{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T06:46:33Z","timestamp":1779345993070,"version":"3.51.4"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2126,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: ChIP-based technology is becoming the leading technology to globally profile thousands of transcription factors and elucidate the transcriptional regulation mechanisms in living cells. It has evolved rapidly in recent years, from hybridization with spotted or tiling microarray (ChIP-chip), to pair-end tag sequencing (ChIP-PET), to current massively parallel sequencing (ChIP-seq). Although there are many tools available for identifying binding sites (peaks) for ChIP-chip and ChIP-seq, few of them are available as easy-accessible online web tools for processing both ChIP-chip and ChIP-seq data for the ChIP-based user community. As such, we have developed a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Our web tool W-ChIPeaks employed a probe-based (or bin-based) enrichment threshold to define peaks and applied statistical methods to control false discovery rate for identified peaks. The web tool includes two different web interfaces: PELT for ChIP-chip, BELT for ChIP-seq, where both were tested on previously published experimental data. The novel features of our tool include a comprehensive output for identified peaks with GFF, BED, bedGraph and .wig formats, annotated genes to which these peaks are related, a graphical interpretation and visualization of the results via a user-friendly web interface.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/motif.bmi.ohio-state.edu\/W-ChIPeaks\/.<\/jats:p>\n               <jats:p>Contact: \u00a0victor.jin@osumc.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq669","type":"journal-article","created":{"date-parts":[[2010,12,8]],"date-time":"2010-12-08T01:46:45Z","timestamp":1291772805000},"page":"428-430","source":"Crossref","is-referenced-by-count":41,"title":["W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data"],"prefix":"10.1093","volume":"27","author":[{"given":"Xun","family":"Lan","sequence":"first","affiliation":[{"name":"1 Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43221 and 2Department of Informatics, University of Washington, Seattle, WA 33333, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Russell","family":"Bonneville","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43221 and 2Department of Informatics, University of Washington, Seattle, WA 33333, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeff","family":"Apostolos","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43221 and 2Department of Informatics, University of Washington, Seattle, WA 33333, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wangcheng","family":"Wu","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43221 and 2Department of Informatics, University of Washington, Seattle, WA 33333, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victor X","family":"Jin","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43221 and 2Department of Informatics, University of Washington, Seattle, WA 33333, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,12,7]]},"reference":[{"key":"2023012511545036700_B1","doi-asserted-by":"crossref","first-page":"716","DOI":"10.4161\/epi.5.8.13014","article-title":"Multivalent epigenetic marks confer microenvironment-responsive epigenetic plasticity to ovarian cancer cells","volume":"5","author":"Bapat","year":"2010","journal-title":"Epigenetics"},{"key":"2023012511545036700_B2","doi-asserted-by":"crossref","first-page":"9654","DOI":"10.1158\/0008-5472.CAN-08-1961","article-title":"N-Myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor","volume":"68","author":"Cotterman","year":"2008","journal-title":"Cancer Res."},{"key":"2023012511545036700_B3","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1038\/nrg2636","article-title":"Insights from genomic profiling of transcription factors","volume":"10","author":"Farnham","year":"2009","journal-title":"Nature Rev. 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