Table 3. Confirmation of genes by RT-PCR testing and comparison with gene microarray results.
|
Real-time reverse transcriptase PCR |
Gene microarray |
||||||
|---|---|---|---|---|---|---|---|
| Gene symbol | Fold change (lesional vs. non-lesional) | Log2 (fold change) | P-value | Fold change (lesional vs. non-lesional) | Log2 (fold change) | False discovery rate | |
| Differentially expressed genes | |||||||
| 1 | IL19 | 1359.74 | 10.41 | 3.43 × 10−17 | 18.29 | 4.19 | <10−15 |
| 2 | DEFB4 | 385.00 | 8.59 | 3.07 × 10−19 | 15.68 | 3.97 | <10−15 |
| 3 | TNIP3 | 341.29 | 8.41 | 1.73 × 10−9 | 23.18 | 4.53 | <10−15 |
| 4 | SERPINB3 | 121.92 | 6.93 | 9.00 × 10−19 | 45.81 | 5.52 | <10−15 |
| 5 | SPRR2C | 33.16 | 5.05 | 7.55 × 10−14 | 243.3 | 7.93 | <10−15 |
| 6 | HPSE | 32.35 | 5.02 | 8.79 × 10−12 | 63.46 | 5.99 | <10−15 |
| 7 | OASL | 29.68 | 4.89 | 1.39 × 10−13 | 238.28 | 7.90 | <10−15 |
| 8 | IVL | 13.95 | 3.80 | 1.29 × 10−7 | 4.63 | 2.21 | <10−15 |
| 9 | OAS2 | 12.95 | 3.70 | 7.54 × 10−10 | 22.19 | 4.03 | <10−15 |
| 10 | PMCH | 12.45 | 3.64 | 1.19 × 10−5 | 2.84 | 1.51 | <10−15 |
| 11 | CTLA4 | 11.21 | 3.49 | 6.05 × 10−5 | 16.31 | 4.03 | <10−15 |
| 12 | HERC6 | 10.67 | 3.42 | 3.40 × 10−6 | 16.13 | 4.01 | <10−15 |
| 13 | CXCL10 | 9.42 | 3.24 | 7.79 × 10−7 | 24.66 | 4.62 | <10−15 |
| 14 | CXCL11 | 9.40 | 3.23 | 1.18 × 10−5 | 2.06 | 1.04 | 4.17 × 10−6 |
| 15 | IL1B | 8.80 | 3.14 | 7.61 × 10−7 | 7.04 | 2.82 | <10−15 |
| 16 | MX1 | 8.44 | 3.08 | 2.19 × 10−8 | 8.71 | 3.12 | <10−15 |
| 17 | NAMPT | 5.93 | 2.57 | 7.75 × 10−8 | 20.59 | 4.36 | <10−15 |
| 18 | STAT1 | 5.81 | 2.54 | 4.37 × 10−7 | 11.79 | 3.56 | <10−15 |
| 19 | CARHSP1 | 5.78 | 2.53 | 3.73 × 10−9 | 7.58 | 2.92 | <10−15 |
| 20 | MMP9 | 5.56 | 2.47 | 8.38 × 10−4 | 2.54 | 1.34 | 4.56 × 10−9 |
| 21 | CCNE1 | 5.54 | 2.47 | 5.33 × 10−5 | 5.71 | 2.51 | <10−15 |
| 22 | CXCL9 | 5.39 | 2.43 | 1.42 × 10−5 | 15.68 | 3.97 | <10−15 |
| 23 | CCL18 | 4.67 | 2.22 | 4.64 × 10−5 | 4.77 | 2.25 | 1.77 × 10−9 |
| 24 | STEAP4 | 4.05 | 2.02 | 3.10 × 10−5 | 8.33 | 3.06 | <10−15 |
| 25 | CCNB1 | 4.00 | 2.00 | 7.16 × 10−6 | 8.74 | 3.13 | <10−15 |
