Table 1. Proportions of the genes with promoters (500 bp upstream of the start codon) containing AGCTGT/G in the submergence- and/or rehydration-responsive gene sets detected in the previously performed microarray analyses.

* 1Gene set	Proportion of genes with at least one AGCTGT/G	Cumulative binomial distribution	*4	Proportion of genes with at least two AGCTGT/G	Cumulative binomial distribution	*4
* 1Total in the genome	0.185	0.504		0.033	0.508
* 2Up-regulated 30 min after submergence in root	0.263	0.986	+	0.068	0.983	+
* 2Up-regulated 30 min after submergence in shoot	0.194	0.652		0.032	0.724
* 2Up-regulated 1 h after submergence in root	0.235	0.989	+	0.056	0.985	+
* 2Up-regulated 1 h after submergence in shoot	0.176	0.5		0.029	0.604
* 2Up-regulated 3 h after submergence in root	0.198	0.839		0.069	∼1	++
* 2Up-regulated 3 h after submergence in shoot	0.147	0.103		0.021	0.239
* 2Up-regulated 6 h after submergence in root	0.194	0.792		0.034	0.58
* 2Up-regulated 6 h after submergence in shoot	0.166	0.159		0.028	0.32
* 2Up-regulated 12 h after submergence in root	0.196	0.849		0.037	0.776
* 2Up-regulated 12 h after submergence in shoot	0.175	0.244		0.028	0.247
* 3Up-regulated by 2-h rehydration and 2-h dehydration	0.293	0.999	++	0.102	∼1	++
* 2Down-regulated 30 min after submergence in root	0.23	0.908		0.027	0.478
* 2Down-regulated 30 min after submergence in shoot	0.143	0.618		0	0.789
* 2Down-regulated 1 h after submergence in root	0.193	0.683		0.017	0.037	*
* 2Down-regulated 1 h after submergence in shoot	0.125	0.409		0	0.582
* 2Down-regulated 3 h after submergence in root	0.187	0.561		0.036	0.729
* 2Down-regulated 3 h after submergence in shoot	0.133	0.11		0.031	0.587
* 2Down-regulated 6 h after submergence in root	0.185	0.498		0.036	0.736
* 2Down-regulated 6 h after submergence in shoot	0.142	0.01	*	0.033	0.569
* 2Down-regulated 12 h after submergence in root	0.18	0.304		0.033	0.529
* 2Down-regulated 12 h after submergence in shoot	0.155	0.008	**	0.026	0.106
* 3Down-regulated by 2-h rehydration after 2-h dehydration	0.16	0.171		0.016	0.0786

*^1–3See Dataset S1 for the exact numbers of the genes and more gene sets, which include the gene sets detected in [26] and [28].

*²These gene sets were prepared using the data in [29]. In this study, the genes that showed at least 2-fold higher expression with P-values <0.05 under the submergence condition than the control condition (non-submergence condition) were defined as up-regulated genes, and the genes that showed at least 2-fold lower expression with P-values <0.05 as down-regulated genes.

*³This gene set was prepared using the data in [27]. In this study, the genes that showed at least 5-fold higher expression after the 2-hour rehydration treatment preceded by the 2-hour dehydration treatment were defined as up-regulated genes, and the genes that showed at least 2-fold lower expression as down-regulated genes.

*⁴++: P>0.99; +: P>0.95; **: P<0.01; *: P<0.05 in cumulative binomial.