{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T22:36:29Z","timestamp":1780612589821,"version":"3.54.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2015,5,7]],"date-time":"2015-05-07T00:00:00Z","timestamp":1430956800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) detects genome-wide DNA\u2013protein interactions and chromatin modifications, returning enriched regions (ERs), usually associated with a significance score. Moderately significant interactions can correspond to true, weak interactions, or to false positives; replicates of a ChIP-seq experiment can provide co-localised evidence to decide between the two cases. We designed a general methodological framework to rigorously combine the evidence of ERs in ChIP-seq replicates, with the option to set a significance threshold on the repeated evidence and a minimum number of samples bearing this evidence.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We applied our method to Myc transcription factor ChIP-seq datasets in K562 cells available in the ENCODE project. Using replicates, we could extend up to 3 times the ER number with respect to single-sample analysis with equivalent significance threshold. We validated the \u2018rescued\u2019 ERs by checking for the overlap with open chromatin regions and for the enrichment of the motif that Myc binds with strongest affinity; we compared our results with alternative methods (IDR and jMOSAiCS), obtaining more validated peaks than the former and less peaks than latter, but with a better validation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>An implementation of the proposed method and its source code under GPLv3 license are freely available at http:\/\/www.bioinformatics.deib.polimi.it\/MSPC\/ and https:\/\/github.com\/Genometric\/MSPC, respectively.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>marco.morelli@iit.it<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary Material are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btv293","type":"journal-article","created":{"date-parts":[[2015,5,9]],"date-time":"2015-05-09T00:29:47Z","timestamp":1431131387000},"page":"2761-2769","source":"Crossref","is-referenced-by-count":83,"title":["Using combined evidence from replicates to evaluate ChIP-seq peaks"],"prefix":"10.1093","volume":"31","author":[{"given":"Vahid","family":"Jalili","sequence":"first","affiliation":[{"name":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan, Italy and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matteo","family":"Matteucci","sequence":"additional","affiliation":[{"name":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan, Italy and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Masseroli","sequence":"additional","affiliation":[{"name":"Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133, Milan, Italy and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco J","family":"Morelli","sequence":"additional","affiliation":[{"name":"Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,5,7]]},"reference":[{"key":"2023020202221611900_btv293-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":"2023020202221611900_btv293-B2","doi-asserted-by":"crossref","first-page":"e1003326","DOI":"10.1371\/journal.pcbi.1003326","article-title":"Practical guidelines for the comprehensive analysis of ChIP-seq data","volume":"9","author":"Bailey","year":"2013","journal-title":"PLoS Comput. 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