Question: Identify TF binding motif for a given gene
0
gravatar for yanweng
4 months ago by
yanweng40
yanweng40 wrote:

If I have a list of gene, is there anyway (software, algorithm?) I can identify the TF binding motif for each gene?

-Objective: find TF motif for each gene

-meaning of "TF motif for gene": the regions which bind by TF to regulate the gene expression; those regions could be in the promoter or enhancer

-what I have found: I just start to read FIMO, not sure if it is the right direction.

ADD COMMENTlink modified 4 months ago • written 4 months ago by yanweng40
1

This biostars post may help: A: TFBS enrichiment analysis

ADD REPLYlink written 4 months ago by Alex Reynolds30k

Please edit your question and add more detail on what your project objective is, what you mean by "motif for gene" as well as details on what you've tried and where exactly you're facing a problem.

ADD REPLYlink modified 4 months ago • written 4 months ago by RamRS27k

This post is a Question, not a Forum discussion. Plus, your question does not seem to have anything to do with the tags you've used. Please tell us how these tags (chip-seq, rnaseq) relate to your question.

ADD REPLYlink written 4 months ago by RamRS27k

I am not sure why you think it's not related.. sequencing, gene, genome are the big areas, not to say the title contains the word "gene"; motif can be accessed by "chip-see"; "rna-seq" gives the gene expression level, which help me near down to the genes I am interested

ADD REPLYlink written 4 months ago by yanweng40
1

Tags are meant to help categorize your question. "motif", "transcription factor binding site" etc might be good tags for this question. The current tags look more like instagram hashtags in that they are like trending topics than indicators of what your question is really about.

ADD REPLYlink written 4 months ago by RamRS27k

Objective: find motif for each gene meaning of "motif for gene": the regions which bind by TF to regulate the gene expression; those regions could be in the promoter or enhancer what I have found: I just start to read FIMO, not sure if it is the right direction.

ADD REPLYlink written 4 months ago by yanweng40

You're looking for TFBS motifs, which are not just "motifs for genes". A motif is a generic term, and your question did not have any indication of what sort of motifs you're looking for.

ADD REPLYlink written 4 months ago by RamRS27k

Yes, I assumed it's TF binding motif. I will modify it to be more specific

ADD REPLYlink written 4 months ago by yanweng40
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