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

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

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
  1. 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.