| Â | GENE Symbol | Probe set ID | 22Rv1 | LNCaP |
|---|
| Â | Â | Â | Log2 (signal) | Log2 Accumulation | Log2 Degradation | Log2 (signal) | Log2 Accumulation | Log2 Degradation |
|---|
| Â | PARD3 | 221526_x_at | 7.1 | 0.9 | 0.1 | 3.2 | 2.9 | 1.6 |
| Â | ANKRD28 | 213035_at | 8.2 | 0.4 | 0.4 | 5.6 | 1.7 | 1.5 |
| Â | CLPTM1 | 211136_s_at | 9.7 | -0.5 | -0.6 | 4.3 | 1.6 | 1.8 |
LNCaP candidate
| VRK3 | 221999_at | 6.5 | 0.3 | 0.5 | 3.9 | 1.5 | 2.5 |
s
| GTPBP2 | 221050_s_at | 8.2 | 0.2 | 0.2 | 5.2 | 1.5 | 2.1 |
| Â | LOC692247 | 1561355_at | 6.9 | 0.1 | 0.3 | 3.9 | 1.5 | 1.5 |
| Â | AFF1 | 227198_at | 10.5 | -0.6 | 0.7 | 5.4 | 1.3 | 1.4 |
| Â | AS3 | 207956_x_at | 5.9 | 2.6 | 1.4 | 10.0 | 0.1 | 0.3 |
22RV1
| TTLL7 | 219882_at | 3.6 | 2.0 | 1.4 | 7.6 | 0.3 | 0.9 |
candidate
| PDSB5 | 204742_s_at | 3.9 | 1.9 | 1.3 | 7.8 | -0.6 | -0.6 |
s
| EIF5 | 208708_x_at | 9.2 | 1.7 | 2.5 | 11.3 | 0.7 | 0.9 |
| Â | EIF2C2 | 225827_at | 3.5 | 1.6 | 1.9 | 6.1 | -0.6 | 0.1 |
- RNAs from LNCaP and 22Rv1 cells were analyzed using Afffymetrix GeneChip Human Genome U133Plus 2.0 Array hybridization after the following treatments: 1) no treatment, 2) incubation with caffeine for four hours, 3) incubation with caffeine and actinomicin D following caffeine treatment for four hours and 4) incubation with actinomycin D following caffeine treatment for four hours. The candidates for sequencing analysis for LNCaP cells were selected by sorting the normalized, Log2 transformed hybridization signal values data using the following criteria: 1) expression of the candidate gene in the untreated LNCaP cells is more than four-times lower than in the untreated 22Rv1 cells used as a control, i.e., Log2(signal LNCaP) - Log2(signal 22Rv1) <2.0; 2). The mRNA level accumulation for candidate genes following incubation with caffeine for four hours should be more than threefold and less than twofold in the LNCaP and 22Rv1 cells, respectively: i.e., Log2 (Accumulation LNCaP) >1.3 and Log2(Accumulation 22Rv1) <1.0; 3). The mRNA levels for candidates after inhibiting both mRNA synthesis and mRNA degradation with actinomycin D and caffeine should be more than threefold and less than twofold higher than after inhibiting mRNA synthesis only with actinomycin D for the LNCaP and 22Rv1 cells, respectively: i.e., Log2 (Degradation LNCaP) >1.3 and Log2 (Degradation22Rv1) <1.0. Candidates for the 22Rv1 cells were selected in the same way, using the LNCaP cell as a control. Five probes for the 22Rv1 and seven probes for the LNCaP cells satisfied the described selection criteria.
