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I have an annotated set of SNPs and I would like to explore the difference in the binding affinity of the transcription factor (TF) if I have a SNP in my locus. As my SNPs are annotated (I know wether it is in an intron variant, downstream gene variant, missions variant, etc...) I might explore the binding affinity of those SNPs that are categorized as intron variant, downstream variant,upstream_gene_variant, non_coding_transcript_variant, 5_prime_UTR_variant and not take into consideration SNPs that are "missense variants". The reason why I want to do so is that transcription factor binding sites (TFBS) might be located before gene and after it.

What do you think about it? Can a TFBS be located in the exon of a gene? What are the locations of the TFBS regarding the exons,introns, 5' UTR etc?

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  • $\begingroup$ Lots of annotated SNPs are located nowhere near any part of any gene, so you would be quite fortunate to (a) find a SNP that maps close to a gene of interest. It would be even rarer for a public SNP to map in top of a relevant TFBS. If you had some SNPs from an unpublished study that might be cool $\endgroup$ – mdperry Mar 29 '15 at 22:47
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I would link your data with the ENCODE dataset. This dataset provides locations of TFBS. It is also accessible via the UCSC genome browser.

For the actual question TFBS are located pretty much everywhere, including exons (as described here), introns and of course intergenic regions (e.g. enhancers, silencers, control locus regions - here a reference).

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  • $\begingroup$ what about the binding affinities? Is there any tool where I can insert my notrmal sequence and a sequence with snp and it will predict the difference? I know sTRAP(trap.molgen.mpg.de) is suitable for that, however the online results differ from r-version results $\endgroup$ – Alina Mar 30 '15 at 11:42
  • $\begingroup$ @Tonja This page contains some suitable software. If you know what TF you are looking at, you might want to look at this page. $\endgroup$ – cagliari2005 Mar 30 '15 at 15:45

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