Table 3. Differentially expressed probes in prostate tissue.
| Fold change | P<0.05* | P<0.005* | P<0.0005* | |
| (a) Differences between benign and malignant TURP tissue | ||||
| Benign v Malignant | >1.0 | 3810 (353) | 683 (7) | 124 (0) |
| >1.5 | 1081 (59) | 400 (2) | 104 (0) | |
| >2.0 | 277 (7) | 140 (0) | 54 (0) | |
| (b) Differences between GSTM1 positive and null genotypes | ||||
| Benign (TURP) | >1.0 | 661 (538) | 19 (17) | 0 (0) |
| >1.5 | 160 (186) | 7 (14) | 0 (0) | |
| >2.0 | 50 (40) | 1 (3) | 0 (0) | |
| Malignant (TURP) | >1.0 | 686 (431) | 8 (13) | 0 (0) |
| >1.5 | 244 (152) | 4 (8) | 0 (0) | |
| >2.0 | 44 (33) | 1 (3) | 0 (0) | |
| Pre-intervention | >1.0 | 730 (484) | 26 (9) | 0 (0) |
| >1.5 | 252 (79) | 16 (3) | 0 (0) | |
| >2.0 | 43 (9) | 8 (1) | 0 (0) | |
| 6 month broccoli | >1.0 | 7976 (351) | 434 (4) | 17 (0) |
| >1.5 | 2790 (91) | 268 (2) | 14 (0) | |
| >2.0 | 316 (8) | 31 (0) | 1 (0) | |
| 6 month peas | >1.0 | 220 (220) | 6 (4) | 0 (0) |
| >1.5 | 33 (41) | 5 (3) | 0 (0) | |
| >2.0 | 5 (10) | 1 (1) | 0 (0) | |
| (c) Differences between paired samples | ||||
| 0–12 months broccoli | >1.0 | 2857 (96) | 151 (0) | 1 (0) |
| >1.5 | 1243 (12) | 141 (0) | 1 (0) | |
| >2.0 | 213 (0) | 62 (0) | 1 (0) | |
| 0–12 months peas | >1.0 | 1199 (42) | 19 (0) | 0 (0) |
| >1.5 | 495 (18) | 19 (0) | 0 (0) | |
| >2.0 | 81 (1) | 4 (0) | 0 (0) | |
Probe numbers that have satisfied the comparison criteria of fold change and P-value cutoffs are shown. Numbers in parentheses represent the median false discovery rate calculated in dChip after 100 permutations of the samples.
P-values were calculated in dChip by a Welch modified two-sample t-test. n = 18 for Benign, n = 14 for Malignant; n = 4 for GSTM1(+) Benign, n = 14 for GSTM1(−) Benign; n = 5 for GSTM1(+) Malignant, n = 9 for GSTM1(−) Malignant; n = 7 for GSTM1(+) Pre-intervention, n = 3 for GSTM1(−) Pre-intervention; n = 6 for GSTM1(+) 6-month broccoli, n = 5 for GSTM1(−) 6-month broccoli; n = 3 for GSTM1(+) 6-month pea and n = 5 for GSTM1(−) 6-month pea intervention.
P-values were calculated in dChip by a Welch modified two-sample paired t-test, n = 4 for each of the diet interventions.