{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T20:14:33Z","timestamp":1767903273683,"version":"3.49.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1311,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Although chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) or tiling array hybridization (ChIP-chip) is increasingly used to map genome-wide\u2013binding sites of transcription factors (TFs), it still remains difficult to generate a quality ChIPx (i.e. ChIP-seq or ChIP-chip) dataset because of the tremendous amount of effort required to develop effective antibodies and efficient protocols. Moreover, most laboratories are unable to easily obtain ChIPx data for one or more TF(s) in more than a handful of biological contexts. Thus, standard ChIPx analyses primarily focus on analyzing data from one experiment, and the discoveries are restricted to a specific biological context.<\/jats:p>\n               <jats:p>Results: We propose to enrich this existing data analysis paradigm by developing a novel approach, ChIP-PED, which superimposes ChIPx data on large amounts of publicly available human and mouse gene expression data containing a diverse collection of cell types, tissues and disease conditions to discover new biological contexts with potential TF regulatory activities. We demonstrate ChIP-PED using a number of examples, including a novel discovery that MYC, a human TF, plays an important functional role in pediatric Ewing sarcoma cell lines. These examples show that ChIP-PED increases the value of ChIPx data by allowing one to expand the scope of possible discoveries made from a ChIPx experiment.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.biostat.jhsph.edu\/\u223cgewu\/ChIPPED\/<\/jats:p>\n               <jats:p>Contact: \u00a0hji@jhsph.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt108","type":"journal-article","created":{"date-parts":[[2013,3,2]],"date-time":"2013-03-02T10:23:13Z","timestamp":1362219793000},"page":"1182-1189","source":"Crossref","is-referenced-by-count":13,"title":["ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data"],"prefix":"10.1093","volume":"29","author":[{"given":"George","family":"Wu","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, 2Department of Pediatrics, Texas Children\u2019s Cancer Center, Baylor College of Medicine, Houston, TX 77030, 3Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY 14611, 4Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, 5Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 and 6Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jason T.","family":"Yustein","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, 2Department of Pediatrics, Texas Children\u2019s Cancer Center, Baylor College of Medicine, Houston, TX 77030, 3Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY 14611, 4Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, 5Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 and 6Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA"},{"name":"1 Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, 2Department of Pediatrics, Texas Children\u2019s Cancer Center, Baylor College of Medicine, Houston, TX 77030, 3Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY 14611, 4Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, 5Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 and 6Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew N.","family":"McCall","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, 2Department of Pediatrics, Texas Children\u2019s Cancer Center, Baylor College of Medicine, Houston, TX 77030, 3Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY 14611, 4Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, 5Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 and 6Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Zilliox","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, 2Department of Pediatrics, Texas Children\u2019s Cancer Center, Baylor College of Medicine, Houston, TX 77030, 3Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY 14611, 4Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, 5Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 and 6Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rafael A.","family":"Irizarry","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, 2Department of Pediatrics, Texas Children\u2019s Cancer Center, Baylor College of Medicine, Houston, TX 77030, 3Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY 14611, 4Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, 5Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 and 6Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karen","family":"Zeller","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, 2Department of Pediatrics, Texas Children\u2019s Cancer Center, Baylor College of Medicine, Houston, TX 77030, 3Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY 14611, 4Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, 5Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 and 6Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chi V.","family":"Dang","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, Johns Hopkins 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Rochester, NY 14611, 4Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, 5Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 and 6Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,3,1]]},"reference":[{"key":"2023012810370822100_btt108-B1","doi-asserted-by":"crossref","first-page":"1653","DOI":"10.1093\/bioinformatics\/btr261","article-title":"DREME: motif discovery in transcription factor ChIP-seq data","volume":"27","author":"Bailey","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810370822100_btt108-B2","doi-asserted-by":"crossref","first-page":"D885","DOI":"10.1093\/nar\/gkn764","article-title":"NCBI GEO: archive for high-throughput functional genomic data","volume":"37","author":"Barrett","year":"2009","journal-title":"Nucleic Acids 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