Table 4.
The number of R-, control, and stress response genes differentially expressed after 15 environmental perturbations. Datasets used can be found in the Supplementary Information.
| Treatment and gene set | Up-regulated | No change | Down-regulated | Sets compared | χ2 value | P-value |
|---|---|---|---|---|---|---|
| Blumeria graminis versus uninfected | ||||||
| R-genes | 6 | 5 | 5 | R versus control | 2.97 | 0.23 |
| Control | 5 | 15 | 6 | R versus stress | 1.48 | 0.48 |
| Stress response | 11 | 7 | 17 | |||
| Hyaloperonospora parasitica arabidopsis Noco2 versus uninfected | ||||||
| R-genes | 33 | 25 | 2 | R versus control | 18.7 | 8.7E-05* |
| Control | 12 | 28 | 14 | R versus stress | 8.65 | 0.013 |
| Stress response | 52 | 26 | 17 | |||
| Powdery mildew (Erisyphe cichoracearum) versus uninfected | ||||||
| R-genes | 35 | 11 | 2 | R versus vontrol | 18.6 | 9.2E-05* |
| Control | 5 | 18 | 1 | R versus stress | 14.7 | 6.3E-04* |
| Stress response | 22 | 31 | 8 | |||
| Pseudomonas syringae pv. DC3000 with avrRpm1versus uninfected | ||||||
| R-genes | 8 | 3 | 3 | R versus control | 2.84 | 0.24 |
| Control | 6 | 4 | 0 | R versus stress | 3.28 | 0.19 |
| Stress response | 10 | 15 | 7 | |||
| Pseudomonas syringae pv. Maculicola with AvrRpt2 versus mock inoculated | ||||||
| R-genes | 36 | 16 | 9 | R versus control | 4.73 | 0.094 |
| Control | 24 | 16 | 17 | R versus stress | 12.1 | 2.3E-03* |
| Stress response | 45 | 10 | 34 | |||
| Pseudomonas syringae pv. tomato with HopZ1a versus mock inoculated | ||||||
| R-genes | 26 | 15 | 11 | R versus control | 0.49 | 0.78 |
| Control | 16 | 8 | 9 | R versus Stress | 1.72 | 0.42 |
| Stress response | 40 | 20 | 27 | |||
| Pseudomonas syringae pv. tomato versus mock inoculated | ||||||
| R-genes | 2 | 10 | 14 | R versus control | 6.37 | 0.041 |
| Control | 4 | 6 | 2 | R versus stress | 10.1 | 6.3E-03 |
| Stress response | 6 | 37 | 10 | |||
| flg22 peptide versus water | ||||||
| R-genes | 4 | 4 | 0 | R versus control | 3.05 | 0.22 |
| Control | 8 | 5 | 5 | R versus stress | 7.35 | 0.03 |
| Stress response | 5 | 6 | 13 | |||
| Salicyclic acid versus Silwet, <24h after treatment | ||||||
| R-genes | 47 | 18 | 4 | R versus control | 11.8 | 2.8E-03* |
| Control | 14 | 17 | 8 | R versus stress | 39.5 | 2.6E-09* |
| Stress response | 33 | 76 | 31 | |||
| Salicyclic acid versus Silwet, >24h after treatment | ||||||
| R-genes | 0 | 18 | 21 | R versus control | 1.24 | 0.54 |
| Control | 0 | 6 | 3 | R versus stress | 9.53 | 0.01 |
| Stress response | 3 | 32 | 11 | |||
| 0.5h or 2h excess light versus low light | ||||||
| R-genes | 5 | 33 | 34 | R versus control | 9.22 | 0.010 |
| Control | 11 | 29 | 13 | R versus stress | 10.6 | 5.1E-03 |
| Stress response | 35 | 57 | 48 | |||
| 37 °C versus 20 °C | ||||||
| R-genes | 7 | 23 | 22 | R versus control | 3.09 | 0.21 |
| Control | 11 | 15 | 13 | R versus stress | 1.19 | 0.55 |
| Stress response | 18 | 39 | 32 | |||
| 4 °C versus 20 °C | ||||||
| R-genes | 13 | 45 | 24 | R versus control | 10.3 | 5.8E-03 |
| Control | 15 | 35 | 16 | R versus stress | 24.8 | 4.0E-06* |
| Stress response | 56 | 65 | 36 | |||
| Drought versus untreated | ||||||
| R-genes | 18 | 30 | 4 | R versus control | 3.50 | 0.17 |
| Control | 8 | 23 | 7 | R versus stress | 8.77 | 0.012 |
| Stress response | 30 | 36 | 25 | |||
| Ozone versus control | ||||||
| R-genes | 8 | 6 | 3 | R versus control | 2.43 | 0.30 |
| Control | 2 | 6 | 3 | R versus stress | 0.69 | 0.71 |
| Stress response | 17 | 9 | 9 | |||
P-values in bold are significant correlations, and asterisks represent significant correlations after correction for multiple testing.