How do I find the associated genes of TFBS when I have the TFBS starting and end positions and sequences?
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?
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Ram
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b.odwyer3 •
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b.odwyer3 •
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- bedtools closest
- bedops closest-features
nearest()in the GenomicRanges package in Bioconductor
...among others.
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Devon Ryan
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Devon Ryan
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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".