TABLE 1.

Known transcription factor binding motifs enriched in promoters (∼1,000 bp upstream of the transcription start site) of genes upregulated in flooded roots showing a higher expression in wild type than in notabilis (Figure 8).

Motif	# In genome promoters	# Total genome promoters	# In promoters upregulated genes	# Total in promoters upregulated genes	Enrichment	p-value (FDR-corrected)	Known binding activity
CACGTG	3824	34417	128	849	1.35692989	0.000215	G box/binding site for AtMYC2
CACGTA	6883	34417	212	849	1.24860024	0.0002044	ABRE
ACGTAT	8196	34417	247	849	1.22168805	0.000198	ACGT/desiccation responsive
ACGTAA	9370	34417	280	849	1.21138938	0.00010403	ACGT/desiccation responsive
ACGTGA	7661	34417	224	849	1.18529889	0.00229434	ACGT/desiccation responsive
GTCATA	13259	34417	373	849	1.14041621	0.0006356	W box/binding site for WRKY3 and WRKY6
ATTATC	21924	34417	600	849	1.10942201	8.42E-06	Consensus GT-1 binding site in many light-regulated genes
ATAGTA	20635	34417	564	849	1.10800049	4.79E-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
AATACT	21847	34417	596	849	1.10590997	1.74E-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
AATATT	27066	34417	736	849	1.10234886	6.94E-10	Motif found both in promoters of rolD