Question

Finding gene targets for a list of transcription factors

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alakatos ▴ 130

@alakatos-6983

Last seen 5.2 years ago

United States

Hello All,

I am reaching out for your advice. Would you please recommend tools preferably in Bioconductor for the following problem: I have a list of transcription factors. At first, I must find all the possible downstream gene targets, then retrieve all the possible interactions (edges) between those genes to build a regulatory network.

All the tools I found do the opposite: finding transcription factors for a list of genes.

Your help and advice are highly appreciated. Thank you in advance. Anita

transcription factors regulatory gene network gene targets • 1.9k views

ADD COMMENT • link updated 5.2 years ago by svlachavas ▴ 840 • written 5.2 years ago by alakatos ▴ 130

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There are quite a few posts about this on Biostars: https://www.biostars.org/p/273985/ (see the 'Similar posts' at right, too).

ADD REPLY • link 5.2 years ago Kevin Blighe ★ 4.0k

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Hi. I had the same problem once using gene lists (as in time course of differentiation) that had TFs in them. I wanted to know TF-target gene interactions. The best way for me was using the cytoscape app called tetramer. I think its hard to build on R. But cytoscape gives you so many options to customise your networks systematically.

ADD REPLY • link 5.2 years ago kasumazim • 0

score 1 · Answer 1 · 2019-09-23

Dear Anita,

even your question is not directly related to the purpose of this group, i would quickly suggest for a solution through R/Bioconductor the R package CoRegNet [http://bioconductor.org/packages/release/bioc/html/CoRegNet.html]-but the relative gene expression data are necessary for the co-regulation network reconstruction..

also, the web tool chea3 has the largest collection of TF-gene interactions (https://amp.pharm.mssm.edu/chea3/).

however, if you directly want to find target genes starting from TFs, i would primarily consider the database TRRUST (https://www.grnpedia.org/trrust/)

Hope that helps.

Best,

Efstathios