Table 6

Genes differentiating clinical stage

Gene symbolGene nameFold changePFDR
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 
Gene symbolGene nameFold changePFDR
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.

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