{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T09:13:09Z","timestamp":1778058789803,"version":"3.51.4"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2019,11,5]],"date-time":"2019-11-05T00:00:00Z","timestamp":1572912000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"INSERM and Aix Marseille Univ and specific grants"},{"name":"A*MIDEX","award":["A-M-AAP-EI-17-63-170228-17.32-SPICUGLIA-HLS"],"award-info":[{"award-number":["A-M-AAP-EI-17-63-170228-17.32-SPICUGLIA-HLS"]}]},{"DOI":"10.13039\/501100006364","name":"Institut National du Cancer","doi-asserted-by":"publisher","award":["PLBIO018-031 INCA_12619"],"award-info":[{"award-number":["PLBIO018-031 INCA_12619"]}],"id":[{"id":"10.13039\/501100006364","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004099","name":"Ligue contre le Cancer","doi-asserted-by":"publisher","award":["Equipe Labellis\u00e9e"],"award-info":[{"award-number":["Equipe Labellis\u00e9e"]}],"id":[{"id":"10.13039\/501100004099","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Franco-Algerian partenariat Hubert Curien (PHC) Tassili","award":["15MDU935"],"award-info":[{"award-number":["15MDU935"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Various bioinformatics analyses provide sets of genomic coordinates of interest. Whether two such sets possess a functional relation is a frequent question. This is often determined by interpreting the statistical significance of their overlaps. However, only few existing methods consider the lengths of the overlap, and they do not provide a resolutive P-value.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we introduce OLOGRAM, which performs overlap statistics between sets of genomic regions described in BEDs or GTF. It uses Monte Carlo simulation, taking into account both the distributions of region and inter-region lengths, to fit a negative binomial model of the total overlap length. Exclusion of user-defined genomic areas during the shuffling is supported.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>This tool is available through the command line interface of the pygtftk toolkit. It has been tested on Linux and OSX and is available on Bioconda and from https:\/\/github.com\/dputhier\/pygtftk under the GNU GPL license.<\/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\/btz810","type":"journal-article","created":{"date-parts":[[2019,10,30]],"date-time":"2019-10-30T20:12:10Z","timestamp":1572466330000},"page":"1920-1922","source":"Crossref","is-referenced-by-count":21,"title":["<i>OLOGRAM<\/i>: determining significance of total overlap length between genomic regions sets"],"prefix":"10.1093","volume":"36","author":[{"given":"Q","family":"Ferr\u00e9","sequence":"first","affiliation":[{"name":"Aix Marseille Univ , INSERM, UMR U1090, TAGC, Marseille, France"},{"name":"Aix Marseille Univ , CNRS, UMR 7020, LIS, Qarma, Marseille, France"},{"name":"Equipe Labellis\u00e9e LIGUE contre le Cancer, Tlemcen University , Tlemcen, Algeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"G","family":"Charbonnier","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ , INSERM, UMR U1090, TAGC, Marseille, France"},{"name":"Equipe Labellis\u00e9e LIGUE contre le Cancer, Tlemcen University , Tlemcen, Algeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"N","family":"Sadouni","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ , INSERM, UMR U1090, TAGC, Marseille, France"},{"name":"Equipe Labellis\u00e9e LIGUE contre le Cancer, Tlemcen University , Tlemcen, Algeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"F","family":"Lopez","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ , INSERM, UMR U1090, TAGC, Marseille, France"},{"name":"Equipe Labellis\u00e9e LIGUE contre le Cancer, Tlemcen University , Tlemcen, Algeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Y","family":"Kermezli","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ , INSERM, UMR U1090, TAGC, Marseille, France"},{"name":"Equipe Labellis\u00e9e LIGUE contre le Cancer, Tlemcen University , Tlemcen, Algeria"},{"name":"The Laboratory of Applied Molecular Biology and Immunology, Tlemcen University , Tlemcen, Algeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S","family":"Spicuglia","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ , INSERM, UMR U1090, TAGC, Marseille, France"},{"name":"Equipe Labellis\u00e9e LIGUE contre le Cancer, Tlemcen University , Tlemcen, Algeria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C","family":"Capponi","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ , CNRS, UMR 7020, LIS, Qarma, Marseille, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"B","family":"Ghattas","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ , CNRS, UMR 7373, IMM, Marseille, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"D","family":"Puthier","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ , INSERM, UMR U1090, TAGC, Marseille, France"},{"name":"Equipe Labellis\u00e9e LIGUE contre le Cancer, Tlemcen University , Tlemcen, Algeria"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,11,5]]},"reference":[{"key":"2023060911595068500_btz810-B1","doi-asserted-by":"crossref","first-page":"3318","DOI":"10.1093\/bioinformatics\/bts607","article-title":"MULTOVL: fast multiple overlaps of genomic regions","volume":"28","author":"Asz\u00f3di","year":"2012","journal-title":"Bioinformatics"},{"key":"2023060911595068500_btz810-B2","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1109\/MCSE.2010.118","article-title":"Cython: the best of both worlds","volume":"13","author":"Behnel","year":"2011","journal-title":"Comput. 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