High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints
Figure 1
GEM improves spatial accuracy in binding event prediction and the resolution of proximal binding events.
A) Fraction of predicted GABP binding events with a motif within the given distance following event discovery by GEM, GPS, SISSRs, MACS, cisGenome, QuEST and PeakRanger. Events shown were predicted by all seven methods and had a GABP motif within 100 bp. B) Fraction of predicted CTCF binding events with a motif within the given distance following event discovery by GEM, GPS, SISSRs, MACS, cisGenome, QuEST, FindPeaks, spp-wtd and spp-mtc. Events shown were predicted by all nine methods and had a CTCF motif within 100 bp. C) Example of a predicted binary GABP event that contains coordinately located GABP motifs. D) Numbers of GABP binding events discovered by GEM, GPS, SISSRs, MACS, cisGenome, QuEST and PeakRanger in 477 regions that contain clustered GABP motifs within 500 bp.