{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T17:37:26Z","timestamp":1775151446591,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) has evolved as a popular technique to study DNA\u2013protein binding or post-translational chromatin\/histone modifications at the genomic level. However, the raw microarray intensities generate a massive amount of data, creating a need for efficient analysis algorithms and statistical methods to identify enriched regions.<\/jats:p>\n               <jats:p>Results: We present a fast, free and powerful, open source R package, rMAT, that allows the identification of regions enriched for transcription factor binding sites in ChIP-chip experiments on Affymetrix tiling arrays.<\/jats:p>\n               <jats:p>Availability: The R-package rMAT is available from the Bioconductor web site at http:\/\/bioconductor.org and runs on Linux, MAC OS and MS-Windows. rMAT is distributed under the terms of the Artistic Licence 2.0.<\/jats:p>\n               <jats:p>Contact: \u00a0arnaud.droit@ircm.qc.ca; raphael.gottardo@ircm.qc.ca<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq023","type":"journal-article","created":{"date-parts":[[2010,1,21]],"date-time":"2010-01-21T01:19:59Z","timestamp":1264036799000},"page":"678-679","source":"Crossref","is-referenced-by-count":25,"title":["rMAT - an R\/Bioconductor package for analyzing ChIP-chip experiments"],"prefix":"10.1093","volume":"26","author":[{"given":"Arnaud","family":"Droit","sequence":"first","affiliation":[{"name":"1 Institut de recherches cliniques de Montreal, 110, avenue des Pins Ouest, Montreal, QC H2W 1R7, Canada and 2 Department of Biostatistics, University of Washington, Seattle, WA 98195\u20137232, USA"}]},{"given":"Charles","family":"Cheung","sequence":"additional","affiliation":[{"name":"1 Institut de recherches cliniques de Montreal, 110, avenue des Pins Ouest, Montreal, QC H2W 1R7, Canada and 2 Department of Biostatistics, University of Washington, Seattle, WA 98195\u20137232, USA"}]},{"given":"Raphael","family":"Gottardo","sequence":"additional","affiliation":[{"name":"1 Institut de recherches cliniques de Montreal, 110, avenue des Pins Ouest, Montreal, QC H2W 1R7, Canada and 2 Department of Biostatistics, University of Washington, Seattle, WA 98195\u20137232, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,1,19]]},"reference":[{"key":"2023012511010313400_B1","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.cell.2005.05.008","article-title":"Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1","volume":"122","author":"Carroll","year":"2005","journal-title":"Cell"},{"key":"2023012511010313400_B2","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and Bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol."},{"key":"2023012511010313400_B3","doi-asserted-by":"crossref","first-page":"12457","DOI":"10.1073\/pnas.0601180103","article-title":"Model-based analysis of tiling-arrays for chip-chip","volume":"103","author":"Johnson","year":"2006","journal-title":"Proc. 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