Figure 3

Sequence conservation surrounding HB and KNI DNA binding sites. Graphs on the left and right sides correspond to results from HB and KNI respectively. In each case, the top pair of graphs were generated from sites filtered by the weak ln(P) cutoff score and the bottom graphs by the strong ln(P) cutoff score (see Methods for details). The x-axis of each graph is the position relative to the consensus binding site, with nucleotides in the core binding site marked with letters and the neighboring 25 bp on each side marked numerically by their position relative to the boundaries of the core binding region. In each upper graph, the y-axis indicates the Chi-squared value from a test in which the null hypothesis is an expected ratio at each nucleotide position of T (0.3), A (0.3), C (0.2), and G (0.2). Chi-squared values shown have been capped at 90 for clarity. Colored bars indicate statistical significance and are based on the lower-bounds of the α-value (Chi-squared values) for 0.05 (7.815, gray), 0.01 (11.345, yellow) and 0.001 (16.266, red). For example, the HB binding region statistically significantly varies from the genome-wide nucleotide distribution one and two bps downstream of the core binding site in the weak cutoff graph, but not in the strong cutoff graph. Each lower graph depicts the frequency of A (green), C (dark blue), G (light blue), and T (purple) at each position.