Differences in nucleotide content of the regions surrounding TF motifs in bound and unbound sequences extracted from in vitro data. (A) Heat map representing the differences in GC content 10 bp upstream of and downstream from the core motifs: Red indicates positions at which the GC content was significantly lower in the bound motifs; blue, positions at which the GC content was significantly higher in the bound compared with the unbound motifs (the color intensity represents the statistical significance). The TFs were grouped by the different TF families (FH, forkhead; HD, homeodomain). The positions correspond to the core-binding motif. (B) Differences between the average GC content (%GC) of the bound and the unbound sequences: Red indicates TFs that prefer binding in regions with high AT content; blue, TFs that prefer binding to regions with high GC content. (C) The GC content (%GC) in each position of the bound (blue) and unbound (black) sequences for two TFs: the EGR4 TF (C2H2 zinc finger; left), and the BARHL2 TF (homeodomain; right). Motif logos representing the aligned bound sequences are shown above.
