Determination of the optimal P
threshold (α) value. For every α, ranging from 0.01 to 0.99 in steps of 0.01, the average nucleosome occupancy (Poccupied) at the true or false positive TFBS site was determined in all four data sets (full lines) and averaged over a range of 1–2 kb upstream (dashed lines). Again, our previous conclusions were confirmed. For low α-values, the average occupancy level of a true TFBS is lower than the average occupancy levels observed with the random sequences (either 0th order or 1st order). Alternatively, the nucleosome occupancy at a false positive TFBS is comparable to the average occupancy observed over a range of 1–2 kb upstream of a true TFBS. For α > 0.1, the nucleosome occupancies for the data sets of random sequences (either 0th order or 1st order), drop quickly reaching very small values. As these values are considerably smaller than the ones obtained with the data set of true TFBSs, this suggests that while low nucleosome occupancy is encoded around true TFBSs, this does not mean nucleosomes should be absent.