Identify TF binding motif for a given gene
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.
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Identify binding motifs within large super enhancer region
written by mkunika •
-
Trascription factor binding sites prediction using FIMO
written by Eisuan •
-
question about TF enrichment analysis
written by tujuchuanli
-
Question about mapping motif binding sites to genome location
written by kanwarjag
-
predict TF binding sites from DNA sequence
written by grant.hovhannisyan
-
Filtering the result of transcription factor binding matrix prediction from PWM with FIMO software
written by bharata1803
-
Differentiating transcription factor binding
written by marianam •
-
Aligning TF binding site to target gene method
written by bharata1803
-
What are the different approaches for reanalysis of chipseq and RNAseq data from GSE
written by macmath
-
Average Distance Between Enhancer And Promoter Of Human Dna
written by Dan12345 •
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
This biostars post may help: A: TFBS enrichiment analysis