Interpreting the biological context of PairMap, PairTrack, PairTrackAnimation and PairLines

[archieandrews10]

I need some help in the interpretation of the biological context of the PairMap, PairTrack, PairTrackAnimation and PairLines. I have done this for a pairs of TFs and I am not sure if I am interpreting it correctly. Do you have any resources that you can point to since https://tf-comb.readthedocs.io/en/latest/examples/plot_pair_footprints.html# does not seem to have any documentation for this.

[hschult]

Hi!

Binding TFs often produce a small region of inaccessible DNA when they bind aka a footprint. The Pair* plots are intended to show this for a given TF-pair. The idea behind the plots is to see how the footprint changes with increasing distance between the two TFs. The bigwig score tells you about the accessibility of the DNA at a specific position (accessible > 0 > blocked).

When you look at a PairMap each row is a genomic location where the TF-pair was found. You would expect to see a pattern at the marked locations if the TF produces a footprint. You can also see whether the TF-pair has a preferred binding distance by looking at the number of times a distance occurs.
The other plots are aggregated views on the same data. Instead of plotting every pair-binding event, you see the mean score for a selection of pair-binding events e.g. a specific binding distance.