Table 1. Genes, differentially expressed in nu61 relative to SCC-61 and common between experiments 1 and 2.
| ID | Name | Symbol | N/S R, experiment 1 | N/S R, experiment 2 | IFN/UTC R, experiment 3 |
|---|---|---|---|---|---|
| 202869_at | 2′,5′-oligoadenylate synthetase 1, 40/46kDa | OAS1*† | 3.286 | 2.282 | 3.922 |
| 205552_s_at | 2′,5′-oligoadenylate synthetase 1, 40/46kDa | OAS1*† | 4.506 | 2.491 | 4.290 |
| 218400_at | 2′-5′-oligoadenylate synthetase 3, 100kDa | OAS3*† | 3.624 | 2.318 | 3.113 |
| 201641_at | Bone marrow stromal cell antigen 2 | BST2*† | 10.343 | 5.196 | 5.744 |
| 204533_at | IFNγ-inducible protein 10 | CXCL10* | 10.319 | 2.820 | 10.619 |
| 204439_at | Chromosome 1 ORF 29 | Clorf29*† | 33.479 | 45.942 | 4.793 |
| 205899_at | Cyclin A1 | CCNA1* | 2.172 | 2.376 | 2.443 |
| 218986_s_at | Hypothetical protein FLJ20035 | FLJ20035* | 8.787 | 6.389 | 3.798 |
| 219352_at | Hypothetical protein FLJ20637 | FLJ20637* | 7.315 | 3.441 | 4.096 |
| 208436_s_at | IFN regulatory factor 7 | IRF7* | 3.254 | 2.713 | 4.814 |
| 204415_at | IFN, α-inducible protein | G1P3* | 3.401 | 5.341 | 5.451 |
| 205483_s_at | IFN, α-inducible protein | G1P2* | 8.500 | 6.452 | 4.967 |
| 202411_at | IFN, α-inducible protein 27 | IFI27*† | 5.425 | 9.462 | 4.231 |
| 209417_s_at | IFN-induced protein 35 | IFI35*† | 4.528 | 2.653 | 4.652 |
| 214059_at | IFN-induced protein 44 | IFI44*† | 5.654 | 3.212 | 3.976 |
| 214453_s_at | IFN-induced protein 44 | IFI44*† | 8.102 | 4.187 | 4.151 |
| 204747_at | IFN-induced protein with tetratricopeptide repeats | IFIT4*† | 6.479 | 2.781 | 6.701 |
| 203153_at | IFN-induced protein with tetratricopeptide repeats 1 | IFIT1*† | 8.606 | 9.055 | 6.124 |
| 202086_at | IFN-inducible protein p78 | MX1*† | 6.204 | 6.327 | 4.240 |
| 205569_at | Lysosomal-associated membrane protein 3 | LAMP3*† | 7.084 | 3.025 | 11.535 |
| 219209_at | Melanoma differentiation-associated protein 5 | MDA5* | 2.617 | 2.761 | 5.238 |
| 202446_s_at | Phospholipid scramblase 1 | PLSCR1*† | 3.498 | 2.428 | 2.398 |
| 200887_s_at | Signal transducer and activator of transcription 1 | STAT1α*† | 2.370 | 2.578 | 2.430 |
| 209969_s_at | Signal transducer and activator of transcription 1 | STAT1β*† | 4.094 | 2.272 | 4.192 |
| 201110_s_at | Thrombospondin 1 | THBS1* | 2.496 | 3.542 | 2.837 |
| 200798_x_at | Myeloid cell leukemia sequence 1 (BCL2-related) | MCL1** | 2.146 | 2.496 | - |
| 200923_at | Lectin | LGALS3BP** | 2.226 | 2.288 | - |
| 201150_s_at | Tissue inhibitor of metalloproteinase 3 | TIMP3** | 2.419 | 2.498 | - |
| 201601_x_at | IFN induced transmembrane protein 1 (9-27) | IFITM1**† | 4.298 | 3.036 | - |
| 201893_x_at | Decorin | DCN** | 0.415 | 0.315 | - |
| 202145_at | Lymphocyte antigen 6 complex, locus E | LY6E** | 4.124 | 2.630 | - |
| 202409_at | Putative insulin-like growth factor 2-associated protein | NA**‡ | 0.046 | 0.377 | - |
| 202736_s_at | LSM4 homolog | LSM4** | 2.336 | 3.756 | - |
| 203148_s_at | Tripartite motif-containing 14 | TRIM14** | 3.270 | 3.175 | - |
