Figure 6
External validation of the predicted binding sites using qPCR. The performance of the binding site detection methods as assessed by independent qPCR validations, either when using all the detected peaks (upper panel) or when focusing on the top 1000 peaks only (lower panel). In total, there were 83, 26 and 17 true positives and 30, 12 and 8 negative validation results for NRSF, FoxA1 and STAT6, respectively. The true positive rate (TP, true positives divided by all positives) and the false positive rate (FP, false positives divided by all negatives) are shown by the bars (median, minimum and maximum in the NRSF data), whereas the solid lines illustrate their distance from the optimal performance [(1-TP)2 + FP2]1/2. The dashed lines show the empirical estimate of false discovery rate (FDR), calculated as the proportion of false positives among all the identified positives.