Position-wise variation properties of three well-characterized developmental TFs from Drosophila melanogaster. (a) Interspecies diversity at bound motif positions and motif flanks. Diversity is expressed as 1-phastcons scores  per position across 15 insect species normalized to these scores for the scrambled versions of the same motifs detected within the respective TF-bound regions. TF 'binding logo' representations of motif PWMs are shown below each plot. (b) Within-species diversity at bound motif positions and motif flanks, expressed as genetic diversity (D)  per position across 162 isogenic lines of D. melanogaster from the DGRP normalized to the same metric for the scrambled versions of the motifs detected within the respective TF-bound regions. Asterisks indicate positions showing significantly reduced variation compared to the scrambled motifs (relative diversity <1; permutation test P < 5e-3). TF 'binding logo' representations of motif PWMs are shown below each plot. The non-normalized versions of the same plots, including both TF-bound and all instances of these motifs and their scrambled versions, are shown in Figure S1 in Additional file 1. (c) Within-species diversity per motif position across the three score ranges labeled grey to red in the increasing order: weak (Twi and Tin, 3 to 5; Bin, 5 to 8), medium (Twi and Tin, 5 to 7; Bin, 8 to 10) and strong (Twi and Tin, >7; Bin, >10). (d) Inverse correlation between individual variation at motif positions (x-axis) and positional information content according to motifs' PWM (y-axis). Variation is expressed in the same terms as in (b). Numbers beside the dots indicate motif positions; r is the Pearson's correlation coefficients for each TF. The same plots for cross-species variation are shown in Figure S2 in Additional file 1.
Spivakov et al. Genome Biology 2012 13:R49 doi:10.1186/gb-2012-13-9-r49