ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments.

ABSTRACT:

Motivation

Detection of allelic imbalances in ChIP-Seq reads is a powerful approach to identify functional non-coding single nucleotide variants (SNVs), either polymorphisms or mutations, which modulate the affinity of transcription factors for chromatin. We present ABC, a computational tool that identifies allele-specific binding of transcription factors from aligned ChIP-Seq reads at heterozygous SNVs. ABC controls for potential false positives resulting from biases introduced by the use of short sequencing reads in ChIP-Seq and can efficiently process a large number of heterozygous SNVs.

Results

ABC successfully identifies previously characterized functional SNVs, such as the rs4784227 breast cancer risk associated SNP that modulates the affinity of FOXA1 for the chromati

SUBMITTER: Bailey SD 

PROVIDER: S-EPMC4668780 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature