Question: Which transcriptin factor bind to specific motif in mouse
0
gravatar for Calangoa
11 months ago by
Calangoa30
Calangoa30 wrote:

Hi there,
How to know which transcription factor bind to a specific motif from RSAT website?
I extracted cgccgcc/ggcggcg over represented up stream of a set of genes from RSAT but it seems there is no way to find TF targeted this motif in this website.

motif • 294 views
ADD COMMENTlink modified 11 months ago by RamRS27k • written 11 months ago by Calangoa30
1
gravatar for ATpoint
11 months ago by
ATpoint36k
Germany
ATpoint36k wrote:

TOMTOM from the MEME suite can match a single sequence to a collection of PFMs which you can e.g. get from JASPAR or HOCOMOCO.

ADD COMMENTlink modified 11 months ago • written 11 months ago by ATpoint36k

Thanks ATpoint. I look at TomTom but I have found motif by RSAT. for now I want to know which TF ( by name forexample EGR1) match to this motif Or a name for this motif. Any suggestion?

ADD REPLYlink modified 11 months ago • written 11 months ago by Calangoa30
1

Yes, run TOMTOM :) What TOMTOM does is to take a sequence, here your cgccgcc and then compares it with all motifs you provide it, e.g. all TF motifs known in databases such as JASPAR or HOCOMOCO. If there is a significant similarity the tool will report it. That way you can check if your sequence significantly resembles any known factor.

ADD REPLYlink written 11 months ago by ATpoint36k

I have search my sequence in TomTOm unfortunatly there is no resemblance with any known TF!!

ADD REPLYlink written 11 months ago by Calangoa30
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