Table 6.
Genes differentiating clinical stage
| Gene symbol | Gene name | Fold change | P | FDR |
|---|---|---|---|---|
| Up-regulated in stage IA/IB | ||||
| HLA-DRB4 | mMajor histocompatibility complex, class II, DR β 4 | 4.53 | .003 | .048 |
| WIF1 | WNT inhibitory factor 1 | 4.41 | < .001 | < .001 |
| CD207 | CD207 antigen, langerin | 3.63 | < .001 | < .001 |
| FCGBP | Fc fragment of IgG binding protein | 2.87 | < .001 | .017 |
| MATN4 | Matrilin 4 | 2.79 | < .001 | < .001 |
| HLA-DQB2 | Major histocompatibility complex, class II, DQ β 2 | 2.74 | < .001 | < .001 |
| CD1A | CD1A antigen, a polypeptide | 2.60 | < .001 | < .001 |
| FCER1A | Fc fragment of IgE, high affinity I, receptor for α polypeptide | 2.45 | < .001 | .029 |
| S100B | S100 calcium-binding protein β (neural) | 2.17 | < .001 | .017 |
| KRT18 | Keratin 18 | 2.06 | .003 | .047 |
| LAMC3 | Laminin γ 3 | 2.05 | .002 | .043 |
| CTSG | Cathepsin G | 2.04 | < .001 | < .001 |
| CMA1 | Chymase 1, mast cell | 2.03 | < .001 | < .001 |
| GSTT1 | Glutathione S-transferase θ 1 | 2.03 | < .001 | .029 |
| HLF | Hepatic leukemia factor | 2.00 | .002 | .039 |
| CD1C | CD1C antigen, c polypeptide | 1.94 | .002 | .043 |
| FRZB | Frizzled-related protein | 1.94 | < .001 | .029 |
| KRT15 | Keratin 15 | 1.86 | .001 | .036 |
| MMP27 | Matrix metalloproteinase 27 | 1.85 | .003 | .044 |
| PADI2 | Peptidyl arginine deiminase, type II | 1.78 | < .001 | .017 |
| SCEL | Sciellin | 1.78 | .002 | .043 |
| TCF7L1 | Tanscription factor 7-like 1 (T-cell specific, HMG-box) | 1.73 | < .001 | .023 |
| LTBP4 | Latent transforming growth factor β–binding protein 4 | 1.70 | < .001 | .033 |
| CTNNBIP1 | Catenin β interacting protein 1 | 1.68 | .003 | .046 |
| COL21A1 | Collagen, type XXI α 1 | 1.67 | .003 | .047 |
| KIT | v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog | 1.66 | < .001 | < .001 |
| S100A1 | S100 calcium-binding protein A1 | 1.64 | < .001 | < .001 |
| NFIB | Nuclear factor I/B | 1.60 | .002 | .039 |
| IL11RA | Interleukin-11 receptor α | 1.59 | < .001 | < .001 |
| MATN2 | Matrilin 2 | 1.53 | < .001 | .017 |
| Up-regulated in stage IIA/III | ||||
| AIM2 | Absent in melanoma 2 | 4.62 | < .001 | < .001 |
| LAG3 | Lymphocyte-activation gene 3 | 4.42 | < .001 | < .001 |
| APOBEC3B | Apolipoprotein B mRNA–editing enzyme, catalytic polypeptide-like 3B | 3.37 | < .001 | .023 |
| SH2D1A | SH2 domain protein 1A, Duncan disease (lymphoproliferative syndrome) | 3.04 | .002 | .039 |
| TNIP3 | TNFAIP3 interacting protein 3 | 2.75 | < .001 | .023 |
| IGH | Ig heavy locus | 2.68 | .002 | .041 |
| IL21R | Interleukin-21 receptor | 2.67 | < .001 | .017 |
| TNFSF14 | Tumor necrosis factor (ligand) superfamily, member 14 | 2.64 | .002 | .039 |
| LILRA3 | Leukocyte Ig-like receptor, subfamily A (without TM domain), member 3 | 2.64 | .002 | .043 |
