Question: transcription factor binding site
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gravatar for priyadhawan11234
4 months ago by
priyadhawan112340 wrote:

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?

rna-seq sequence gene genome • 182 views
ADD COMMENTlink modified 4 months ago by Jean-Karim Heriche23k • written 4 months ago by priyadhawan112340
1
gravatar for Jean-Karim Heriche
4 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche23k wrote:

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).

ADD COMMENTlink written 4 months ago by Jean-Karim Heriche23k
1

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.

ADD REPLYlink written 4 months ago by ATpoint40k

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

ADD REPLYlink modified 4 months ago • written 4 months ago by priyadhawan112340
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