Influence of TF-TF cooperative interactions on TF-DNA occupancy.

<p><b>A.</b> ROC curve and Genome Surveyor tracks of the single motif model and best TF-TF interaction model for the data set “KR_Bseq_s5”, where CC(KR) = 0.487, CC(KR+VFL) = 0.774, AUC(KR) = 0.701, and AUC(KR+VFL) = 0.801. <b>B.</b> Inter-site spacing bias for a selection of putative TF-TF cooperative interactions. The statistical significance of inter-site spacing bias in the top 250 ChIP peaks (blue) or 250 non-peaks (red) of a data set is measured by the Fisher's Exact Test, for different spacing ranges (x-axis). TF pairs are named in legend (inset) with primary TF appearing first. <b>C.</b> Experimental validation of predicted direct TF-TF interactions. (Left) Candidate interacting TF pairs were produced by <i>in vitro</i> transcription/translation of renilla luciferase (Luc) and maltose binding protein (MBP) tagged proteins; luciferase activity co-isolated with the MBP-tagged protein was determined. (Right) For each heteromeric pair, interaction was tested in two configurations, with either TF1 or TF2 tagged with MBP. Results for each configuration alone and the average of both experiments are shown. A Luminescence Intensity Ratio (LIR) cutoff of 7 was used for positive interactions. Error bars indicate the Standard Deviation.