Table 2.
Genes found differentially expressed in HPV-positive SCCHN versus normal oral epithelium
| Gene Title | Gene Symbol | Pooled variance t- Test fold change | SAM- Test fold change |
|---|---|---|---|
| Up-regulated genes | |||
| Apoptosis | |||
| lectin, galactoside-binding, soluble, 1 (galectin 1) | LGALS1 | 3.22 | 2.44 |
| Cell Adhesion | |||
| collagen, type XI, alpha 1 | COL11A1 | 6.29 | 8.84 |
| Cell Cycle Regulation | |||
| cyclin E2 | CCNE2 | 4.23 | 2.23 |
| cyclin-dependent kinase inhibitor 2A | CDKN2A | 16.59 | 8.04 |
| proliferating cell nuclear antigen | PCNA | 7.78 | 2.04 |
| retinoblastoma-like 1 (p107) | RBL1 | 6.09 | 2.37 |
| Chromatin assembly and modification | |||
| centromere protein F, 350/400ka (mitosin) | CENPF | 3.60 | 2.00 |
| SWI/SNF related, matrix associated, member 3 | SMARCA3 | 5.54 | 2.45 |
| Development | |||
| IGF-II mRNA-binding protein 3 | IMP-3 | 3.28 | 5.06 |
| DNA Repair | |||
| flap structure-specific endonuclease 1 | FEN1 | 3.3 | 2.28 |
| RAD51 associated protein 1 | RAD51AP1 | 3.65 | 2.14 |
| topoisomerase (DNA) II alpha 170kDa | TOP2A | 4.07 | 3.60 |
| DNA Replication | |||
| CDC7 cell division cycle 7 (S. cerevisiae) | CDC7 | 5.38 | 2.34 |
| MCM2 minichromosome maintenance deficient 2, mitotin | MCM2 | 4.39 | 3.36 |
| MCM3 minichromosome maintenance deficient 3 | MCM3 | 3.86 | 2.00 |
| Miscellaneous | |||
| lumican | LUM | 4.18 | 3.41 |
| mesoderm specific transcript homolog (mouse) | MEST | 8.88 | 3.01 |
| squamous cell carcinoma antigen recognised by T cells 3 | SART3 | 8.44 | 2.10 |
| Transcription Regulation | |||
| interferon regulatory factor 1 | IRF1 | 6.28 | 2.66 |
| Wnt Receptor Signaling Pathway | |||
| secreted frizzled-related protein 4 | SFRP4 | 4.45 | 5.61 |
|
| |||
| Down-regulated genes | |||
| Cell Adhesion | |||
| alpha-2-glycoprotein 1, zinc | AZGP1 | −3.07 | −13.77 |
| Cell Cycle Regulation | |||
| Ras association (RalGDS/AF-6) domain family 1 | RASSF1 | −3.96 | −2.51 |
| Cell Differentiation | |||
| deleted in malignant brain tumors 1 | DMBT1 | −4.04 | −9.31 |
| NDRG family member 2 | NDRG2 | −2.64 | −2.56 |
| transglutaminase 3 | TGM3 | −7.14 | −7.55 |
| Cellular Metabolism | |||
| aldehyde dehydrogenase 1 family, member A1 | ALDH1A1 | −4.60 | −4.85 |
| sulfotransferase family, cytosolic, 2B, member 1 | SULT2B1 | −2.33 | −3.00 |
| UDP glucuronosyltransferase 1 family, A10 / A8 / A7 / A6 | UGT1A | −3.71 | −2.56 |
| DNA Repair | |||
| mutL homolog 3 (E. coli) | MLH3 | −2.53 | −2.06 |
| Immune response | |||
| chemokine (C-C motif) ligand 14 / chemokine ligand 15 | CCL14/CCL15 | −5.23 | −2.10 |
| interleukin 18 (interferon-gamma-inducing factor) | IL18 | −4.47 | −4.18 |
| trefoil factor 3 (intestinal) | TFF3 | −2.61 | −10.42 |
| Miscellaneous | |||
| envoplakin | EVPL | −3.26 | −3.55 |
| huntingtin interacting protein-1-related | HIP1R | −3.72 | −2.65 |
| kallikrein 11 | KLK11 | −3.70 | −7.28 |
| kallikrein 13 | KLK13 | −4.41 | −12.15 |
| protease, serine, 3 (mesotrypsin) | PRSS3 | −3.88 | −7.21 |
| Signal Transduction | |||
| fibroblast growth factor binding protein 1 | FGFBP1 | −2.12 | −3.27 |
| insulin-like growth factor binding protein 6 | IGFBP6 | −3.69 | −7.74 |
| Transcription Regulation | |||
| BarH-like homeobox 2 | BARX2 | −2.96 | −3.71 |