Journal article

is-rSNP: a novel technique for in silico regulatory SNP detection

Geoff Macintyre, James Bailey, Izhak Haviv, Adam Kowalczyk

BIOINFORMATICS | OXFORD UNIV PRESS | Published : 2010

Abstract

MOTIVATION: Determining the functional impact of non-coding disease-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) is challenging. Many of these SNPs are likely to be regulatory SNPs (rSNPs): variations which affect the ability of a transcription factor (TF) to bind to DNA. However, experimental procedures for identifying rSNPs are expensive and labour intensive. Therefore, in silico methods are required for rSNP prediction. By scoring two alleles with a TF position weight matrix (PWM), it can be determined which SNPs are likely rSNPs. However, predictions in this manner are noisy and no method exists that determines the statistical sig..

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