{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T11:26:54Z","timestamp":1778239614484,"version":"3.51.4"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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 (\u22655.18.1) and R (\u22653.1.1) installed. The script requires the PERL Statistics::R module.<\/jats:p>\n               <jats:p>Contact: \u00a0mlupien@uhnres.utoronto.ca<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv321","type":"journal-article","created":{"date-parts":[[2015,5,21]],"date-time":"2015-05-21T02:30:54Z","timestamp":1432175454000},"page":"3057-3059","source":"Crossref","is-referenced-by-count":24,"title":["ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments"],"prefix":"10.1093","volume":"31","author":[{"given":"Swneke D.","family":"Bailey","sequence":"first","affiliation":[{"name":"1 Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, 2Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and 3Ontario Institute for Cancer Research, Toronto, ON, Canada"},{"name":"1 Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, 2Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and 3Ontario Institute for Cancer Research, Toronto, ON, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carl","family":"Virtanen","sequence":"additional","affiliation":[{"name":"1 Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, 2Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and 3Ontario Institute for Cancer Research, Toronto, ON, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benjamin","family":"Haibe-Kains","sequence":"additional","affiliation":[{"name":"1 Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, 2Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and 3Ontario Institute for Cancer Research, Toronto, ON, Canada"},{"name":"1 Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, 2Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and 3Ontario Institute for Cancer Research, Toronto, ON, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mathieu","family":"Lupien","sequence":"additional","affiliation":[{"name":"1 Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, 2Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and 3Ontario Institute for Cancer Research, Toronto, ON, Canada"},{"name":"1 Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, 2Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and 3Ontario Institute for Cancer Research, Toronto, ON, Canada"},{"name":"1 Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada, 2Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada and 3Ontario Institute for Cancer Research, Toronto, ON, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,5,20]]},"reference":[{"key":"2023020202240189400_btv321-B1","doi-asserted-by":"crossref","first-page":"6186","DOI":"10.1038\/ncomms7186","article-title":"ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters","volume":"2","author":"Bailey","year":"2015","journal-title":"Nat. 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