Table III. ult1-3 restoration of misregulated genes in LFYasEMF1 plants at 7 DAG.
| Category | No. of Genes Investigated | Change in Gene Expression | No. of Genes Misregulated in LFYasEMF1a | No. of Genes with Expression Restored to Wild-Type Level in LFYasEMF1 ult1-3b | Example of Genes with Expression Restored to Wild-Type Level in LFYasEMF1 ult1-3c |
|---|---|---|---|---|---|
| Abscisic acid | 12 | Up | 2 | 1 | RNA-binding protein |
| Down | 0 | 0 | |||
| Auxin | 107 | Up | 8 | 4 | Auxin-responsive family protein |
| Down | 13 | 11 | SAUR24, GH3.17, IAA14, SAUR19 | ||
| Cold | 19 | Up | 3 | 0 | |
| Down | 0 | 0 | |||
| Ethylene | 56 | Up | 14 | 8 | RRTF1, ERF5, ERF73, ERF-1, ORA59, MBF1C |
| Down | 0 | 0 | |||
| Expansin | 20 | Up | 0 | 0 | |
| Down | 5 | 3 | EXPA1, EXPA5, EXPA10 | ||
| Flower organ identity | 14 | Up | 10 | 10d | AG, SEP1, SEP2, SEP3, AP1, AP3, PI, SHP1, SHP2, STK |
| Down | 1 | 0 | |||
| Flowering time | 98 | Up | 12 | 9 | AGL24, TFL1, TEM1, ATC, MAF3, CO, SPL3, CPL3, FPF1 |
| Down | 11 | 8 | SPL1, SPL5, FLD, DNF, TOE1, FRI, GID1B, GA1 | ||
| GA | 13 | Up | 1 | 1 | GASA6 |
| Down | 1 | 0 | |||
| Heat | 50 | Up | 9 | 3 | HSFB2A, HSFA7A |
| Down | 4 | 2 | HSFC1, HSP23.6-MITO | ||
| Histone | 36 | Up | 5 | 4 | HTA12 |
| Down | 0 | 0 | |||
| Photoreceptor | 28 | Up | 2 | 1 | ELIP1 |
| Down | 3 | 2 | PAT1, IOS1 | ||
| Photosynthesis | 54 | Up | 1 | 1 | PSII 5-kD protein |
| Down | 2 | 1 | Chlorophyll a/b-binding protein | ||
| Seed | 119 | Up | 25 | 12 | Protease inhibitor genes, XYP1, M17, LEC1 |
| Down | 5 | 3 | SIP1, SIP2, EM1 | ||
| Stress | 46 | Up | 2 | 2 | STZ |
| Down | 2 | 0 | |||
| Transcription factor | 588 | Up | 77 | 48 | No apical meristem (NAM) family genes |
| Down | 46 | 22 | |||
| Total | 1,260 | 264 | 156 |
a
Genes more than 2-fold up- or down-regulated in LFYasEMF1 plants at 7 DAG. Fold changes are calculated using the signal intensity, which measures the change in expression level for each probe set between wild-type and mutant or transgenic plants. bGenes up- or down-regulated in LFYasEMF1 plants that were restored to wild-type expression levels (less than 2-fold) by ult1-3 at 7 DAG. cFor a complete list, see Supplemental Table S1. dEight of the 10 flower organ identity genes remained up-regulated by more than 2-fold in LFYasEMF1 ult1-3 plants but are included here because their up-regulation is greatly reduced (Supplemental Table S1).