Table 2.
Functional gene classes enriched in Merkel cell polyomavirus-negative compared to -positive tumors.
| KEGG pathway1, probe-set | Gene | Description | Fold2 |
|---|---|---|---|
| Axon guidance | |||
| 229288_at | EPHA7 | EPH receptor A7 | 4.41 |
| 214607_at | PAK3 | p21 protein (Cdc42/Rac)-activated kinase 3 | 4.72 |
| 231325_at | UNC5D | unc-5 homolog D (C. elegans) | 4.29 |
| 200965_s_at | ABLIM1 | actin binding LIM protein 1 | 3.53 |
| 227449_at | EPHA4 | EPH receptor A4 | 3.27 |
| 230425_at | EPHB1 | EPH receptor B1 | 4.06 |
| 209589_s_at | EPHB2 | EPH receptor B2 | 2.50 |
| 236088_at | NTNG1 | netrin G1 | 2.36 |
| 213169_at | SEMA5A | semaphorin 5A | 2.03 |
| 223610_at | SEMA5B | semaphorin 5B | 2.16 |
| 32541_at | PPP3CC | protein phosphatase 3, catalytic subunit, gamma isozyme | 0.49 |
| 212298_at | NRP1 | neuropilin 1 | 0.48 |
| 240425_x_at | ROBO2 | roundabout, axon guidance receptor, homolog 2 (Drosophila) | 0.43 |
| 227955_s_at | EFNA5 | ephrin-A5 | 0.29 |
| 213603_s_at | RAC2 | rho family, small GTP binding protein Rac2 | 0.36 |
| 206941_x_at | SEMA3E | semaphorin 3E | 0.11 |
| Pathways in cancer | |||
| 208606_s_at | WNT4 | wingless-type MMTV integration site family, member 4 | 3.94 |
| 203638_s_at | FGFR2 | fibroblast growth factor receptor 2 | 2.75 |
| 210512_s_at | VEGFA | vascular endothelial growth factor A | 2.73 |
| 205463_s_at | PDGFA | platelet-derived growth factor alpha polypeptide | 2.25 |
| 230288_at | FGF14 | fibroblast growth factor 14 | 2.06 |
| 227271_at | FGF11 | fibroblast growth factor 11 | 2.07 |
| 227314_at | ITGA2 | integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) | 2.25 |
| 221029_s_at | WNT5B | wingless-type MMTV integration site family, member 5B | 2.04 |
| 239178_a | FGF9 | fibroblast growth factor 9 (glia-activating factor) | 0.43 |
| 203132_at | RB1 | retinoblastoma 1 | 0.41 |
| 223709_s_at | WNT10A | wingless-type MMTV integration site family, member 10A | 0.28 |
| Notch signaling pathway | |||
| 224215_s_at | DLL1 | delta-like 1 (Drosophila) | 4.99 |
| 201218_at | CTBP2 | C-terminal binding protein 2 | 2.71 |
| 203394_s_at | HES1 | hairy and enhancer of split 1, (Drosophila) | 2.50 |
| 32137_at | JAG2 | jagged 2 | 2.35 |
| 216268_s_at | JAG1 | jagged 1 | 2.25 |
| Neuroactive ligand-receptor interaction | |||
| 209990_s_at | GABBR2 | gamma-aminobutyric acid (GABA) B receptor, 2 | 7.94 |
| 231192_at | LPAR3 | lysophosphatidic acid receptor 3 | 5.98 |
| 221107_at | CHRNA9 | cholinergic receptor, nicotinic, alpha 9 | 4.41 |
| 231384_at | GRIN2A | glutamate receptor, ionotropic, N-methyl D-aspartate 2A | 2.69 |
| 209793_at | GRIA1 | glutamate receptor, ionotropic, AMPA 1 | 2.62 |
| 213506_at | F2RL1 | coagulation factor II (thrombin) receptor-like 1 | 2.30 |
| 229944_ at | OPRK1 | opioid receptor, kappa 1 | 2.14 |
| 229309_at | ADRB1 | adrenergic, beta-1-, receptor | 2.0 |
| 230593_at | GRIK3 | glutamate receptor, ionotropic, kainate 3 | 2.03 |
| 206128_at | ADRA2C | adrenergic, alpha-2C-, receptor | 0.41 |
| 205279_s_at | GLRB | glycine receptor, beta | 0.38 |
| 211772_x_at | CHRNA3 | cholinergic receptor, nicotinic, alpha 3 | 0.36 |
| 229686_at | P2RY8 | purinergic receptor P2Y, G-protein coupled, 8 | 0.39 |
| 213845_at | GRIK2 | glutamate receptor, ionotropic, kainate 2 | 0.38 |
| 207307_at | HTR2C | 5-hydroxytryptamine (serotonin) receptor 2C | 0.38 |
1
KEGG pathways for each gene group are shown in italics. Note that although a functional class/pathway may be upregulated as a whole by KEGG analysis, some individual genes within a class may not display upregulation.
2
Fold change represents relative array transcript expression in MCPyV-negative Merkel cell carcinoma (MCC) relative to MCPyV-positive MCC. A central value for each probe-set was determined by averaging log-transformed data, and taking the anti-logarithm.