Figure 3

Structural conservation shows positional preferences in TFBSs. Real conservation rates of structures are shown for each position of TFBSs (black). Low levels correspond to high conservation rates. Average conservation rates of structures in 10,000 randomized experiments in which TFBSs are generated from real PWMs are also shown (red). Error bars were calculated by standard deviation. The names of TF-structure correspondences are also indicated. TFs show significantly higher conservation in their corresponding structures than those based on 10,000 randomized experiments in the following specific positions in TFBSs (P < 0.05, after Bonferroni correction for multiple testing): (A) The thirteenth and fourteenth positions; (B) The first and sixth positions; (C) The fourth position; (D) The first, second, third, fourth and fifth positions; (E) The second, third, fourth and fifth positions; (F) The first, second, third, fourth, fifth, seventh and eighth positions; (G) The third and fourth positions; (H) The third and fourth positions; (I) The third position; (J) The first, fourth, fifth, sixth, seventh, eighth and ninth positions; (K) The second, third, fourth and fifth positions.