Genes regulated by transcription factors

Question

[pankaj27data]

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?

[zizigolu]

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

[Critical°Period]

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 ?

Answer 1

[Alex Reynolds]

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.

[Critical°Period]

Thank you ! I will definitively try this :)