Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules

Table 4 Comparison of p-values and cutoff for different sets of DNA sequences

regulatory regions bicoid regulated	minimal pvalue	Cut-off	regulatory regions not regulated by bicoid	minimal pvalue	Cut-off	random seq.	minimal pvalue	Cut-off
Btd crm	3.24E-05	3.4	Gt p. enh.	0.023	2.7	seq. 1	0.16	2.6
Hb P2	4.13E-05	3.7	Hb upstream enh.	0.053	4.4	seq. 2	0.12	1.7
Kni cis element	0.01	5.3	Eve stripe 4+6 enh.	0.41	3.6	seq. 3	0.25	1.2
Kr CD-1 enh.	0.0001	5.1	Eve stripe 3+7 enh.	0.58	2.5	seq. 4	0.065	1.6
Otd early enh.	0.024	5	Ftz upstream enh.	0.037	5.8	seq. 5	0.11	1
Sal blastoder. enh.	8.62E-04	6.5	Ftz	0.28	3.3	seq. 6	0.0087	3.8
Tll PD enh.	0.26	4.2	Ubx PBX enh.	0.196	6.7	seq. 7	0.024	2.9
Tll AD+PD enh.	0.025	8.1	Ubx BXD enh.	0.698	4.6	seq. 8	0.17	3.4
Eve stripe 2 enh.	4.04E-05	5.1	Ubx BX enh. (BRE)	0.05	7.5	seq. 9	0.092	2.8
Eve stripe 1 enh.	8.09E-06	5.2	Ems upstream enh.	0.276	4.4	seq. 10	0.052	3.6
Eve stripe 5 enh.	0.27	3.8	En stripe enh. (intr. 1)	0.049	5	seq. 11	0.13	1.7
Median	8.62E-04	5.1	Median	0.196	4.4	Median	0.1128	2.6

Comparison of minimal p-values and best found cutoffs for bicoid PWM calculated (i) in regulatory regions which are regulated by bicoid, (ii) in regulatory regions which are not regulated by bicoid, and (iii) in random sequences of the same length and with the same dinucleotide distribution as in the even-skipped stripe 2 enhancer.

ISSN: 1748-7188