ | 0.02 | 2.21 × 10−9 |
| SLC6A4 | 0.16 | 5.56 × 10−8 | HBB | 0.05 | 1.62 × 10−8 |
| AGER | 0.17 | 2.99 × 10−9 | MRC1 | 0.06 | 4.02 × 10−8 |
| AGER | 0.17 | 2.59 × 10−9 | MRC1 | 0.06 | 4.02 × 10−8 |
| AGER | 0.18 | 1.93 × 10−9 | FABP4‡ | 0.07 | 5.11 × 10−8 |
| TMEM100 | 0.19 | 2.07 × 10−9 | PECAM1 | 0.08 | 4.97 × 10−8 |
| GKN2 | 0.20 | 8.62 × 10−7 | GMFG | 0.09 | 6.40 × 10−8 |
| CPB2 | 0.21 | 2.53 × 10−7 | A2M | 0.10 | 5.10 × 10−7 |
| FCN3 | 0.22 | 1.74 × 10−8 | FMO2§ | 0.11 | 5.11 × 10−8 |
| FIGF | 0.22 | 1.08 × 10−6 | LDB2 | 0.11 | 2.21 × 10−9 |
| WIF1 | 0.22 | 1.70 × 10−6 | ABI3BP | 0.11 | 4.02 × 10−8 |
| SFTPC‡ | 0.22 | 3.18 × 10−5 | AQP4 | 0.12 | 4.21 × 10−6 |
| ANKRD1 | 0.23 | 1.24 × 10−7 | CALCRL | 0.12 | 1.14 × 10−6 |
| ADH1B | 0.23 | 3.50 × 10−6 | ANKRD1 | 0.13 | 5.90 × 10−7 |
| RTKN2 | 0.24 | 3.42 × 10−10 | LRRK2 | 0.13 | 1.94 × 10−4 |
| CLDN18 | 0.24 | 8.95 × 10−7 | PTPRB | 0.13 | 5.17 × 10−7 |
| ST8SIA6 | 0.25 | 1.22 × 10−10 | HBA1 | 0.14 | 6.08 × 10−8 |
| FHL1 | 0.25 | 3.20 × 10−9 | HBA1 | 0.14 | 6.08 × 10−8 |
| TCF21 | 0.26 | 1.17 × 10−8 | MSR1 | 0.14 | 1.39 × 10−6 |
| PKHD1L1 | 0.26 | 4.10 × 10−10 | EPAS1 | 0.14 | 4.97 × 10−8 |
Macro: n = 32 T, n = 32 NT, n = 31 pairs. LCM: n = 21 T, n = 20 NT, n = 17 pairs. Repeated gene names indicate redundant probe sets.
∗
Fold change (FC) reflects the ratio of transcript levels in T versus NT alveolar, by microarray.
†
Benjamini–Hochberg false-discovery rate (FDR)–adjusted significance.
‡
Genes common to both Macro and LCM signatures.
§
FMO2 for a functional protein is reclassified as FMO4 (flavin containing monooxygenase 4).