Table 2.
Enumerative selection of overrepresented motifs harbouring known cis-elements in the promoters of OsWRKY13-regulated genes
| Overrepresented motif sequencea | Strandb | P-valuec | Known homologous cis-element | |||
|---|---|---|---|---|---|---|
| Elementd | Transcription factor type | Potential signalling pathway | Reference | |||
| Upregulated | ||||||
| GTTGACC | bs | 1.20e-06 | W-box | WRKY | biotic/abiotic response, development | 18, 19, 21 |
| GTTGACT | bs | 9.05e-06 | W-box | WRKY | biotic/abiotic response, development | 18, 19, 21 |
| GTTGAC | bs | 1.21e-06 | W-box (core) | WRKY | biotic/abiotic response, development | 18, 19, 21 |
| TTGACCTC | bs | 3.80e-06 | W-box | WRKY | biotic/abiotic response, development | 18, 19, 21 |
| TGCTGCCGC | ss | 7.52e-06 | PRE2 | Rad51-like | biotic response | 22 |
| ATGGTGAA | ss/bs | 4.99e-06 | GTGA motif | unknown | pollen development | 45 |
| GTGCAGAAAT | ss | 3.92e-06 | POLLEN1LELAT52 | unknown | pollen development | 46 |
| ATTCTGTCAG | bs | 6.82e-06 | BIHD1OS | homeodomain | defence response | 47 |
| Downregulated | ||||||
| CGTACG | bs/ss | 2.13e-06 | CURECORECR | SBP domain family | copper response | 48 |
| GTACGTAC | bs/ss | 3.05e-06 | ACGTATERD1, ACGTABOX | AP2/EREBP, bZIP | dehydration response, seed development | 49, 50 |
| A(C/G)AGTGAC | bs/ss | 3.81e-06 | GTGA motif | unknown | pollen development | 45 |
| GAAAGTCCGG | bs/ss | 6.06e-06 | DOFCOREZM/EECCRCAH1 (-) | ZF-DOF | carbon metabolism | 51 |
| GGTTAGTTA | bs | 7.19e-07 | Myb1 | MYB | defence response | 40 |
| TATTGGTTGT | ss | 2.91e-06 | REALPHALGLHCB21 (-), AREOSREP1 | unknown | Phytochrome regulation gibberellin response | 52, 53 |
| CTACTGGC | bs | 4.27e-06 | CACTFTPPCA1 | unknown | carbon metabolism | 54 |
| GTGCAATTAT | ss | 6.69e-06 | CAATBOX1 | unknown | tissue-specific response | 55 |
a The known cis-elements in the overrepresented sequences are in bold.
b The letters "bs" or "ss" designate whether the element was detected as overrepresented on both strands (bs) or just on the sense strand (ss); "bs/ss" refers to consensus sequence from bs and ss with priority on both strands and "ss/bs" with priority on the sense strand.
c The P-value of motif with bs/ss or ss/bs annotation was calculated by average of the P-values for bb and ss.
d Dash indicates that the complementary sequence of the known cis-element is harboured by the conserved motif.