Question: Find gene affected by specific regulatory region
gravatar for Mr Locuace
14 months ago by
Mr Locuace100
Mr Locuace100 wrote:

I have some some SNPs mapping regulatory elements (TFBS, enhancer, promoter-flanking region) that are 72 -45 Kb away from a particular gene A. I want to know if there is a bioinformatic tool that predicts whether such elements affect the transcription of gene A. Thanks !

ADD COMMENTlink written 14 months ago by Mr Locuace100

I argue that you do not need a special tool but sufficient data for this, which means a cohort of samples to either do or do not harbour that SNP and matched expression data to perform regression analysis between presence/absence of that SNP and the target gene expression. Do you have these kind of data? If not I suggest you browse the literature and this forum for suggestions on predicting the interaction between distal regions and gene promoters. There are plenty of tools with different strategies to do that, best would probably be to browse PubMed for a review.

ADD REPLYlink written 14 months ago by ATpoint44k
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