AtSNP: transcription factor binding affinity testing for regulatory SNP detection.

ABSTRACT:

Motivation

Genome-wide association studies revealed that most disease-associated single nucleotide polymorphisms (SNPs) are located in regulatory regions within introns or in regions between genes. Regulatory SNPs (rSNPs) are such SNPs that affect gene regulation by changing transcription factor (TF) binding affinities to genomic sequences. Identifying potential rSNPs is crucial for understanding disease mechanisms. In silico methods that evaluate the impact of SNPs on TF binding affinities are not scalable for large-scale analysis.

Results

We describe A: ffinity T: esting for regulatory SNP: s (atSNP), a computationally efficient R package for identifying rSNPs in silico. atSNP implements an importance sampling algorithm coupled with a first-order Markov model for the backg

SUBMITTER: Zuo C 

PROVIDER: S-EPMC4643619 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature