We have 470 mouse TFs and 21989 mouse protein-coding genes and we got promoter sequences (2000 nt) of these protein-coding genes.
Used the following command to run Match:
./match ../data/matrix.dat ../data/promoter.sequences result ../data/minFP_good.prf
and then use core matrix threshold 1.0 and similarity matrix threshold 0.95 to filter results.
We found that some TFs targeted huge amount of genes as follows:
Name of TF; Number of targeted genes
Could you please give us some suggestions on how to get reasonable number of TF-targets?
Thanks a lot!