{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:42Z","timestamp":1772138082241,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,12,12]],"date-time":"2016-12-12T00:00:00Z","timestamp":1481500800000},"content-version":"vor","delay-in-days":4,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ERC starting grant Relieve-IMDs"},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Computational evaluation of variability across DNA or RNA sequencing datasets is a crucial step in genomic science, as it allows both to evaluate reproducibility of biological or technical replicates, and to compare different datasets to identify their potential correlations. Here we present fCCAC, an application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). We show how this method differs from other measures of correlation, and exemplify how it can reveal shared covariance between histone modifications and DNA binding proteins, such as the relationship between the H3K4me3 chromatin mark and its epigenetic writers and readers.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>An R\/Bioconductor package is available at http:\/\/bioconductor.org\/packages\/fCCAC\/.<\/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\/btw724","type":"journal-article","created":{"date-parts":[[2016,11,16]],"date-time":"2016-11-16T15:05:49Z","timestamp":1479308749000},"page":"746-748","source":"Crossref","is-referenced-by-count":3,"title":["fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets"],"prefix":"10.1093","volume":"33","author":[{"given":"Pedro","family":"Madrigal","sequence":"first","affiliation":[{"name":"Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK"},{"name":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hixton, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,12,8]]},"reference":[{"key":"2023020204502597900_btw724-B1","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. Biol"},{"key":"2023020204502597900_btw724-B2","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/nprot.2011.420","article-title":"A computational pipeline for comparative ChIP-seq analyses","volume":"7","author":"Bardet","year":"2011","journal-title":"Nat. Protoc"},{"key":"2023020204502597900_btw724-B3","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1101\/gad.255984.114","article-title":"Activin\/nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark","volume":"29","author":"Bertero","year":"2015","journal-title":"Genes. Dev"},{"key":"2023020204502597900_btw724-B4","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"ENCODE Project Consortium","year":"2012","journal-title":"Nature"},{"key":"2023020204502597900_btw724-B5","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1038\/nsmb.1778","article-title":"PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1\/2 demethylation","volume":"17","author":"Feng","year":"2010","journal-title":"Nat. Struct. Mol. Biol"},{"key":"2023020204502597900_btw724-B6","doi-asserted-by":"crossref","first-page":"2976","DOI":"10.1093\/nar\/gkt1249","article-title":"Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments","volume":"42","author":"Kheradpour","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020204502597900_btw724-B7","doi-asserted-by":"crossref","first-page":"1752","DOI":"10.1214\/11-AOAS466","article-title":"Measuring reproducibility of high-throughput experiments","volume":"5","author":"Li","year":"2011","journal-title":"Ann. Appl. Stat"},{"key":"2023020204502597900_btw724-B8","doi-asserted-by":"crossref","first-page":"20.","DOI":"10.1186\/s13040-015-0051-7","article-title":"Uncovering correlated variability in epigenomic datasets using the Karhunen-Loeve transform","volume":"8","author":"Madrigal","year":"2015","journal-title":"BioData Min"},{"key":"2023020204502597900_btw724-B9","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1128\/MCB.00864-13","article-title":"The demethylase JMJD2C localizes to H3K4me3-positive transcription start sites and is dispensable for embryonic development","volume":"34","author":"Pedersen","year":"2014","journal-title":"Mol. Cell Biol"},{"key":"2023020204502597900_btw724-B10","doi-asserted-by":"crossref","DOI":"10.1007\/b98888","volume-title":"Functional Data Analysis","author":"Ramsay","year":"2005"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/5\/746\/49037881\/bioinformatics_33_5_746.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/5\/746\/49037881\/bioinformatics_33_5_746.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T23:52:03Z","timestamp":1675295523000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/5\/746\/2627422"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,12,8]]},"references-count":10,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2017,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw724","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/060780","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,3,1]]},"published":{"date-parts":[[2016,12,8]]}}}