| 26 | S100P | 3.63 | 1.86 | 5.24 × 10−4 | 3.2 | 1.68 | 7.60 × 10−14 |
| 27 | CCNA2 | 3.62 | 1.85 | 2.34 × 10−4 | 14.28 | 3.84 | <10−15 |
| 28 | CEBPD | 2.03 | 1.02 | 1.34 × 10−2 | 7.43 | 2.89 | <10−15 |
| 29 | ADAM10 | 1.58 | 0.66 | 7.64 × 10−2 | 4.41 | 2.14 | <10−15 |
| 30 | SNCA | −1.27 | −0.35 | 4.99 × 10−1 | −3.71 | −1.89 | <10−15 |
| 31 | NR1H3 | −1.61 | −0.69 | 1.74 × 10−2 | −2.69 | −1.43 | <10−15 |
| 32 | NTRK2 | −1.68 | −0.75 | 5.43 × 10−2 | −9.22 | −3.20 | <10−15 |
| 33 | KRT33A | −1.84 | −0.88 | 4.28 × 10−1 | −2.19 | −1.13 | 6.00 × 10−4 |
| 34 | CD207 | −2.09 | −1.06 | 1.75 × 10−1 | −2.96 | −1.57 | 2.04 × 10−11 |
| 35 | KRT73 | −2.14 | −1.10 | 8.42 × 10−3 | −2.17 | −1.12 | 6.86 × 10−5 |
| 36 | KRT18 | −2.17 | −1.12 | 3.87 × 10−4 | −9.17 | −3.20 | <10−15 |
| 37 | LPL | −2.21 | −1.14 | 8.42 × 10−3 | −6.25 | −2.64 | 7.02 × 10−13 |
| 38 | KRT19 | −2.45 | −1.29 | 1.28 × 10−3 | −8.35 | −3.06 | <10−15 |
| 39 | ACTA2 | −2.75 | −1.46 | 7.41 × 10−4 | −3.69 | −1.88 | <10−15 |
| 40 | APOC1 | −3.12 | −1.64 | 5.55 × 10−3 | −7.62 | −2.93 | <10−15 |
| 41 | MUC1 | −3.55 | −1.83 | 1.51 × 10−3 | −6.10 | −2.61 | 2.15 × 10−11 |
| 42 | FADS2 | −5.83 | −2.54 | 2.02 × 10−2 | −6.43 | −2.68 | 1.29 × 10−11 |
| 43 | FADS1 | −5.96 | −2.58 | 6.69 × 10−4 | −15.95 | −4.00 | 2.27 × 10−15 |
| Borderline genes | |||||||
| 44 | IL22 | 168.03 | 7.39 | 5.67 × 10−14 | 1.19 | 0.25 | 2.56 × 10−2 |
| 45 | S100A7 | 44.94 | 5.49 | 2.01 × 10−12 | 1.62 | 0.70 | <10−15 |
| 46 | CD69 | 2.43 | 1.28 | 1.82 × 10−2 | 1.71 | 0.77 | 1.62 × 10−6 |
| 47 | CD209 | 1.49 | 0.57 | 3.52 × 10−1 | 1.58 | 0.66 | 2.40 × 10−3 |
| 48 | JAK2 | 1.46 | 0.55 | 1.42 × 10−1 | 1.47 | 0.56 | 2.21 × 10−7 |
| 49 | ITGAM | −1.15 | −0.20 | 7.92 × 10−1 | 1.63 | 0.70 | 5.00 × 10−4 |
| 50 | ITGAX | −1.25 | −0.32 | 6.63 × 10−1 | 1.69 | 0.76 | 1.49 × 10−8 |
Abbreviations: DEGs, differentially expressed genes; RT-PCR, real-time reverse transcriptase PCR. Genes 1–43 were chosen among those DEGs by microarray analysis, with the exception of gene 29 (ADAM10), which was borderline. Additional borderline genes (44–50) were also confirmed.