Table 1. Most common cis-acting promoter elements within the most differentially up-regulated genes in Arabidopsis germinated seeds at stage II treated with PEG^a.

TF sites containing ABRE-motif	Consensus sequence b	P	S	P-value
ABFs biding site motif	CACGTGGCACGTGGC	36	41	<10−10
AtMYC2 BS in RD22	CACATGACATG	102	142	<10−4
ABRE-like biding site motif	BACGTGKMACGTGKM	137	275	<10−10
ACGTABREMOTIFA2OSEM	ACGTGKCCGTGKC	128	217	<10−10
CACGTGMOTIF	CACGTGACGTG	104	302	<10−10
GADOWNAT	ACGTGTCCGTGTC	88	129	<10−10
GBOXLERBCS	MCACGTGGCCACGTGGC	32	36	<10−10
ABRE binding site motif	YACGTGGCACGTGGC	55	64	<10−10
ABREATRD22	RYACGTGGYRYACGTGGYR	34	37	<10−10
GBF1/2/3 BS in ADH1	CCACGTGGCACGTGG	14	28	<10−5
Z-box promoter motif	ATACGTGTTACGTGT	20	20	<10−6
TF sites containing DRE-motif
DREB1A/CBF3	RCCGACNTCCGACNT	38	46	<10−7
DRE core motif	RCCGACCCGAC	91	122	<10−10
Other TF sites
MYCATERD1	CATGTGATGTG	102	142	<10−4
RY-repeat promoter motif	CATGCATGATGCATG	19	38	<10−4
Evening Element promoter motif	AAAATATCTAAATATCT	32	38	<10−4

^aAnalysis performed with Athena [21].

^bWhere B = T/G/C; K = T/G; M = A/C; Y = T/C; R = A/G and N = A/T/G/C.

The number of promoters containing at least one instance of the TF binding site and the total number of TF binding sites in the selected set of sequences are given in the ‘P’ and ‘S’ columns, respectively. The p-value for enrichment is a measure of how overrepresented a motif is in the selected set of genes versus the overall occurrence in the genome.