TABLE 3.
Comparison of gene expression values obtained with macroarray hybridization and real-time RT-PCR
| Gene product (ORF) | Log2 ratio between value after the indicated time (min) of CPT treatment and reference point value (array/RT-PCR)
|
Correlation coefficienta (RP/RS) | ||
|---|---|---|---|---|
| 30 | 60 | 120 | ||
| Ubiquitin carboxyl-terminal hydrolase (AN7422.2) | 0.17/0.32 | 0.15/2.12 | 0.84/3.59 | 0.82/0.46 |
| Ubiquitin-like modifier (AN1191.2) | −0.22/1.48 | −0.12/1.90 | 0.39/3.24 | 0.99/0.94 |
| Histone acetyltransferase (AN3071.2) | 0.45/0.06 | 0.52/0.43 | 0.95/1.35 | 0.99/0.89 |
| Ubiquitin-activating enzyme Ned8 (AN2416.2) | −0.14/1.28 | −0.25/1.23 | 0.49/1.39 | 0.99/0.94 |
| Histone H2A variant (AN8039.2) | 0.25/1.72 | −0.13/1.04 | −0.54/0.78 | 0.96/0.89 |
| Rad52 (AN4407.2) | 0.27/1.29 | 2.07/3.35 | 0.23/2.83 | 0.68/0.49 |
| PARP (AN3129.2) | 1.17/3025 | 3.06/3.88 | 3.39/4.46 | 0.94/0.94 |
| Rad2 (AN2764.2) | −1.10/1.65 | −0.12/1.08 | 0.37/0.63 | −0.99/−0.98 |
| Rad26 (AN7103.2) | 0.36/2.18 | −0.08/3.71 | 0.68/4.38 | 0.20/0.50 |
| Rad18 (uvsH) (AN7309.2) | 0.60/1.57 | −0.55/2.37 | 0.69/3.76 | 0.22/0.43 |
| MutS (AN1708.2) | 0.78/1.17 | 0.79/4.55 | −0.06/4.30 | −0.06/0.43 |
| Smad (AN2893.2) | 0.07/1.33 | 1.76/2.41 | 2.66/2.65 | 0.98/0.89 |
| Prohibitin (AN6073.2) | 1.21/1.06 | 0.34/1.63 | 0.74/3.47 | −0.27/−0.50 |
| Sulfur metabolite repression control protein SconB (AN6359.2) | 0.69/0.97 | 0.12/2.01 | 0.49/2.38 | −0.58/−0.37 |
| Helicase (AN2285.2) | −1.09/0.19 | −0.91/2.91 | 1.91/3.76 | 0.72/0.89 |
| Topoisomerase I (AN0253.2) | 0.96/2.06 | −0.05/1.50 | −0.21/2.12 | 0.30/−0.41 |
| UvsC (Rad51 homologue) (AN1237.2) | 0.43/1.43 | 0.67/1.98 | 1.20/0.33 | −0.17/0.08 |
| Ribonucleotide reductase small subunit (AN0067.2) | 1.08/0.09 | 1.23/0.92 | 0.39/2.12 | −0.83/−0.49 |
| Ribonucleotide-diphosphate reductase large chain (AN4380.2) | 0.43/1.52 | 0.94/1.97 | 1.17/3.31 | 0.91/0.89 |
| Myb-like DNA binding protein Myb-1 (AN0279.2) | 0.76/0.32 | 0.69/1.14 | −0.69/1.19 | −0.58/−0.99 |
| Tetratrico peptide repeat (AN3617.2) | 2.75/2.26 | 3.28/3.64 | 4.23/7.78 | 0.99/0.87 |
| HpmS2 (AN4365.2) | 0.73/0.99 | 1.58/2.03 | 1.22/2.55 | 0.72/0.50 |
| Cell division cycle 2 homolog protein kinase (NPKA) (AN6044.2) | −0.22/1.07 | 0.74/0.97 | −0.29/3.30 | −0.58/0.94 |
a
Correlation coefficients calculated after comparison of the array and RT-PCR data for each gene. We calculated both Pearson's (RP) and Spearman's (RS) correlation coefficients for each pair of curves. The former is more adequate for comparisons in which the data assume a normal distribution, while the latter is more appropriate for data sets which do not follow a normal distribution. The highest R value is in boldface.