transcription factor binding site

Question

[priyadhawan11234]

I have list of some transcription factors (pax1, deaf1 ....). How to know the binding sites of these transcription factors in human as well as in mouse?

Answer 1

[Jean-Karim Heriche]

There are a number of databases that provide consensus binding sequences (e.g. JASPAR) which you can then use to scan genomic regions of interest to identify binding sites. The result of such scans can also be found in some databases (e.g. Ensembl).
There are also other databases that provide this information on the basis of experiments (e.g. from ChIP-seq in GTRD).

[ATpoint]

If you want to scan given region(s) for potential binding sites using a consensus sequence (PFM/PWM) then use the FIMO tool from the MEME suite. It requires sequences in fasta format and motifs in MEME format which can be downloaded from e.g. JASPAR or (my personal preference) the HOCOMOCO database.

[priyadhawan11234]

in JASPAR, for some transcription factors it is giving this result - " No Binding sites available for this model. "