AR binding upon small molecule antagonism. (A) Number of high-confidence AR binding sites in various conditions. (B) Percent (%) impact of AR antagonists with increasing dosage. To quantify the molecular effects of AR antagonists, “maximum” and “minimum” AR binding were defined using non-antagonist-treated R1881(+) and R1881(−) cistromes and the % impact was based on their differentially occupied sites. (C) AR antagonists preferentially disrupted weaker binding sites. R1881(+)-defined binding sites were sorted by descending MACS binding score (in cases of a tie, they were further sorted by descending fold enrichment values), which approximates binding affinity. (D) AR antagonists had a greater effect on weaker binding sites. Fold changes were computed as −1/signal ratio and plotted as moving average with a window size of 100. Shown in black are linear trend lines. (E) Motif score distribution of the 15 bp perfect palindrome (Additional file:1 Fig. S3B) for AR-bound sequences and 100 groups of randomly selected comparable sequences. The binding sites still occupied in the presence of the AR antagonists tend to have higher quality sequence motif (P < 0.01 for both compounds).