Figure 4.
An example of indirect DNA association by a TF. The Rap1 motif is the only significantly enriched motif in all three Fhl1 ChIP-chip data sets: Fhl1_RAPA, Fhl1_SM, and Fhl1_YPD. The Fhl1 motif has only moderate AUC values and associated P-values that do not pass our significance criteria. We infer that in such cases many sequences identified as “bound” in the ChIP-chip experiments are actually indirectly bound by the profiled factor (here, Fhl1) through an interacting factor (here, Rap1).
