Standard and effective affinity range for different transcription factors. (a) Estimation of the affinity range for the different transcription factors analyzed in this work. For each transcription factor, the affinity range is represented as the distribution of affinities for all its experimentally determined binding sites. The affinity of each binding site is estimated using the Rsequence · BvH ranking index. (b) Estimation of the effective affinity range. For each transcription factor, the effective affinity range is represented as the distribution of normalized affinities for all its experimentally determined binding sites. Normalized affinities are estimated by normalizing the Rsequence · BvH ranking index for each site with the number of false positives required to find that site. For comparison purposes, in both affinity range plots Rsequence · BvH values (Y-axis) are normalized to the length of the binding motif for each transcription factor and ranges (X-axis) are shown as the percentage of experimentally determined sites (collection).
Erill and O'Neill BMC Bioinformatics 2009 10:57 doi:10.1186/1471-2105-10-57