Table 6.
genes transcriptionally up-regulated by both ripening and cold.
| Probeset ID | Avg. signal 17°C | Avg. signal 4°C | Fold change | Adjusted P. Value | Best potato match | Annotation |
| Les.1936.1.S1_at | 11.58 | 1990.21 | 171.51 | 0.00129 | TA27416_4113 | Early light inducible protein (Solanum lycopersicum) [64]; TC116636 |
| Les.4223.1.S1_at | 4.79 | 330.56 | 69.20 | 0.00189 | TA28833_4113 | alternative oxidase 1a (Solanum lycopersicum) [64]; TC116692 |
| Les.4829.1.S1_at | 14.26 | 586.14 | 40.29 | 0.00189 | CV498197 | 2-oxoglutarate-dependent dioxygenase (Solanum lycopersicum) [64]; TC115851 |
| Les.3338.1.S1_at | 7.75 | 222.86 | 29.98 | 0.00300 | TA24335_4113 | S-adenosyl-L-methionine synthetase 1 (Daucus carota) [105] |
| Les.220.1.S1_at | 8.10 | 226.46 | 28.2 | 0.00182 | TA25585_4113 | AER (Nicotiana tabacum) [106] |
| LesAffx.49935.1.S1_at | 20.28 | 510.32 | 26.62 | 0.00384 | TA28438_4113 | Pyruvate decarboxylase (Solanum tuberosum) [64]; TC1163 |
| Les.3551.1.S1_at | 17.51 | 390.08 | 22.9 | 0.00255 | CV475083 | Ethylene-responsive transcriptional coactivator (ER24)(Solanum lycopersicum) [76] |
| Les.2988.1.S1_at | 84.47 | 1601.26 | 18.92 | 0.00182 | TA25065_4113 | Cinnamic acid 4-hydroxylase (Capsicum annuum) [64]; TC124119 |
| LesAffx.44987.1.S1_at | 13.27 | 222.49 | 16.76 | 0.00175 | TA38177_4113 | Solanesyl diphosphate synthase (Hevea brasiliensis (Para rubber tree) geranyl diphosphate synthase (Arabidopsis thaliana) [64]; TC116882 |
| Les.3651.1.S1_at | 108.84 | 1738.28 | 16.03 | 0.00224 | TA24332_4113 | S-adenosyl-L-methionine synthetase (Nicotiana tabacum) [107] |
| Les.2560.1.S1_at | 7.42 | 103.61 | 13.90 | 0.00226 | TA25537_4113 | Ethylene-forming enzyme (Solanum lycopersicum) [64]; TC123934 |
| Les.4412.1.A1_at | 10.95 | 133.78 | 12.10 | 0.00209 | TA26173_4113 | Leucoanthocyanidin dioxygenase 2, putative (Arabidopsis thaliana) [108] |
| Les.5956.1.S1_s_at | 130.33 | 1406.81 | 10.88 | 0.00276 | TA23754_4113 | Cold-stress inducible protein (CI7) (Solanum tuberosum) [64]; TC116013 |
| Les.4150.1.S1_at | 173.18 | 1515.29 | 8.74 | 0.00287 | TA29480_4113 | Mitochondrial small heat-shock protein (Solanum lycopersicum) [64]; TC124001 |
| Les.5826.1.S1_at | 136.17 | 1105.79 | 8.12 | 0.00226 | TA28749_4113 | Cathepsin B-like cysteine proteinase (Solanum tuberosum) [64]; TC124060 |
| LesAffx.1959.1.S1_at | 28.53 | 224.93 | 7.88 | 0.00224 | TA25003_4113 | Glutathione S-transferase. class-phi (Solanum commersonii) [64]; TC116034 |
| LesAffx.47187.1.S1_at | 41.05 | 293.51 | 7.14 | 0.00236 | TA36088_4113 | Universal stress protein/early nodulin ENOD18-like [64]; TC123970 |
| Les.3171.3.S1_a_at | 18.56 | 120.71 | 6.50 | 0.00249 | TA30735_4113 | Phytoene synthase. chloroplast precursor (Capsicum annuum) [64]; TC115970 |
