{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T07:18:45Z","timestamp":1760080725978,"version":"3.41.2"},"reference-count":64,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2022,8,12]],"date-time":"2022-08-12T00:00:00Z","timestamp":1660262400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62171166","62001145"],"award-info":[{"award-number":["62171166","62001145"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural Science Foundation for Distinguished Young Scholars of Heilongjiang Province of China","award":["JQ2020C004"],"award-info":[{"award-number":["JQ2020C004"]}]},{"name":"Research Foundation of the First Affiliated Hospital of University of South China for Advanced Talents","award":["20210002-1005"],"award-info":[{"award-number":["20210002-1005"]}]},{"name":"Wu Liande Youth Training Fund of Harbin Medical University","award":["JFWLD202001"],"award-info":[{"award-number":["JFWLD202001"]}]},{"name":"Key Laboratory of Myocardial Ischemia, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang Province, China","award":["KF202005"],"award-info":[{"award-number":["KF202005"]}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2019M661311"],"award-info":[{"award-number":["2019M661311"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010009","name":"Heilongjiang Provincial Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["LBH-Z19075"],"award-info":[{"award-number":["LBH-Z19075"]}],"id":[{"id":"10.13039\/501100010009","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The rapid development of genomic high-throughput sequencing has identified a large number of DNA regulatory elements with abundant epigenetics markers, which promotes the rapid accumulation of functional genomic region data. The comprehensively understanding and research of human functional genomic regions is still a relatively urgent work at present. However, the existing analysis tools lack extensive annotation and enrichment analytical abilities for these regions. Here, we designed a novel software, Genomic Region sets Enrichment Analysis Platform (GREAP), which provides comprehensive region annotation and enrichment analysis capabilities. Currently, GREAP supports 85 370 genomic region reference sets, which cover 634 681 107 regions across 11 different data types, including super enhancers, transcription factors, accessible chromatins, etc. GREAP provides widespread annotation and enrichment analysis of genomic regions. To reflect the significance of enrichment analysis, we used the hypergeometric test and also provided a Locus Overlap Analysis. In summary, GREAP is a powerful platform that provides many types of genomic region sets for users and supports genomic region annotations and enrichment analyses. In addition, we developed a customizable genome browser containing &amp;gt;400\u00a0000\u00a0000 customizable tracks for visualization. The platform is freely available at http:\/\/www.liclab.net\/Greap\/view\/index.<\/jats:p>","DOI":"10.1093\/bib\/bbac329","type":"journal-article","created":{"date-parts":[[2022,8,12]],"date-time":"2022-08-12T12:48:01Z","timestamp":1660308481000},"source":"Crossref","is-referenced-by-count":6,"title":["GREAP: a comprehensive enrichment analysis software for human genomic regions"],"prefix":"10.1093","volume":"23","author":[{"given":"Yongsan","family":"Yang","sequence":"first","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing, 163319, China"},{"name":"West China Biomedical Big Data Center, West China Hospital, Sichuan University , China"}]},{"given":"Fengcui","family":"Qian","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"School of Computer, University of South China , Hengyang, Hunan, 421001, China"},{"name":"Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang, China"}]},{"given":"Xuecang","family":"Li","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing, 163319, China"}]},{"given":"Yanyu","family":"Li","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing, 163319, China"}]},{"given":"Liwei","family":"Zhou","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing, 163319, China"}]},{"given":"Qiuyu","family":"Wang","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"School of Computer, University of South China , Hengyang, Hunan, 421001, China"},{"name":"Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang, China"}]},{"given":"Xinyuan","family":"Zhou","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing, 163319, China"}]},{"given":"Jian","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing, 163319, China"}]},{"given":"Chao","family":"Song","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"School of Computer, University of South China , Hengyang, Hunan, 421001, China"},{"name":"Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang, China"}]},{"given":"Zhengmin","family":"Yu","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang, China"}]},{"given":"Ting","family":"Cui","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang, China"}]},{"given":"Chenchen","family":"Feng","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing, 163319, China"}]},{"given":"Jiang","family":"Zhu","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing, 163319, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9141-393X","authenticated-orcid":false,"given":"Desi","family":"Shang","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"School of Computer, University of South China , Hengyang, Hunan, 421001, China"},{"name":"Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang, China"}]},{"given":"Jiaqi","family":"Liu","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"School of Computer, University of South China , Hengyang, Hunan, 421001, China"},{"name":"Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang, China"}]},{"given":"Mengfei","family":"Sun","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing, 163319, China"}]},{"given":"Yuexin","family":"Zhang","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing, 163319, China"}]},{"given":"Huifang","family":"Tang","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4700-5496","authenticated-orcid":false,"given":"Chunquan","family":"Li","sequence":"additional","affiliation":[{"name":"The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University , Daqing, 163319, China"},{"name":"School of Computer, University of South China , Hengyang, Hunan, 421001, China"},{"name":"Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China , Hengyang, Hunan, 421001, China"},{"name":"Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China , Hengyang, Hunan, 421001, China"},{"name":"The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China , Hengyang, China"}]}],"member":"286","published-online":{"date-parts":[[2022,8,12]]},"reference":[{"key":"2022092013223753800_ref1","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":"Consortium EP","year":"2012","journal-title":"Nature"},{"key":"2022092013223753800_ref2","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1038\/518314a","article-title":"Epigenomics: roadmap for regulation","volume":"518","author":"Romanoski","year":"2015","journal-title":"Nature"},{"key":"2022092013223753800_ref3","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nature25169","article-title":"Therapeutic targeting of ependymoma as informed by oncogenic enhancer 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features","volume":"11","author":"Wang","year":"2018","journal-title":"BMC Med Genomics"},{"key":"2022092013223753800_ref36","doi-asserted-by":"crossref","first-page":"D1028","DOI":"10.1093\/nar\/gky1096","article-title":"Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers","volume":"47","author":"Gao","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2022092013223753800_ref37","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1093\/nar\/gkx1311","article-title":"LncMAP: pan-cancer atlas of long noncoding RNA-mediated transcriptional network perturbations","volume":"46","author":"Li","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2022092013223753800_ref38","doi-asserted-by":"crossref","first-page":"D1034","DOI":"10.1093\/nar\/gky905","article-title":"LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases","volume":"47","author":"Bao","year":"2019","journal-title":"Nucleic Acids 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