I'm analysing ATAC-seq data from cancer tissue and normal tissue. I am now analysing the results from Homer after doing the motif finding step. My supervisor has put special interest (if not all) in the "de novo" motifs found. If I understand correctly, these are unknown motifs that are matched by their similarity to known motifs by Homer, but the results in the known motifs tab are also enriched.
My question is: are de novo motifs more "valuable" when trying to find TF that may be involved with cancer? Also, when checking the results, what do you consider a good difference between % in target and % in background? Do you relay only in P-value?
Thanks in advance