Hi, all
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
SPIB 14402
ZFP354C 14291
KLF6 13982
SOX9 13449
SRY 13449
SOX10 13224
SATB1 13150
FOXO1 13107
COL11A2 13022
PARP1 13022
EFNA2 12924
ELF1 12924
SPI1 12922
...
Could you please give us some suggestions on how to get reasonable number of TF-targets?
Thanks a lot!
Aimin