Dataset Information
ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments.
Ontology highlight
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 chromatin.Availability and implementation
The code is open-source under an Artistic-2.0 license and versioned on GitHub (https://github.com/mlupien/ABC/). ABC is written in PERL and can be run on any platform with both PERL (?5.18.1) and R (?3.1.1) installed. The script requires the PERL Statistics::R module.Contact
mlupien@uhnres.utoronto.caSupplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Bailey SD
PROVIDER: S-EPMC4668780 | biostudies-literature | 2015 Sep
REPOSITORIES: biostudies-literature
Publications
ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments.
Bioinformatics (Oxford, England) 20150520 18
<h4>Motivation</h4>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 u ...[more]