Table 1.
Classification of differentially expressed genes based on Affymetrix microarrays
| B84 × B73 | B37 × B73 | Oh43 × B73 | Oh43 × Mo17 | Mo17 × B73 | B73 × Mo17 | |
| #DE genes* | 326 | 726 | 1407 | 993 | 1180 | 1144 |
| # Pass filtration** | 290 | 655 | 1071 | 885 | 1064 | 1055 |
| #Nonadditive*** | 88 (30.3%) | 159 (24.3%) | 296 (27.6%) | 233 (26.3%) | 247 (23.2%) | 266 (25.2%) |
| HP or LP**** | 5 | 32 | 58 | 47 | 44 | 55 |
| AHP***** | 0 | 1 | 3 | 1 | 0 | 1 |
| BLP****** | 0 | 2 | 3 | 1 | 2 | 1 |
*Differentially expressed genes (based on ANOVA FDR < 0.05)
**filters: 1) at least one genotype avg signal > 50; fold-change of at least 1.2 between any two genotypes (parent1-parent2 or parent1-hybrid or parent2-hybrid comparisons)
***based on two-tailed t-test between midparent and hybrid (p < 0.05)
****based on two-tailed t-tests (p < 0.05); hybrid must be significantly different than midparent and not significantly different from either high or low parent
*****AHP: above high parent; based on one-tailed t-test between high parent and hybrid (p < 0.05) and d/a > 1
******BLP: below low parent; based on one-tailed t-test between low parent and hybrid (p < 0.05) and d/a < -1