Table 3.
Lists of Differentially Expressed Genes in the Horizontal and Vertical Comparisons: Nonmetastatic Tumor (versus LN Metastases (P < 0.005, fc > 1.5)
| P value | fc | Gene description | Accession no. | Probe set |
|---|---|---|---|---|
| Top 20 genes up-regulated in the nonmetastatic tumor (versus the LN metastases) | ||||
| 0.000024 | 1.56 | Dual specificity phosphatase 4 | BC002671.1 | 204015_s_at |
| 0.000028 | 3.08 | Transforming growth factor, β-induced, 68 kd | NM_000358.1 | 201506_at |
| 0.00003 | 1.99 | Ras-GTPase-activating protein SH3-domain-binding protein | BG500067 | 201503_at |
| 0.000035 | 1.85 | Non-POU domain containing, octamer-binding | NM_007363.2 | 200057_s_at |
| 0.00004 | 1.56 | Superoxide dismutase 1, soluble (amyotrophic lateral sclerosis 1 (adult) | NM_000454.1 | 200642_at |
| 0.000048 | 2.54 | KIAA0843 protein | NM_014945.1 | 205730_s_at |
| 0.000052 | 80.77 | Cancer/testis antigen 1 | AF038567.1 | 211674_x_at |
| 0.000056 | 1.85 | Nuclear pore complex interacting protein | NM_006985.1 | 204538_x_at |
| 0.000068 | 1.67 | Integrin, α 6 | NM_000210.1 | 201656_at |
| 0.000074 | 3.11 | Plectin 1, intermediate filament binding protein 500 kd | Z54367 | 216971_s_at |
| 0.00008 | 2.15 | DEAD (Asp-Glu-Ala-Asp) box polypeptide 41 | NM_016222.1 | 217840_at |
| 0.000085 | 1.6 | ATPase, H+ transporting, lysosomal 16 kd, V0 subunit c | NM_001694.1 | 200954_at |
| 0.000088 | 1.96 | Cytoplasmic FMR1 interacting protein 1 | BC005097.1 | 208923_at |
| 0.000089 | 1.91 | Parvulin | BE674061 | 214224_s_at |
| 0.000094 | 2.19 | Sialyltransferase 4C (β-galactoside α-2,3-sialyltransferase) | NM_006278.1 | 203759_at |
| 0.000095 | 2.36 | STIP1 homology and U-Box containing protein 1 | NM_005861.1 | 217934_x_at |
| 0.000096 | 2.49 | Mahogunin, ring finger 1 | AB011116.1 | 212576_at |
| 0.000099 | 2.23 | Nonmetastatic cells 4, protein expressed in | AL523860 | 212739_s_at |
| 0.000104 | 1.97 | MAX interacting protein 1 | NM_005962.1 | 202364_at |
| 0.000121 | 2.54 | Regulator of G-protein signaling 10 | NM_002925.2 | 204316_at |
| Top 20 genes up-regulated in the LN metastases (versus the nonmetastatic tumor) | ||||
| 0 | 6.63 | Osteopontin | M83248.1 | 209875_s_at |
| 0.000007 | 3.4 | Ornithine decarboxylase 1 | NM_002539.1 | 200790_at |
| 0.000007 | 2.2 | RAB27A, member RAS oncogene family | BE502030 | 209514_s_at |
| 0.00001 | 13 | Baculoviral IAP repeat-containing 7 (livin) | NM_022161.1 | 220451_s_at |
| 0.00001 | 6.23 | Sulfotransferase family, cytosolic, 1C, member 1 | AF026303.1 | 205342_s_at |
| 0.00001 | 3.94 | Preferentially expressed antigen in melanoma | NM_006115.1 | 204086_at |
| 0.00001 | 3.67 | KIAA0930 protein | AK025608.1 | 217118_s_at |
| 0.00001 | 2.4 | Mitochondrial ribosomal protein L35 | NM_016622.1 | 218890_x_at |
| 0.000013 | 39.88 | Chromosome 1 open reading frame 34 | BC004399.1 | 210652_s_at |
| 0.000021 | 3.73 | GREB1 protein | NM_014668.1 | 205862_at |
| 0.000023 | 2.45 | Malate dehydrogenase 1, NAD (soluble) | NM_005917.1 | 200978_at |
| 0.000023 | 2.24 | Adaptor-related protein complex 2, σ 1 subunit | NM_021575.1 | 208074_s_at |
| 0.000024 | 2.42 | N-Acylsphingosine amidohydrolase (acid ceramidase) 1 | U47674.1 | 210980_s_at |
| 0.000025 | 2.07 | Adaptor-related protein complex 2, σ 1 subunit | BC006337.1 | 211047_x_at |
| 0.000027 | 1.9 | Sorting nexin 10 | NM_013322.1 | 218404_at |
| 0.000028 | 11.05 | Aldehyde dehydrogenase 1 family, member A1 | NM_000689.1 | 212224_at |
| 0.00003 | 6.06 | Serine (or cysteine) proteinase inhibitor, clade F, member 1 | NM_002615.1 | 202283_at |
| 0.00003 | 2.92 | Neutral sphingomyelinase (N-SMase) activation associated factor | NM_003580.1 | 203269_at |
| 0.000032 | 4519.89 | G antigen 4 | NM_001473.1 | 207663_x_at |
| 0.000032 | 2.36 | N-acylsphingosine amidohydrolase (acid ceramidase) 1 | AI934569 | 213702_x_at |