Table 3. Altered transcript expression in PTC samples as compared to benign counterparts from different donors.
| Gene | P-value (PTC vs benign) | P-value with FDR (PTC vs benign) | Fold change | Total number of samples | Number of samples with expression value > 50 (linear scale) |
|---|---|---|---|---|---|
| Without consideration of clinical aggressiveness | |||||
| BCL2 | 5.86 × 10−11 | 3.51 × 10−10 | −3.17 | 34 | 34 |
| BMAL1 | 5.56 × 10−10 | 2.50 × 10−9 | 4.44 | 34 | 34 |
| CHEK1 | 8.88 × 10−4 | 1.45 × 10−3 | 2.97 | 34 | 32 |
| c-KIT | 4.60 × 10−7 | 1.38 × 10−6 | –10.80 | 34 | 32 |
| c-MET | 5.15 × 10−13 | 9.27 × 10−12 | 5.96 | 34 | 34 |
| PPARγ | 6.33 × 10−6 | 1.42 × 10−5 | −3.96 | 34 | 31 |
| TG | 2.71 × 10−6 | 6.96 × 10−6 | −3.85 | 34 | 34 |
| TIMP1 | 1.02 × 10−11 | 9.18 × 10−11 | 6.27 | 34 | 34 |
| VEGFR1 | 2.42 × 10−4 | 4.36 × 10−4 | –2.18 | 34 | 34 |
| ALDH1 | 3.97 × 10−8 | 6.75 × 10−7 | –5.69 | 20 | 20 |
| DIO2 | 2.51 × 10−3 | 5.34 × 10−3 | –3.61 | 20 | 20 |
| With consideration of clinical aggressiveness: more aggressive PTC (group II in Table 1) | |||||
| AKT2 | 6.75 × 10−5 | 1.35 × 10−4 | −2.01 | 32 | 32 |
| BCL2 | 1.28 × 10−10 | 7.70 × 10−10 | −3.24 | 32 | 32 |
| BMAL1 | 1.74 × 10−9 | 7.82 × 10−9 | 4.05 | 32 | 32 |
| CHEK1 | 1.30 × 10−3 | 1.79 × 10−3 | 3.01 | 32 | 30 |
| CRY2 | 1.40 × 10−8 | 5.02 × 10−8 | −2.02 | 32 | 32 |
| c-KIT | 3.22 × 10−7 | 9.65 × 10−7 | −12.21 | 32 | 30 |
| c-MET | 2.48 × 10−12 | 4.47 × 10−11 | 5.99 | 32 | 32 |
| PPARγ | 1.61 × 10−6 | 3.61 × 10−6 | −4.46 | 32 | 29 |
| TG | 1.14 × 10−6 | 2.92 × 10−6 | −4.23 | 32 | 32 |
| TIMP1 | 5.38 × 10−11 | 4.85 × 10−10 | 5.91 | 32 | 32 |
| VEGFR1 | 7.51 × 10−5 | 1.35 × 10−4 | −2.37 | 32 | 32 |
| ALDH1 | 1.49 × 10−7 | 2.53 × 10−6 | −5.64 | 19 | 19 |
| DIO2 | 3.81 × 10−3 | 8.10 × 10−3 | −3.65 | 19 | 19 |
The fold changes between the transcript expression levels in PTC and benign (B) samples were calculated as follows: Fc (fold change) PTC/B = 2(average log(PTC)-average log(B)) where PTC and B are normalized expression values obtained by NanoString analysis for the respective samples.