Figure 1.

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 [64] 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) [78] 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