{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T01:45:48Z","timestamp":1778636748559,"version":"3.51.4"},"reference-count":34,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2020,2,14]],"date-time":"2020-02-14T00:00:00Z","timestamp":1581638400000},"content-version":"vor","delay-in-days":44,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Joint School of Life Sciences"},{"DOI":"10.13039\/100009659","name":"Guangzhou Medical University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>A gene regulatory process is the result of the concerted action of transcription factors, co-factors, regulatory non-coding RNAs (ncRNAs) and chromatin interactions. Therefore, the combination of protein\u2013DNA, protein\u2013protein, ncRNA\u2013DNA, ncRNA\u2013protein and DNA\u2013DNA data in a single graph database offers new possibilities regarding generation of biological hypotheses. GREG (The Gene Regulation Graph Database) is an integrative database and web resource that allows the user to visualize and explore the network of all above-mentioned interactions for a query transcription factor, long non-coding RNA, genomic range or DNA annotation, as well as extracting node and interaction information, identifying connected nodes and performing advanced graphical queries directly on the regulatory network, in a simple and efficient way. In this article, we introduce GREG together with some application examples (including exploratory research of Nanog\u2019s regulatory landscape and the etiology of chronic obstructive pulmonary disease), which we use as a demonstration of the advantages of using graph databases in biomedical research.<\/jats:p><jats:p>Database URL: https:\/\/mora-lab.github.io\/projects\/greg.html, www.moralab.science\/GREG\/<\/jats:p>","DOI":"10.1093\/database\/baz162","type":"journal-article","created":{"date-parts":[[2020,1,3]],"date-time":"2020-01-03T12:08:04Z","timestamp":1578053284000},"source":"Crossref","is-referenced-by-count":4,"title":["GREG\u2014studying transcriptional regulation using integrative graph databases"],"prefix":"10.1093","volume":"2020","author":[{"given":"Songqing","family":"Mei","sequence":"first","affiliation":[{"name":"School of Basic Medical Sciences, Guangzhou Medical University, Panyu Campus of Guangzhou Medical University, Xinzao, 511436 Guangzhou, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaowei","family":"Huang","sequence":"first","affiliation":[{"name":"Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Panyu Campus of Guangzhou Medical University, Xinzao, 511436 Guangzhou, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chengshu","family":"Xie","sequence":"first","affiliation":[{"name":"Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Panyu Campus of Guangzhou Medical University, Xinzao, 511436 Guangzhou, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1344-1131","authenticated-orcid":false,"given":"Antonio","family":"Mora","sequence":"first","affiliation":[{"name":"Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Panyu Campus of Guangzhou Medical University, Xinzao, 511436 Guangzhou, P.R. China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,2,13]]},"reference":[{"key":"2020021321302334400_ref1","volume-title":"GREG\u2014the Gene Regulation Graph Database","author":"Mei","year":"2018"},{"key":"2020021321302334400_ref2","doi-asserted-by":"crossref","first-page":"2560","DOI":"10.1093\/bioinformatics\/btv158","article-title":"4DGenome: a comprehensive database of chromatin interactions","volume":"31","author":"Teng","year":"2015","journal-title":"Bioinformatics"},{"key":"2020021321302334400_ref3","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1186\/1471-2105-9-405","article-title":"iRefIndex: a consolidated protein interaction database with provenance","volume":"9","author":"Razick","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2020021321302334400_ref4","doi-asserted-by":"crossref","first-page":"D729","DOI":"10.1093\/nar\/gky1094","article-title":"Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis","volume":"47","author":"Zheng","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020021321302334400_ref5","first-page":"2018","article-title":"LnChrom: a resource of experimentally validated lncRNA-chromatin interactions in human and mouse","author":"Yu","year":"2018","journal-title":"Database (Oxford)"},{"key":"2020021321302334400_ref6","doi-asserted-by":"crossref","first-page":"D92","DOI":"10.1093\/nar\/gkt1248","article-title":"starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data","volume":"42","author":"Li","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2020021321302334400_ref7","article-title":"GENCODE reference annotation for the human and mouse genomes","author":"Frankish","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2020021321302334400_ref8","author":"Pareja Tobes","year":"2015"},{"key":"2020021321302334400_ref9","doi-asserted-by":"crossref","first-page":"3868","DOI":"10.1093\/bioinformatics\/btv460","article-title":"cyNeo4j: connecting Neo4j and Cytoscape","volume":"31","author":"Summer","year":"2015","journal-title":"Bioinformatics"},{"key":"2020021321302334400_ref10","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1186\/s12918-018-0616-4","article-title":"BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources","volume":"12","author":"Messina","year":"2018","journal-title":"BMC Syst. 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