Question

Which transcriptin factor bind to specific motif in mouse

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4.8 years ago

Calangoa ▴ 30

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 • 1.2k views

ADD COMMENT • link updated 4.8 years ago by Ram 43k • written 4.8 years ago by Calangoa ▴ 30

score 1 · Answer 1 · 2019-07-22

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4.8 years ago

ATpoint 82k

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 COMMENT • link 4.8 years ago by ATpoint 82k

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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 REPLY • link 4.8 years ago by Calangoa ▴ 30

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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 REPLY • link 4.8 years ago by ATpoint 82k

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

ADD REPLY • link 4.8 years ago by Calangoa ▴ 30