Table 1.
A coregulated set of T3E-induced genes responsive to ABA identified by hierarchial clustering
| AGI number | Function (name) | ABA/stress reference | ARE | FC |
|---|---|---|---|---|
| ABA biosynthetic genes | ||||
| At3g14440 | ABA synthesis (NCED3) | Qin and Zeevaart (1999) | B | 17.0 |
| Protein phosphatase 2C clade A | ||||
| At5g59220 | PP2C | Xin et al (2005) | 2D | 10.0 |
| At1g72770 | PP2C (HAB1) | Saez et al (2004) | 2A2D | 2.1 |
| At1g07430 | PP2C | AB4D | 8.7 | |
| At3g11410 | PP2C (AtPP2CA) | Kuhn et al (2006) | AC2D | 4.2 |
| At5g57050 | PP2C (ABI2) | Merlot et al (2001) | B | 3.2 |
| At4g26080 | PP2C (ABI1) | Merlot et al (2001) | C | 2.9 |
| NAC domain transcription factors | ||||
| At5g39610 | NAC TF (AtNAC6) | He et al (2005) | 3.6 | |
| At1g52890 | NAC TF (ANACO19) | Tran et al (2004) | 3C2D | 2.9 |
| At3g15500 | NAC TF (AtNAC3) | Tran et al (2004) | C3D | 7.9 |
| At4g27410 | NAC TF (RD26) | Fujita et al (2004) | A2CD | 4.5 |
| Transcription factors of various families | ||||
| At1g66550 | WRKY TF (WRKY67) | D | 10.2 | |
| At5g49450 | bZIP family TF | 2D | 4.3 | |
| At1g24440 | C3HC4 zinc finger? | 3.1 | ||
| Other signalling pathways | ||||
| At1g69260 | ABI5 binding protein | Lopez et al (2003) | 2C2D | 3.1 |
| At1g05100 | MAP3K (MAPKKK18) | BC3D | 10.9 | |
| At2g02710 | PAC motif containing | BD | 2.1 | |
| At5g62540 | Ubiquitin conjugating | D | 2.2 | |
| Assorted physiological processes | ||||
| At2g03760 | Steroid sulphotransferase | 7.0 | ||
| At5g13750 | Transporter (ZIFL1) | C2D | 2.7 | |
| At3g11340 | UDP glucosyl transferase | 2.4 | ||
| At3g46660 | UDP glucosyl transferase | D | 5.3 | |
| At3g06500 | β-Fructofuranosidase | B3D | 4.3 | |
| At4g21680 | Oligopeptide transporter | 2.5 | ||
| At1g05560 | UDP-glucose transferase | Tran et al (2004) | D | 3.3 |
| At1g26770 | Expansin (AtEXPA10) | 4.4 | ||
| At5g13820 | Telomeric DNA-binding-1 | Nagaoka and Takano (2003) | C3D | 3.2 |
| At3g14660 | Cytochrome P450 | C | 2.1 | |
| Genes of unknown function | ||||
| At3g01650 | Copine related | 3.3 | ||
| At1g24600 | Expressed protein | A2D | 3.2 | |
| At3g48350 | Cysteine proteinase like | 3D | 8.1 | |
| At3g28007 | Nodulin MtN3 family | 4D | 2.7 | |
| At3g29575 | Expressed protein | 4C3D | 3.3 | |
| At1g69480 | ERD1/XPR1/SYG1 | BC | 3.4 | |
| At2g28400 | Expressed protein | 3.2 | ||
| At4g33980 | Expressed protein | 3C | 2.4 | |
| At5g04250 | OTU cysteine protease? | C3D | 5.1 | |
| At5g54730 | WD40 repeat protein | 3D | 3.9 | |
| At5g42900 | Expressed protein | C2D | 11.5 | |
| At1g33110 | MATE efflux protein | 3.1 | ||
| At5g64230 | Expressed protein | D | 6.2 | |
| At5g65660 | HPRG protein | 2D | 2.8 | |
| At1g58270 | MATH domain protein | 2A4D | 3.0 | |
| At3g07350 | Expressed protein | ACD | 6.5 | |
| At3g28210 | Zinc-finger protein | Xin et al (2005) | D | 2.1 |
| At5g13360 | Auxin responsive GH3 | D | 2.1 | |
| At5g64250 | 2-Nitropropane diox. | 2.7 | ||
| Each of the 880 genes, significantly differentially expressed in response to T3E at 12 hpi, were median-centred and logged before clustering. This table presents a cluster of 47 genes containing a significant over-representation of ABA response elements in their promoters (1 kb upstream). Most genes of known function had previously been associated with abiotic stress. ARE—presence or absence of an ABA response element as defined in the PLACE database (Higo et al, 1999). Scoring is non-redundant and the number of occurrences precedes the motif. (A) ABREMOTIFAOSOSEM—TACGTGTC; (B) ABREATCONSENSUS—[CT]ACGTGGC; (C) ACGTABREMOTIFA2OSEM—ACGTG[GT]C; (D) ABRELATEDD1—ACGTG. FC—fold change. | ||||