A ChIP-Seq Benchmark Shows That Sequence Conservation Mainly Improves Detection of Strong Transcription Factor Binding Sites
Figure 3
ROC score correlates with motif length and information content.
A) ROC score for PWM scanning as a function of motif length. B) ROC score for PWM scanning as a function of motif information content. Longer, information-rich motif achieve better scores. Note that YY1 has the second longest motif (V$YY1_01), but this motif also has the second lowest information content, which likely explains its lower score compared to the most information rich motif (V$NRSF_Q4). C) ROC curves for all methods on the E2F4 dataset in the promoter benchmark. The V$E2F_Q2 motif is one of the least informative motifs and the performance of the prediction methods on the E2F4 dataset is relatively low. D) ROC curves for all methods on the NRSF dataset in the promoter benchmark. The V$NRSF_Q4 motif is the most informative motif and the NRSF dataset is among the highest scoring datasets.