Using Transfac Match to predict TF-gene binding relations

Question

[liaimin815]

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