The effect of relative motif orientation on motif synergy
motif orientation
a Orientation analysis of the most synergistic motif pair, PAC and mRRPE (left) and of two randomly
chosen motifs, designated M1
and M2 (corresponding to motif number 352 and 169 on the motif list on the accompanying WWW site)
(right). The figures show the distribution of differences between the location of PAC (relative
to Start) and that of mRRPE (relative to Start) in promoters containing single copies of each
motif (left) and the differences between the location of M1 (relative to Start) and that of M2
(relative to Start) (right). Of the 79 promoters containing a single copy of PAC and mRRPE, mRRPE
is closer to Start in 51 promoters. In the random pair, a more balanced distribution is obtained
as M1 is closer to Start in 14 promoters while M2 is closer to Start in 12 promoters.
b
An
orientation bias statistic using a cumulative binomial probability was calculated for the
probability of obtaining more or the same extent of bias by chance, assuming no a priori bias.
The probability for the observed orientation bias is 0.002 for mRRPE and PAC and 0.14 for M1 and M2.
(B) Histograms of the logarithm of the orientation bias scores for all 115 synergistic motif pairs
(thick line) and for a random control set (thin line) of 115 motif pairs. The P-value on the
hypothesis that the two histograms are identical is 10-14 according to the Wilcoxon rank sum test.