TABLE 2.
Known transcription factor binding motifs enriched in promoters (∼1,000 bp upstream of the transcription start site) of genes downregulated in flooded roots showing a lower expression in wild type than in notabilis (Figure 8).
| Motif | # In genome promoters | # Total genome promoters | # In promoters downregulated genes | # Total in promoters downregulated genes | Enrichment | p-value (FDR-corrected) | Known binding activity |
| GGCCCA | 3947 | 34417 | 110 | 631 | 1.52008968 | 5.05E-06 | “Site II element” found in the promoter regions of cytochrome genes (Cytc-1, Cytc-2) in Arabidopsis; overrepresented in the promoters of nuclear genes encoding components of the oxidative phosphorylation (OxPhos) machinery from both Arabidopsis and rice |
| AGTACT | 6900 | 34417 | 170 | 631 | 1.34382737 | 1.53E-05 | GTAC is the core of a CuRE (copper-response element) found in Cyc6 and Cpx1 genes in Chlamydomonas; also involved in oxygen response of these genes |
| TACGTA | 5002 | 34417 | 118 | 631 | 1.28671384 | 0.00216669 | “A-box” according to the nomenclature of ACGT elements by Foster et al. (1994) [FASEB J, 8:192–200]; one of ACGT elements; found in ocs gene |
| GTACTA | 10009 | 34417 | 235 | 631 | 1.28062161 | 5.08E-06 | GTAC is the core of a CuRE (copper-response element) found in Cyc6 and Cpx1 genes in Chlamydomonas; also involved in oxygen response of these genes |
| ACGTAA | 9370 | 34417 | 209 | 631 | 1.2166071 | 0.00056655 | ACGT/desiccation responsive |
| GTAGTA | 11059 | 34417 | 238 | 631 | 1.17382878 | 0.00156573 | Tetranucleotide (CACT) is a key component of Mem1 (mesophyll expression module 1) found in the cis-regulatory element in the distal region of the phosphoenolpyruvate carboxylase (ppcA1) of the C4 dicot F. trinervia |
| CTAATA | 20787 | 34417 | 435 | 631 | 1.14140848 | 4.31E-06 | The sequence critical for cytokinin-enhanced protein binding in vitro, found in -490 to -340 of the promoter of the cucumber (CS) POR (NADPH-protochlorophyllide reductase) gene |
| TAAGTA | 19684 | 34417 | 409 | 631 | 1.13332274 | 4.80E-05 | Tetranucleotide (CACT) is a key component of Mem1 (mesophyll expression module 1) found in the cis-regulatory element in the distal region of the phosphoenolpyruvate carboxylase (ppcA1) of the C4 dicot F. trinervia |
| ATAGTA | 20635 | 34417 | 426 | 631 | 1.12602693 | 4.54E-05 | Tetranucleotide (CACT) is a key component of Mem1 (mesophyll expression module 1) found in the cis-regulatory element in the distal region of the phosphoenolpyruvate carboxylase (ppcA1) of the C4 dicot F. trinervia |
| CAATTA | 23958 | 34417 | 484 | 631 | 1.10189054 | 3.82E-05 | “CAAT promoter consensus sequence” found in legA gene of pea |
| ACAATA | 24128 | 34417 | 487 | 631 | 1.10090866 | 3.65E-05 | “CAAT promoter consensus sequence” found in legA gene of pea |