TABLE 3.
Most upregulated and downregulated genes on the Clontech +TPA arrays after KSHV infectiona
| Regulation | Rank | C-SD | I(%) | I-R | Gene name | Unigene | Intensity
|
|
|---|---|---|---|---|---|---|---|---|
| Uninfected | Infected | |||||||
| Up | 1 | +7.6 | — | — | Metallothionein (MTH1) | Hs.83326 | 4,470 | 25,030 |
| 2 | +6.3 | — | — | Exodus 2 beta chemokine | Hs.57907 | 3,110 | 17,360 | |
| 3 | +5.4 | 93.1 | +1.7 | RAD23A UV excision repair protein (HHR23A) | Hs.180455 | 1,440 | 7,780 | |
| 4 | +4.9 | — | — | Osteopontin | Hs.313 | 740 | 8,200 | |
| 5 | +4.7 | — | — | DCR3 decoy receptor 3 | Hs.278556 | 1,270 | 9,280 | |
| 6 | +4.6 | 99.7 | +2.8, +2.6 | RDC1 G-protein-coupled receptor homolog | Hs.23016 | 1,470 | 11,770 | |
| 7 | +4.2 | — | — | Tripeptidyl-peptidase 1 (TPP) | Hs.20478 | 4,130 | 10,620 | |
| 8 | +4.1 | NR | Proteasome component C9 | Hs.251531 | 990 | 5,110 | ||
| 9 | +3.9 | ND | Calgranulin B (migration inhibitory factor MRP14) | Hs.112405 | 570 | 4,340 | ||
| 10 | +3.6 | 17.4 | −1.2 | TIMP1 inhibitor of metalloproteinases | Hs.5831 | 25,420 | 33,390 | |
| 11 | +3.6 | NR | Cytochrome P450 II A6 | Hs.183584 | 1,020 | 5,890 | ||
| 12 | +3.6 | NR | Bcl3 (B-cell lymphoma 3) | Hs.31210 | 4,570 | 11,400 | ||
| 13 | +3.5 | — | — | TIMP4 inhibitor of metalloproteinases | Hs.190787 | 1,620 | 5,060 | |
| 14 | +3.3 | 86.9 | +1.5 | Interferon-induced leucine zipper protein | Hs.50842 | 4,960 | 8,540 | |
| 15, 27 | +3.2, +2.5 | 89.5 | +1.6 | IRF7 (interferon regulatory factor 7) | Hs.166120 | 940 | 2,960 | |
| 16 | +3.2 | 10.0 | −1.3 | RAMP2 (receptor activation modifier 2) | Hs.155106 | 8,050 | 16,220 | |
| 17 | +3.1 | 96.1 | +1.8 | CDC25B—cell division cycle protein | Hs.153752 | 3,560 | 7,050 | |
| 18 | +3.1 | 00.2 | −4.5 | PAI-1 endothelial plasminogen activator inhibitor-1 | Hs.82085 | 4,960 | 8,550 | |
| 19 | +3.0 | — | — | Smooth muscle cell LIM protein | Hs.10526 | 480 | 3,880 | |
| 20 | +2.8, +1.3 | 94.3 | +1.7 | Neurogranin | Hs.26944 | 3,560 | 6,450 | |
| 22 | +2.7 | NR | ICAM2 (intracellular adhesion molecule 2) | Hs.83733 | 2,730 | 6,300 | ||
| 26 | +2.5 | — | — | H105E3 | Hs.57698 | 11,845 | 18,370 | |
| 28 | +2.5 | NR | Fibrinogen Bβ | Hs.166120 | 15,610 | 23,120 | ||
| 33 | +2.4 | — | — | VWF | Hs.110802 | 11,650 | 17,760 | |
| 36 | +2.4 | — | — | RIG-E (stem cell antigen 2) | Hs.77667 | 6,400 | 11,120 | |
| Down | 1 | −5.0 | NR | Nucleobindin | Hs.172609 | 15,960 | 4,830 | |
| 2 | −4.9 | 81.5 | −1.2 | CXCR4 stromal cell alpha chemokine receptor | Hs.89414 | 13,840 | 4,910 | |
| 3 | −4.6 | NR | IL-8 | Hs.624 | 14,520 | 5,450 | ||
| 4 | −4.4 | — | — | Notch3 homologue | 14,090 | 3,470 | ||
| 5 | −4.0 | 82.7 | −1.2 | GRK4 G-protein-coupled receptor kinase (GPRK2L) | Hs.32959 | 17,090 | 4,980 | |
| 6 | −3.8 | 99.8 | −4.3 | Thrombin receptor (coagulation factor II) | Hs.128087 | 9,670 | 2,890 | |
| 7 | −3.8 | NR | Inhibin β-B subunit | Hs.1735 | 12,070 | 2,250 | ||
| 8 | −3.7 | 97.2 | −1.7 | Cytosolic dynein heavy chain | I.23958 | 17,790 | 6,150 | |
| 9 | −2.9 | NR | Thy1 membrane glycoprotein | Hs.125359 | 26,260 | 13,350 | ||
| 10 | −2.9 | 19.2 | +1.4 | Phosphatidylethanolamine-binding protein | Hs.80423 | 9,810 | 2,380 | |
| 11 | −2.9 | NR | Machado-Joseph disease protein 1 (MJD1) | Hs.66521 | 3,970 | 190 | ||
| 12 | −2.8 | 93.0 | −1.4 | Junction plakoglobin, desmoplakin III | Hs.2340 | 10,110 | 4,760 | |
| 13 | −2.8 | — | — | Glycine amidinotransferase | Hs.75335 | 5,870 | 180 | |
| 14 | −2.8 | NR | Guanine nucleotide exchange factor MSS4 | Hs.90875 | 15,320 | 6,330 | ||
| 15 | −2.7 | 95.8 | −1.5 | c-Maf transcription factor | Hs.30250 | 4,870 | 530 | |
| 16 | −2.6 | — | — | Gastric triacylglycerol lipase | Hs.159177 | 3,910 | 11,360 | |
| 17 | −2.6 | 91.9 | −1.4 | Reelin | Hs.12246 | 7,900 | 1,540 | |
| 18 | −2.6 | 93.2 | −1.4 | LIM and SH3 domain protein LASP-1 | Hs.75080 | 5,380 | 12,260 | |
| 19 | −2.5 | 93.4 | −1.4 | Phospholipase C-gamma-2 | Hs.75648 | 2,710 | 560 | |
| 20 | −2.5 | — | — | Phosphomevalonate kinase | Hs.30954 | 10,110 | 3,250 | |
| 21 | −2.5 | NR | CD40 receptor associated factor | Hs.89676 | 4,870 | 1,620 | ||
| 23 | −2.4 | NR | Cyclin A1 (CNN1) | Hs.86137 | 1,750 | 230 | ||
| 29 | −2.2, −1.8 | — | — | WNT 13 | Hs.258575 | 9,420 | 5,890 | |
| 31 | −2.1 | NR | bFGF-R (basic fibroblast growth factor receptor) | Hs.748 | 9,030 | 5,560 | ||
| 32 | −2.1 | — | — | GRK5 (G-protein receptor kinase 5) | Hs.311569 | 5,140 | 2,700 | |
a
See Table 2, footnote a.