TABLE 2.
Partial list of cellular genes that were dependent on viral replicationa
| Gene type | I.M.A.G.E. identification | Gene product | Fold change
|
|
|---|---|---|---|---|
| FHT vs FACT | M vs FACT | |||
| Protein synthesis | 303048 | Ribosomal protein S6 | 2.8+ | 1.8+ |
| X69150 | Ribosomal protein S18 | 2.6+ | 1.7+ | |
| 214565 | ESTs, ribosomal protein S14 | 2.7+ | 2.2+ | |
| 141854 | Eukaryotic translation elongation factor 1 gamma | 1.7+ | 1.9+ | |
| 562867 | Homolog of yeast ribosome biogenesis regulatory protein | 2.7+ | 2.0+ | |
| 897982d | Translation initiation factor eIF-3 p110 subunit | 5.8− | 4.0− | |
| 34849d | Eukaryotic translation elongation factor 2 | 4.2− | 4.0− | |
| 788511 | Ribosomal protein S6 kinase, 90 kDa, polypeptide 2 | 4.8− | 2.7− | |
| 40567de | Human homolog translational activator GCN1 | 8.5− | 4.7− | |
| Cytokine and growth factor signaling | 310406de | IL-6 | 18.2+ | 7.9+ |
| 811920 | IL-11 receptor alpha chain | 2.3− | 1.9− | |
| 289606 | IL-15 | 3.7− | 2.0− | |
| 897570 | Tumor necrosis factor type 1 receptor-associated protein | 5.1− | 2.4− | |
| 810444d | B94 protein | 2.4− | 1.8− | |
| 788185 | TRAIL receptor 2 | 2.4− | 1.8− | |
| 813184 | B12 protein | 2.4− | 1.8− | |
| 811900 | Lymphotoxin-beta receptor precursor | 3.7− | 2.6− | |
| 136821cd | TGF-β 1 precursor | 3.9− | 2.5− | |
| 768168b | Bone morphogenetic protein 6 precursor | 3.3− | 1.9− | |
| 898092d | Connective tissue growth factor | 5.2+ | 3.0+ | |
| 79712de | Insulin-like growth factor 2 receptor | 2.8− | 2.8− | |
| 898218c | Insulin-like growth factor-binding protein | 4.4− | 4.8− | |
| 85093de | KIAA0062 gene, similar to estrogen regulated LIV-1 protein | 6.8− | 3.4− | |
| 297122e | Epidermal growth factor receptor (v-erb-b) oncogene homolog | 4.6− | 4.6− | |
| 768496d | Cytokine receptor (EBI3) | 3.9− | 5.2− | |
| Transcription factors and DNA binding proteins | 898221 | Immediate-early response protein NOT | 2.7+ | 1.7+ |
| 812965 | v-myc avian myelocytomatosis viral oncogene homolog | 4.7+ | 4.2+ | |
| 770670 | Putative DNA binding protein A20 | 8.1+ | 3.7+ | |
| 146577 | TGF-β-inducible early protein | 2.6+ | 3.8+ | |
| 377320e | Zinc finger protein | 5.6− | 2.5− | |
| 771220 | Transcription factor p65, NF-κB | 4.3− | 3.2− | |
| 755821bd | Transcription factor 11 | 2.8− | 2.1− | |
| 725680d | Transcription factor ERF-1 | 11.7− | 2.0− | |
| 785816bd | Nuclear factor NF90 | 5.9− | 3.8− | |
| 40781d | Interleukin enhancer-binding factor | 4.3− | 3.1− | |
| 240367 | Transcriptional repressor (CTCF) | 3.8− | 2.6− | |
| 712840 | Transcription factor Stat5b | 2.6− | 1.9− | |
| 137387d | ESTs,f transcription factor AP-2 | 10.0− | 3.5− | |
| 161950d | ESTs, weakly similar to hairless protein | 4.5− | 2.8− | |
| 770910de | Epithelial cell-spectrum transcription factor ESE-1b | 5.2− | 3.7− | |
| 783681de | KIAA0312 gene, upstream regulatory element binding protein | 6.4− | 3.4− | |
| Processing and export of mRNA | 67074 | ESTs, pre-mRNA splicing factor RNA helicase PRP22 | 4.5− | 2.6− |
| 814119de | RNA helicase (HRH1) | 4.3− | 2.7− | |
| 741841 | CHL1 potential helicase (CHLR1) | 5.7− | 7.1− | |
| 809535 | Splicing factor, arginine/serine-rich 2 | 5.5− | 2.8− | |
| 811108 | Pre-mRNA splicing factor SF2, P32 subunit precursor | 3.6− | 2.5− | |
| 123400 | Human FUSE binding protein 2 (FBP2) | 3.3− | 2.1− | |
| 825224 | Export protein Rae1 (RAE1) | 4.2− | 3.2− | |
| 714426 | Cleavage stimulation factor, 3′ pre-RNA, subunit 2, 64 kDa | 2.8− | 1.8− | |
| 50188 | Zinc finger protein | 4.1− | 3.0− | |
| 823663d | Fragile X mental retardation syndrome-related protein (FXR2) | 4.3− | 2.1− | |
| 25588 | RNA-binding protein CUG-BP/hNab50 | 3.7− | 2.4− | |
| 811911d | Hlark | 3.5− | 2.5− | |
| 121621d | Heterogenous nuclear ribonucleoprotein U | 7.0− | 3.0− | |
| 309032 | Cleavage and polyadenylation specificity factor | 3.9− | 2.4− | |
| 366558 | RanGTPase activating protein 1 | 4.7− | 3.0− | |
| Ubiquitin pathway | 210405 | Proteasome activator hPA28 subunit beta | 1.9+ | 1.7+ |
| X63237 | Human ubiquitin | 2.6+ | 1.7+ | |
| 898262d | Ubiquitin activating enzyme E1 | 11.3− | 4.0− | |
| 134172 | ESTs, ubiquitin-conjugating enzyme E2-17 KD 11 | 3.7− | 1.9− | |
| 789232 | Antisecretory factor-1 | 1.9− | 3.0− | |
| 613126 | Isopeptidase T-3 (ISOT-3) | 3.0− | 2.7− | |
The gene names and fold changes are based on the results from the 8-h time point. The ratios were generated by taking the means of eight measurements at the two appropriate conditions, mock infection (M) versus FACT and FHT versus FACT (Fig. 3). A complete list of genes and the ratios for each individual experiment as well as the other condition (mock infection versus FHT) are available at http://thor.csi.washington.edu/katzelab/papers/Geiss2000/index.htm in Table S3.
The I.M.A.G.E clone was present in two copies on the array.
The clone was present twice on the array and regulated at both time points.
The cDNA was regulated in both FHT and FUVI experiments.
The mRNA was also differentially regulated in a replication-dependent manner at the 4-h time point.
ESTs, expressed sequence tags.