SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps
Fig 3
SeqGL identifies binding signals in ChIP-seq occupancy profiles.
(A) Heatmaps show predicted binding signals and ChIP occupancy of PAX5 and co-factors. SeqGL analysis of PAX5 ChIP-seq predicts BATF and PU.1 as the most significant binding partners of PAX5. The top panel shows the group scores associated to three TFs from the PAX5 model, and the bottom panel shows the corresponding ChIP-seq read counts. This shows that a number of PAX5 ChIP-seq peaks are indirect and obtained through DNA binding of partners rather than PAX5 itself. The dashed boxes highlight the specific examples illustrated in Fig 3B. (B) Specific examples of PAX5 profiles show various modes of binding detected by SeqGL. The left panel shows direct binding of a TF (PAX5 recognizing its motif). The middle panel shows that the sequence signal is associated to BATF, and hence the PAX5 peak at this location is either due to interaction of the two factors and/or long distance looping. The right panel shows an example of co-binding of PAX5 and PU.1, each recognizing its respective binding motif.