Figure 6
From: Flanking sequence context-dependent transcription factor binding in early Drosophila development
Low stringency HB binding site predictions in the IAB7b CRM. PWMs corresponding to the 7 bp core predicted binding region (PBR, red) or the core PBR with flanking sequences of various sizes (black) were used to predict HB binding sites in the 828 bp IAB7b enhancer with an initial cutoff threshold ln(p-value) = -6.77 (corresponding to the 25th percentile). For each individual PWM, a secondary cutoff at the 0th, 25th, 50th or 75th percentile of all the ranked sites (see Methods for details) was also applied. At this lower stringency primary cutoff score there are many more false positive binding sites predicted (orange circles). The core PBR fails to predict the true positive HB binding site (purple circle). The most robust predictions are made with the -19 to +7 PWM at the 25th percentile secondary cutoff, which predicts the true positive HB site and just three false positive sites (normalized value = 1.00, the relative performance of all other PWMs that predict the true positive HB site is measured against this value).