| |
GENE Symbol
|
Probe set ID
|
22Rv1
|
LNCaP
|
|---|
| | | |
Log2 (signal)
|
Log2 Accumulation
|
Log2 Degradation
|
Log2 (signal)
|
Log2 Accumulation
|
Log2 Degradation
|
|---|
| |
PARD3
|
221526_x_at
|
7.1
|
0.9
|
0.1
|
3.2
|
2.9
|
1.6
|
| |
ANKRD28
|
213035_at
|
8.2
|
0.4
|
0.4
|
5.6
|
1.7
|
1.5
|
| |
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
|
| |
LOC692247
|
1561355_at
|
6.9
|
0.1
|
0.3
|
3.9
|
1.5
|
1.5
|
| |
AFF1
|
227198_at
|
10.5
|
-0.6
|
0.7
|
5.4
|
1.3
|
1.4
|
| |
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
|
| |
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.
