Question: transcription factor binding site
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gravatar for priyadhawan11234
5 weeks 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 • 122 views
ADD COMMENTlink modified 5 weeks ago by Jean-Karim Heriche22k • written 5 weeks ago by priyadhawan112340
1
gravatar for Jean-Karim Heriche
5 weeks ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche22k 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 5 weeks ago by Jean-Karim Heriche22k
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 5 weeks ago by ATpoint36k

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

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by priyadhawan112340
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