Question

How do I find the associated genes of TFBS when I have the TFBS starting and end positions and sequences?

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9.8 years ago

b.odwyer3 • 0

My problem is I have a list of sequence for the binding sites of transcription factors I'm interested in but I want to find genes that are related to them. How do I find genes a certain amount of bp upstream or downstream of a tfbs?

ChIP-Seq gene • 3.0k views

ADD COMMENT • link updated 2.5 years ago by Ram 43k • written 9.8 years ago by b.odwyer3 • 0

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If you only have the name of the TF, then there a plenty of tools to predict the targets of those TFs. Google for "Transcription factor target genes tools".

ADD REPLY • link updated 2.5 years ago by Ram 43k • written 9.8 years ago by Ashutosh Pandey 12k

Ram · Answer 1 · 2014-07-07

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9.8 years ago

Devon Ryan 104k

bedtools closest
bedops closest-features
nearest() in the GenomicRanges package in Bioconductor

...among others.

ADD COMMENT • link updated 2.5 years ago by Ram 43k • written 9.8 years ago by Devon Ryan 104k