{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,11]],"date-time":"2026-07-11T00:00:38Z","timestamp":1783728038083,"version":"3.55.0"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2023,10,3]],"date-time":"2023-10-03T00:00:00Z","timestamp":1696291200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100022232","name":"Department of Clinical Medicine, Aalborg University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100022232","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HL126901"],"award-info":[{"award-number":["R01HL126901"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HL149302"],"award-info":[{"award-number":["R01HL149302"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The cases of inflammatory bowel disease (IBD) are increasing rapidly around the world. Due to the multifactorial causes of IBD, there is an urgent need to understand the pathogenesis of IBD. As such, the usage of high-throughput techniques to profile genetic mutations, microbiome environments, transcriptome and proteome (e.g. lipidome) is increasing to understand the molecular changes associated with IBD, including two major etiologies of IBD: Crohn disease (CD) and ulcerative colitis (UC). In the case of transcriptome data, RNA sequencing (RNA-seq) technique is used frequently. However, only protein-coding genes are analyzed, leaving behind all other RNAs, including non-coding RNAs (ncRNAs) to be unexplored. Among these ncRNAs, long non-coding RNAs (lncRNAs) may hold keys to understand the pathogenesis of IBD as lncRNAs are expressed in a cell\/tissue-specific manner and dysregulated in a disease, such as IBD. However, it is rare that RNA-seq data are analyzed for lncRNAs. To fill this gap in knowledge, we re-analyzed RNA-seq data of CD and UC patients compared with the healthy donors to dissect the expression profiles of lncRNA genes. As inflammation plays key roles in the pathogenesis of IBD, we conducted loss-of-function experiments to provide functional data of IBD-specific lncRNA, lung cancer associated transcript 1 (LUCAT1), in an in vitro model of macrophage polarization. To further facilitate the lncRNA research in IBD, we built a web database, IBDB (https:\/\/ibd-db.shinyapps.io\/IBDB\/), to provide a one-stop-shop for expression profiling of protein-coding and lncRNA genes in IBD patients compared with healthy donors.<\/jats:p>","DOI":"10.1093\/bfgp\/elad044","type":"journal-article","created":{"date-parts":[[2023,10,4]],"date-time":"2023-10-04T08:12:57Z","timestamp":1696407177000},"page":"395-405","source":"Crossref","is-referenced-by-count":5,"title":["Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease"],"prefix":"10.1093","volume":"23","author":[{"given":"Rania","family":"Velissari","sequence":"first","affiliation":[{"name":"Faculty of Biology , Medicine and Health, , Oxford Rd, Manchester M13 9PL , UK"},{"name":"University of Manchester , Medicine and Health, , Oxford Rd, Manchester M13 9PL , UK"},{"name":"Bioinformatics Research Network , Atlanta, GA 30317 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mirolyuba","family":"Ilieva","sequence":"additional","affiliation":[{"name":"Center for RNA Medicine , Department of Clinical Medicine, , DK-2450 Copenhagen SV , Denmark"},{"name":"Aalborg University , Department of Clinical Medicine, , DK-2450 Copenhagen SV , Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Dao","sequence":"additional","affiliation":[{"name":"Bioinformatics Research Network , Atlanta, GA 30317 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henry E","family":"Miller","sequence":"additional","affiliation":[{"name":"Bioinformatics Research Network , Atlanta, GA 30317 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jens Hedelund","family":"Madsen","sequence":"additional","affiliation":[{"name":"Center for RNA Medicine , Department of Clinical Medicine, , DK-2450 Copenhagen SV , Denmark"},{"name":"Aalborg University , Department of Clinical Medicine, , DK-2450 Copenhagen SV , Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Gorodkin","sequence":"additional","affiliation":[{"name":"Center for non-coding RNA in Technology and Health , Department of Veterinary and Animal Sciences, , Ridebanevej 9, DK-1870 Frederiksberg C , Denmark"},{"name":"University of Copenhagen , Department of Veterinary and Animal Sciences, , Ridebanevej 9, DK-1870 Frederiksberg C , Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masanori","family":"Aikawa","sequence":"additional","affiliation":[{"name":"Cardiovascular Division , Center for Interdisciplinary Cardiovascular Sciences, , Boston, MA , USA"},{"name":"Brigham and Women's Hospital and Harvard Medical School , Center for Interdisciplinary Cardiovascular Sciences, , Boston, MA , USA"},{"name":"Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School , Boston, MA , USA"},{"name":"Center for Excellence in Vascular Biology, Brigham and Women's Hospital and Harvard Medical School , Boston, MA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hideshi","family":"Ishii","sequence":"additional","affiliation":[{"name":"Department of Medical Data Science , Center of Medical Innovation and Translational Research, Graduate School of Medicine, , Suita 565-0871 , Japan"},{"name":"Osaka University , Center of Medical Innovation and Translational Research, Graduate School of Medicine, , Suita 565-0871 , Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shizuka","family":"Uchida","sequence":"additional","affiliation":[{"name":"Center for RNA Medicine , Department of Clinical Medicine, , DK-2450 Copenhagen SV , Denmark"},{"name":"Aalborg University , Department of Clinical Medicine, , DK-2450 Copenhagen SV , Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,10,3]]},"reference":[{"key":"2024072104363148700_ref1","doi-asserted-by":"crossref","first-page":"765474","DOI":"10.3389\/fmed.2021.765474","article-title":"Treatment of inflammatory bowel disease: a comprehensive review","volume":"8","author":"Cai","year":"2021","journal-title":"Front Med (Lausanne)"},{"key":"2024072104363148700_ref2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2019\/7247238","article-title":"A comprehensive review and update on the pathogenesis of inflammatory bowel disease","volume":"2019","author":"Guan","year":"2019","journal-title":"J Immunol Res"},{"key":"2024072104363148700_ref3","doi-asserted-by":"crossref","first-page":"1603990","DOI":"10.3389\/phrs.2021.1603990","article-title":"A review of inflammatory bowel disease: a model of microbial, immune and neuropsychological integration","volume":"42","author":"Tavakoli","year":"2021","journal-title":"Public Health Rev"},{"key":"2024072104363148700_ref4","article-title":"RNA modification in inflammatory bowel diseases","volume":"10","author":"Nakayama","year":"2022","journal-title":"Biomedicine"},{"key":"2024072104363148700_ref5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s12276-018-0188-9","article-title":"The emerging role of lncRNAs in inflammatory bowel disease","volume":"50","author":"Yarani","year":"2018","journal-title":"Exp Mol Med"},{"key":"2024072104363148700_ref6","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/ibd\/izaa089","article-title":"Inflammatory bowel disease through the lens of single-cell RNA-seq technologies","volume":"26","author":"Corridoni","year":"2020","journal-title":"Inflamm Bowel Dis"},{"key":"2024072104363148700_ref7","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1038\/s43588-021-00114-y","article-title":"The Inflammatory Bowel 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