Table 2.
Summary of Downregulated Genes with Up to Five Mismatches
| amiR-lfy-1 | amiR-mads-1 | amiR-mads-2 | ||
|---|---|---|---|---|
| Predicted targets, represented on array | 1 | 6 | 18 | |
| Predicted targets, present in control | 1 | 4 | 13 | |
| Predicted targets, present in control and downregulated in amiRNA overexpressers | 1 | 1 | 6 | |
| All genes present in control without predicted targets | 15,367 | 15,364 | 15,355 | |
| All genes downregulated without predicted targets | 342 | 141 | 287 | |
| Genes with five mismatches, present in control | 32 | 89 | 311 | |
| Observed downregulated | Predicted targets | 1 | 1 | 5 |
| Others | 1 | 3 | 5 | |
| Expected downregulated without predicted targets | 0.7 | 0.8 | 5.6 | |
| χ2 | 0.1 | 6.4 | 0.5 | |
Significantly downregulated genes were determined using LIMMA (Smyth et al., 2005), with an expression change of at least 1.5-fold at an estimated 1% false discovery rate (FDR) (Benjamini and Yekutieli, 2001). A χ2 test was used to determine statistical significance of the difference between expected and observed downregulated genes among the nontargets (genes with five or less mismatches, but not predicted targets). A minimal χ2 value of 6.63 corresponds to significant differences at α = 0.01. Use of the logit-T algorithm produced qualitatively similar results. A total of 15,368 genes were called present in Col-0 inflorescences. For amiR-lfy-1, we used the sequence of the 21-mer deduced from the mapping of the cleavage product, which was shifted by two nucleotides from the intended amiRNA.