Table 3.
Differentially expressed genes predicting for HPV-positive versus HPV-negative samples
| Gene | This study NanoString P value | TCGA HPV+ (n = 36) % Diff expa | TCGA HPV− (n = 243) % diff expa |
|---|---|---|---|
| OGG1 | 3.89E-05 | 11.1 | 1.4 |
| CSF3R | 0.0002 | 0 | 3.2 |
| WNT10B | 0.0006 | 19.4 | 5.0 |
| WNT1 | 0.0009 | 2.8 | 0.7 |
| PDGFA | 0.0020 | 2.8 | 9.0 |
| IL4 | 0.0035 | 5.6 | 4.3 |
| E2F3 | 0.0057 | 11.1 | 9.3 |
| SIAH1 | 0.0072 | 2.8 | 7.2 |
| GATA1 | 0.0086 | 5.6 | 4.7 |
| RB1 | 0.0091 | 13.9 | 8.6 |
| PTGS2 | 0.0097 | 0 | 2.5 |
| BLM | 0.0112 | 11.1 | 6.5 |
| CDKN2A | 0.0113 | 5.6 | 1.1 |
| IRF1 | 0.0147 | 5.6 | 3.2 |
| TFE3 | 0.0155 | 0 | 6.8 |
| BCL2A1 | 0.0221 | 0 | 1.8 |
| TNF | 0.0223 | 0 | 1.8 |
| REL | 0.0225 | 13.9 | 6.1 |
| CEBPA | 0.0241 | 8.3 | 5.7 |
| FGR | 0.0270 | 5.6 | 4.7 |
| SYK | 0.0275 | 33.3 | 6.5 |
| IL1A | 0.0278 | 0 | 5.7 |
| PLG | 0.0357 | 0 | 2.9 |
| CDKN2C | 0.0360 | 47.2 | 6.5 |
| NRAS | 0.0366 | 0 | 3.6 |
| MAP3K8 | 0.0409 | 16.7 | 5.0 |
| CSF3 | 0.0418 | 0 | 1.8 |
| CSF1R | 0.0443 | 2.8 | 1.8 |
| MST1R | 0.0469 | 11.1 | 3.9 |
| XPC | 0.0493 | 8.3 | 3.2 |
One way ANOVA with no batch affect correction was performed on the NanoString gene expression dataset for the eight samples used in this study as described in the Methods section. An unadjusted P value cut-off of 0.05 with fold change cut-off of ≥10 was used to generate this HPV classifier gene list. Frequency of differential expression by RNA-Seq in the TCGA HNSCC dataset (in revision July 2014) was assessed as separate HPV-positive and HPV-negative cohorts using cBioPortal. This gene list was parsed based on NanoString P values and frequency in HPV-positive and HPV-negative TCGA cohorts to arrive at the 11 gene classifier
aHNSCC RNA-Seq (TCGA, in revision, July 2014)