| 204019_s_at | Likely ortholog of mouse Src homology 3 domain YSC-like 1 | SH3YL1** | 0.218 | 0.253 | - |
| 204417_at | Galactosylceramidase | GALC** | 2.190 | 2.968 | - |
| 204470_at | Chemokine (C-X-C motif) ligand 1 | CXCL1** | 3.093 | 2.470 | - |
| 204614_at | Serine (or cysteine) proteinase inhibitor | SERPINB2** | 0.358 | 0.428 | - |
| 205623_at | Aldehyde dehydrogenase 3 family | ALDH3A1** | 0.325 | 0.317 | - |
| 205829_at | Hydroxysteroid (17-β) dehydrogenase 1 | HSD17B1** | 3.428 | 4.291 | - |
| 206376_at | Homolog of rat orphan transporter v7-3 | NTT73** | 2.102 | 2.322 | - |
| 208282_x_at | Deleted in azoospermia 2 | DAZ2** | 2.138 | 3.192 | - |
| 208729_x_at | MHC, class 1, B | HLA-B** | 2.377 | 2.371 | - |
| 209301_at | Carbonic anhydrase II | CA2** | 2.655 | 2.480 | - |
| 211529_x_at | MHC, class 1, A | HLA-A** | 2.683 | 2.583 | - |
| 212463_at | CD59 | CD59** | 0.516 | 0.447 | - |
| 213194_at | Roundabout, axon guidance receptor, homolog 1 | ROBO1**† | 5.562 | 4.970 | - |
| 213294_at | Hypothetical protein FLJ38348 | FLJ38348** | 2.401 | 2.276 | - |
| 214657_s_at | Trophoblast-derived noncoding RNA | TncRNA** | 0.505 | 0.405 | - |
| 215239_x_at | Zinc finger protein 273 | ZNF273** | 0.463 | 0.414 | - |
| 216922_x_at | Deleted in azoospermia | DAZ** | 2.320 | 2.968 | - |
| 218669_at | RAP2C, member of RAS oncogene family | RAP2C** | 0.520 | 0.070 | - |
Shown are 52 genes, common between two independent experiments in vivo. Numbers represent the ratios of expression of genes in nu61 relative to SCC-61 (columns 5 and 6) or ratios of gene expression in nu61 exposed to IFNs relative to the untreated cells (column 7). Each target was counted as separate gene or potential gene isoform. OAS1, IFI44, and Stat1 are represented by two targets each. Stat1 targets correspond to α (200887_s_at) and β (209969_s_at) isoforms. Asterisks represent 25 genes overlapped with experiment 3 (response to IFN in vitro). Double asterisks represent 27 genes, not inducible by IFN in experiment 3. Daggers indicate the genes confirmed by the real-time PCR analysis. Not included here but also confirmed by the real-time PCR genes are: ISG15 (IFN-stimulated protein, 15 kDa), MX2 (IFN-regulated resistance GTP-binding protein MxB), TRIM22 (tripartite motif-containing 22), USP18 (ubiquitin-specific protease 18), CLCA4 (chloride channel, calcium-activated, member 4), HAIK1 (type 1 intermediate filament cytokeratin), KLK7 (kallikrein 7), PPP1R3C (protein phosphatase 1, regulatory subunit 3C), IGF2 (insulin-like growth factor 2), and RIL (LIM domain protein). Quantitative RT-PCR was performed with the pooled RNA samples, obtained from the first experiment (see text), and genes not shown here were selected based on the levels of expression, exceeding ±3 SD cutoff level (see Materials and Methods and Fig. 1) and producing primers, able to generate positive products in quantitative RT-PCR amplification reactions. Overall correlation between DNA array data and quantitative RT-PCR data, measured as Pearson's correlation coefficient, was 0.894.
NA, not available