I have a list of transcription factors (genes) which are differentially regulated (based on RNA-seq data) in the treatment vs control group.
Is it somehow possible to find the genes regulated by these transcription factors?
I have a list of transcription factors (genes) which are differentially regulated (based on RNA-seq data) in the treatment vs control group.
Is it somehow possible to find the genes regulated by these transcription factors?
You could run FIMO on your entire genome for TFs (transcription factors; DNA-binding proteins) of interest, which gives you binding sites: genomic intervals where those TFs bind.
https://bioinformatics.stackexchange.com/a/2491/776
A gene's "proximal promoter" could be defined as a window 500-2500nt upstream of the strand-specific gene's TSS.
You can then map or intersect your gene's proximal promoter regions with those TF binding sites with BEDOPS bedmap
or bedops
, respectively:
https://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html
https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html
The use of bedmap
is recommended to assign TFs to a promoter of interest. This tool will return both the promoter region and any TFs that overlap it by the specified overlap criteria.
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I guess you could use iregulon app in cytoscape that finds transcription factors up stream of a list of genes. If you feed your gene list or TFs that would return these regulations. Also genei3 R package is very versatile tool to find regulAtory events.
Also Aracne is a tool that it's stand alone version easy installed on Windows could be used. I have used all of these options and playing with them is really gives fun and interesting results
Hello, I was asking myself the same question, if I have a list of transcription factors, and their binding sequence how can I find the genes that are regulated by them ?