The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates

Table 1 Non-degenerate motifs found by the evolutionary selex (EvoSelex) method

Motif	Cluster size	Annotation	Reference	EvoSelex Z-score	Comparative P value
CpG region motifs
CCAATC	11	CAAT-BOX	[40]	28.1	6.4e-6
GGGCGG	6	SP1	[41]	24.9	1.8e-8
TGACGTCA	3	CRE	[42]	23.8	2.8e-9
CGGAAG*	5	ETS	[43]	23.4	3.6e-9
CACGTG*	1	E-Box	[44]	23.1	3.3e-7
ACTACA*	3			20.4	6.0e-5
GTGACG	2	CRE related	[42]	16.5	5.0e-4
CTTTGT	2			16.1	0.5
CCCTCCCCC	5	SP1 related	[41]	15.9	0.05
GCGCAGGCGC	2			15.5	1.0e-3
GCGCGC	1			15.5	4.6e-13
AACTTT	4			15.4	0.3
CCTTTAA	3			15.3	0.01
TGCGCA	1			14.6	2.7e-5
CTCGCGAGA	1			14.6	4.13e-8
TTGGCT	1			13.9	0.01
TATAAA	1	TATA-box	[45]	13.7	0.49
AAGATGGCGG	1			13.6	0.001
TTTGTT	3			13.4	0.13
ATGCAAAT	1			13.3	1.0e-4
TAATTA	1			13.1	0.06
TTTAAG	1			13.1	0.5
CGCATGCG	1			13.1	1.1e-5
ATAAAT	1			12.6	0.02
TTTAAA	1			12.6	0.02
GCCATTTT	1			11.7	8.5e-7
ATAAAA	1			11.7	0.6
TAAATA	1			11.6	0.5
CAGGTG	1	Helix-turn-helix	[46]	11.2	0.2
CTAGCAAC	1			11.0	4.0e-3
TGACGC	1	CRE	[42]	10.9	1.6e-4
CATTGT	1			10.7	0.14
GCCATCTT	1			10.6	8.4e-5
ATTTAT	1			10.6	0.02
ATGAAT	1			10.2	9.0e-3
Non-CpG region motifs
TAATTA	1			20.3	0.064
CAGCTG	1			18.4	0.31
TGAGTCA	2	TRE	[47]	18.1	8.0e-3
CAGGAAGT	5	ETS	[43]	14.9	0.79
CCCTCCC	2			14.4	2.68e-10
AATAAA	2			14.0	0.31
AATTAA	2	Homeodomain related	[48]	13.5	0.17
AGAAAA	2			12.9	0.44
ATAAAA	1			12.7	0.68
TTTCCA	2			12.5	0.04
TATAAATAG	1	TATA-box	[45]	12.2	0.01
AGGAAA	1			12.2	0.091
TTTCCT	1			12.2	0.091
TTCAAA	1			12.1	0.079
TGACCT	1			11.7	0.040
ATTTGCAT	1			11.3	1.0e-4
TTGTTT	1			10.9	0.011
TTTAAA	2			10.7	0.020
TTTCAG	1			10.4	0.31

The first column gives the motif consensus. *The three tested motifs in the experimental validation. The second column gives the number of related motifs when by hand analysis was used to remove additional redundancy. The third column gives a brief text description when we found a matched motif, and the literature reference for these cases is shown in the fourth column. The fifth column gives the Z-score (the number of standard deviations from the expected mean) for the conserved versus occurrence ratio on the basis of the binomial distribution. The sixth column is the probability of observing the overlap between fish and human promoters containing this motif. The table is sorted by Z-score.

ISSN: 1474-760X