| CCR4 | Chemokine (C-C motif) receptor 4 | 2.52 | < .001 | .023 |
| G1P2 | Interferon α–inducible protein (clone IFI-15K) | 2.49 | < .001 | .029 |
| ISG20 | Interferon-stimulated gene 20 kDa | 2.42 | < .001 | < .001 |
| TNIK | TRAF2 and NCK interacting kinase | 2.39 | < .001 | .017 |
| IGL | Ig lambda locus, constant, variable and joining regions | 2.36 | .002 | .042 |
| PRKCQ | Protein kinase C θ | 2.24 | .002 | .041 |
| OAS2 | 2′-5′-oligoadenylate synthetase 2, 69/71 kDa | 2.18 | < .001 | < .001 |
| OAS1 | 2′,5′-oligoadenylate synthetase 1, 40/46 kDa | 2.12 | .002 | .039 |
| IGKC; IGKV1-5 | Ig κ constant and variable 1-5 | 2.09 | .003 | .050 |
| CCR7 | Chemokine (C-C motif) receptor 7 | 2.08 | .001 | .036 |
| ZAP70 | ζ-chain (TCR)–associated protein kinase 70 kDa | 2.05 | .002 | .041 |
| CCND2 | Cyclin D2 | 2.00 | .002 | .039 |
| GBP1 | Guanylate-binding protein 1, interferon-inducible, 67 kDa | 1.95 | .003 | .046 |
| ZC3HAV1 | Zinc finger CCCH type, antiviral 1 | 1.91 | < .001 | < .001 |
| IL2RB | Interleukin-2 receptor β | 1.90 | .002 | .041 |
| PTPRCAP | Protein tyrosine phosphatase, receptor type, C-associated protein | 1.90 | .003 | .048 |
| C1GALT1 | Core 1 synthase | 1.89 | < .001 | .017 |
| C5R1 | Complement component 5 receptor 1 (C5a ligand) | 1.88 | < .001 | .033 |
| PIM2 | pim-2 oncogene | 1.88 | .003 | .050 |
| ITGB7 | Integrin β7 | 1.84 | .002 | .042 |
| DDX58 | DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 | 1.84 | .002 | .041 |
| RARRES3 | Retinoic acid receptor responder (tazarotene induced) 3 | 1.83 | .003 | .047 |
| IFRG28 | 28 kDa interferon-responsive protein | 1.82 | .001 | .036 |
| MX2 | Myxovirus (influenza virus) resistance 2 (mouse) | 1.75 | .002 | .043 |
| SP100 (IFI41) | Nuclear antigen Sp100 | 1.71 | < .001 | < .001 |
| VAV1 | vav 1 oncogene | 1.68 | .001 | .036 |
| LCP2 | Lymphocyte cytosolic protein 2 | 1.65 | .002 | .042 |
| NFATC2IP | NFAT, cytoplasmic, calcineurin-dependent 2 interacting protein | 1.65 | < .001 | < .001 |
| DUSP5 | Dual specificity phosphatase 5 | 1.64 | < .001 | .017 |
| IL10 | Interleukin-10 | 1.64 | .002 | .042 |
| BAX | BCL2-associated X protein | 1.63 | .002 | .043 |
| FYB | FYN binding protein (FYB-120/130) | 1.61 | < .001 | .023 |
| NUP98 | Nucleoporin 98 kDa | 1.60 | .002 | .041 |
| HSPD1 | heat shock 60 kDa protein 1 (chaperonin) | 1.56 | .003 | .048 |
| IFNAR2 | Interferon (α, β, and ω) receptor 2 | 1.53 | < .001 | < .001 |
| RAP140 | Retinoblastoma-associated protein 140 (CTCL tumor antigen se89-1) | 1.52 | < .001 | .033 |
| FGFR1OP | FGFR1 oncogene partner | 1.51 | < .001 | < .001 |
Selected genes with up-regulated expression in the specified stages are shown, with fold change greater than or equal to 1.5, P value less than or equal to .05, and FDR less than or equal to .05.