| Les.3813.1.S2_at | 142.73 | 855.96 | 6.38 | 0.01985 | TA23078_4113 | S-adenosylmethionine decarboxylase proenzyme [64]; TC123879 |
| Les.3085.1.S1_at | 28.13 | 178.22 | 6.28 | 0.00391 | BG888309 | Flavonol synthase/flavanone 3-hydroxylase (Solanum tuberosum) [64]; TC116718 |
| Les.3285.1.S1_at | 311.71 | 1908.05 | 6.13 | 0.00384 | TA27830_4113 | Acyl carrier protein (Capsicum chinense) [64]; TC124728 |
| LesAffx.34336.1.S1_at | 65.09 | 382.59 | 6.12 | 0.00895 | TA46602_4113 | 70 kD heat-shock protein (Arabidopsis thaliana) [64]; TC126413 |
| Les.4573.1.S1_at | 28.35 | 150.86 | 5.50 | 0.00889 | TA28898_4113 | Guanylate kinase (Nicotiana tabacum) [64]; TC115887 |
| LesAffx.69795.1.S1_at | 27.80 | 148.00 | 5.32 | 0.00458 | TA37100_4113 | Putative methionine sulfoxide reductase B (Oryza sativa) [109] |
| Les.274.1.S1_at | 8.38 | 29.61 | 3.53 | 0.01158 | BQ046569 | Ripening regulated protein DDTFR10/A (Solanum lycopersicum) [64]; TC116368 |
| Les.824.1.S1_at | 64.19 | 169.95 | 2.79 | 0.04315 | TA30812_4113 | Glucose-6-phosphate 1-dehydrogenase precursor (Solanum tuberosum) [64]; TC116406 |
| Les.2702.1.S1_a_at | 7.53 | 20.97 | 2.66 | 0.03637 | TA26908_4113 | Acid invertase (Solanum tuberosum) [64]; TC123895 |
| Les.205.1.S1_at | 174.85 | 461.58 | 2.64 | 0.00847 | TA24762_4113 | 14-3-3 protein (Solanum tuberosum) [64]; TC116260 |
| Les.2992.1.S1_a_at | 87.62 | 225.46 | 2.58 | 0.01367 | BQ504492 | Callus-expressing factor (Nicotiana tabacum) JERF3; [99] |
| Les.3933.1.S1_at | 1933.65 | 4519.78 | 2.33 | 0.00978 | TA24146_4113 | Adenosylhomocysteinase (Solanum lycopersicum) [64]; TC116044 |
| LesAffx.10807.1.S1_at | 18.17 | 35.73 | 1.96 | 0.01649 | TA28665_4113 | Heat-shock cognate 70 kDa protein (Petunia hybrida) [64]; TC126297 |
| LesAffx.32723.1.S1_at | 40.30 | 68.27 | 1.69 | 0.03380 | TA26759_4113 | BZIP transcription factor ATB2 (Glycine max) [64]; TC124112 |
| Les.283.1.S1_at | 138.53 | 228.92 | 1.65 | 0.03786 | CV477421 | Induced stolon tip protein (Capsicum annuum) [64]; TC124196 |
| Les.303.1.S1_at | 5852.89 | 9264.98 | 1.57 | 0.04951 | TA24257_4113 | Enolase (Solanum lycopersicum) [64]; TC123931 |
Selected entries from a set of genes, which are transcriptionally up-regulated by both ripening (various databases as indicated) and cold (our GeneChip dataset). TED database [64] refers to a recent list of tomato ripening-up-regulated genes (transition from mature green to breaker stage) and the ID of the corresponding tomato Tentative Consensus (TC) entry is reported. Fold changes represent the ratios of stress to control average signals (two biological replicates for both control and stress conditions). Further details are as described in Table 2.