{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,14]],"date-time":"2024-06-14T00:57:15Z","timestamp":1718326635661},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2017,4,7]],"date-time":"2017-04-07T00:00:00Z","timestamp":1491523200000},"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":[[2017,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) generates local accumulations of sequencing reads on the genome (\u201cpeaks\u201d), which correspond to specific protein\u2013DNA interactions or chromatin modifications. Peaks are detected by considering their total area above a background signal, usually neglecting their shapes, which instead may convey additional biological information. We present FunChIP, an R\/Bioconductor package for clustering peaks according to a functional representation of their shapes: after approximating their profiles with cubic B-splines, FunChIP minimizes their functional distance and classifies the peaks applying a k-mean alignment and clustering algorithm. The whole pipeline is user-friendly and provides visualization functions for a quick inspection of the results. An application to the transcription factor Myc in 3T9 murine fibroblasts shows that clusters of peaks with different shapes are associated with different genomic locations and different transcriptional regulatory activity.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The package is implemented in R and is available under Artistic Licence 2.0 from the Bioconductor website (http:\/\/bioconductor.org\/packages\/FunChIP).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx201","type":"journal-article","created":{"date-parts":[[2017,4,6]],"date-time":"2017-04-06T20:06:34Z","timestamp":1491509194000},"page":"2570-2572","source":"Crossref","is-referenced-by-count":5,"title":["FunChIP: an R\/Bioconductor package for functional classification of ChIP-seq shapes"],"prefix":"10.1093","volume":"33","author":[{"given":"Alice C L","family":"Parodi","sequence":"first","affiliation":[{"name":"MOX\u2014Department of Mathematics, Politecnico di Milano, Milan, Italy"}]},{"given":"Laura M","family":"Sangalli","sequence":"additional","affiliation":[{"name":"MOX\u2014Department of Mathematics, Politecnico di Milano, Milan, Italy"}]},{"given":"Simone","family":"Vantini","sequence":"additional","affiliation":[{"name":"MOX\u2014Department of Mathematics, Politecnico di Milano, Milan, Italy"}]},{"given":"Bruno","family":"Amati","sequence":"additional","affiliation":[{"name":"Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan, Italy"},{"name":"Department of Experimental Oncology, European Institute of Oncology, Milan, Italy"}]},{"given":"Piercesare","family":"Secchi","sequence":"additional","affiliation":[{"name":"MOX\u2014Department of Mathematics, Politecnico di Milano, Milan, Italy"}]},{"given":"Marco J","family":"Morelli","sequence":"additional","affiliation":[{"name":"Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan, Italy"}]}],"member":"286","published-online":{"date-parts":[[2017,4,7]]},"reference":[{"key":"2023020206203283100_btx201-B1","doi-asserted-by":"crossref","first-page":"349.","DOI":"10.1186\/s12859-015-0787-6","article-title":"Peak shape clustering reveals biological insights","volume":"16","author":"Cremona","year":"2015","journal-title":"BMC Bioinformatics"},{"key":"2023020206203283100_btx201-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":"2023020206203283100_btx201-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-14-834","article-title":"Characterising chip-seq binding patterns by model-based peak shape deconvolution","volume":"14","author":"Mendoza-Parra","year":"2013","journal-title":"BMC Genomics"},{"key":"2023020206203283100_btx201-B4","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","article-title":"Silhouettes: a graphical aid to the interpretation and validation of cluster analysis","volume":"20","author":"Rousseeuw","year":"1987","journal-title":"J. Comput. Appl. Math"},{"key":"2023020206203283100_btx201-B5","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1038\/nature13537","article-title":"Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis","volume":"511","author":"Sab\u00f2","year":"2014","journal-title":"Nature"},{"key":"2023020206203283100_btx201-B6","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1016\/j.csda.2009.12.008","article-title":"k-mean alignment for curve clustering","volume":"54","author":"Sangalli","year":"2010","journal-title":"Comput. Stat. Data Anal"},{"key":"2023020206203283100_btx201-B7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0011471","article-title":"Evaluation of algorithm performance in chip-seq peak detection","volume":"5","author":"Wilbanks","year":"2010","journal-title":"PLoS ONE"},{"key":"2023020206203283100_btx201-B8","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1111\/j.1541-0420.2010.01441.x","article-title":"Pics: probabilistic inference for chip-seq","volume":"67","author":"Zhang","year":"2011","journal-title":"Biometrics"},{"key":"2023020206203283100_btx201-B9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of chip-seq (macs)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/16\/2570\/49040571\/bioinformatics_33_16_2570.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/16\/2570\/49040571\/bioinformatics_33_16_2570.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T06:20:49Z","timestamp":1675318849000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/16\/2570\/3111843"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,4,7]]},"references-count":9,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2017,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx201","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,8,15]]},"published":{"date-parts":[[2017,4,7]]}}}