Table IV.
Occurrence of promoter motifs in differentially expressed genes showing response to P starvation with fold change ≥2
Upstream regions (1,000 bp) of differentially expressed genes were analyzed for the occurrence of the various motifs. The frequency in the 1,000-bp upstream regions was analyzed for the whole genome using the Patmatch tool at TAIR (http://www.arabidopsis.org/index.jsp). For references to motifs, see Rubio et al. (2001)a; Hammond et al., (2003)b; and Tang et al. (2001)c. Overrepresented motifs were identified using promomer at BAR (http://bbc.botany.utoronto.ca/).
| Name/Sequence | Genes Induced by P Starvation (169 Genes)
|
Genes Repressed by P Starvation (16 Genes)
|
Genome % Genes with Motif | ||||
|---|---|---|---|---|---|---|---|
| Genes with Motif | Motifs | % Genes with Motif | Genes with Motif | Motifs | % Genes with Motif | ||
| aPHR1, GNATATNC | 80 | 128 | 47.3 | 2 | 3 | 12.5 | 18.1 |
| bP responsive, ATGCCAT | 12 | 13 | 7.1 | 0 | 0 | 0 | 4.3 |
| bPHO, CACGT(G/C) | 45 | 56 | 26.6 | 7 | 8 | 43.8 | 22.1 |
| bPHO-like, (G/T/A)(C/T/A)GTGG | 44 | 51 | 26 | 5 | 5 | 31.25 | 24.8 |
| bTATA box, TATAAATA | 31 | 32 | 18.3 | 2 | 3 | 12.5 | 16 |
| bTC-rich, TCTCTCT | 43 | 52 | 25.4 | 2 | 4 | 12.5 | 24.8 |
| bNIT2, TATC(A/T)(A/T) | 143 | 388 | 84.6 | 11 | 41 | 68.8 | 86.3 |
| bNIT2-like, AAATATCT | 14 | 14 | 8.2 | 3 | 3 | 18.8 | 8 |
| bHLH, CA(T/G)(A/C)TG | 89 | 128 | 52.7 | 9 | 13 | 56.3 | 49.8 |
| cHD-ZIP, CATTAATTAG | 0 | 0 | 0.0 | 0 | 0 | 0.0 | 0.0 |
| Overrepresented motif searches | |||||||
| AGTTTT | 86 | 144 | 50.9 | 12 | 32 | 75.0 | 58.7 |
| GAATAT | 101 | 171 | 59.8 | 6 | 8 | 37.5 | 37.8 |
| ANGAATATNC | 26 | 30 | 15.4 | 1 | 1 | 6.3 | 2.6 |