How to handle redundant motif in enrichment results (AP-1 family)

[syeong8]

Hi, I'm working on scATAC-seq motif analysis using Signac, and I encountered an issue related to motif name redundancy.

When running motif enrichment test by FindMotifs() function, I observe that the motif.name column in the results contains many variations of AP-1 family motifs, such as FOSL1, FOSL1::JUND, FOSL2::JUN, BATF::JUN, FOS::JUN, JUNB, ....
While this reflects the structure of the JASPAR PWM database, it makes the plot difficult to interpret since dozens of highly similar AP-1 motifs dominate the top-ranked results.

I'd like to ask:

1. Is there a recommended way to collapse redundant motifs? for example by consolidating them under a single representative gene name?
2. Does Signac provide any built-in method to map motif names to gene names?

Thank you in advance for your help! :)

[timoast]

There are TF motif clustering collections available, for example:

JASPAR: https://jaspar.elixir.no/matrix-clusters/vertebrates/?detail=false
Vierstra lab: https://www.vierstra.org/resources/motif_clustering
Hocomoco non-redundant set: https://hocomoco14.autosome.org/downloads_v14

To convert motif IDs to TF names you can use the ConvertMotifID() function