Entering edit mode
4.7 years ago
yanweng
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80
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.
This biostars post may help: A: TFBS enrichiment analysis
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.
This post is a
Question, not aForumdiscussion. 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.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
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.
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.
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.
Yes, I assumed it's TF binding motif. I will modify it to be more specific