{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,11]],"date-time":"2025-12-11T20:51:59Z","timestamp":1765486319103,"version":"3.37.3"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2019,10,3]],"date-time":"2019-10-03T00:00:00Z","timestamp":1570060800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"Federal Ministry of Education and Research","doi-asserted-by":"publisher","award":["FKZ 031L0129B"],"award-info":[{"award-number":["FKZ 031L0129B"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Era-Net","award":["01KT1801"],"award-info":[{"award-number":["01KT1801"]}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Long non-coding RNAs (lncRNAs) are of fundamental biological importance; however, their functional role is often unclear or loosely defined as experimental characterization is challenging and bioinformatic methods are limited. We developed a novel integrated method protocol for the annotation and detailed functional characterization of lncRNAs within the genome. It combines annotation, normalization and gene expression with sequence-structure conservation, functional interactome and promoter analysis. Our protocol allows an analysis based on the tissue and biological context, and is powerful in functional characterization of experimental and clinical RNA-Seq datasets including existing lncRNAs. This is demonstrated on the uncharacterized lncRNA GATA6-AS1 in dilated cardiomyopathy.<\/jats:p>","DOI":"10.1093\/bib\/bbz066","type":"journal-article","created":{"date-parts":[[2019,5,16]],"date-time":"2019-05-16T11:14:07Z","timestamp":1558005247000},"page":"1391-1396","source":"Crossref","is-referenced-by-count":5,"title":["A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs"],"prefix":"10.1093","volume":"21","author":[{"given":"Meik","family":"Kunz","sequence":"first","affiliation":[{"name":"Chair of Medical Informatics, Friedrich-Alexander University of Erlangen-N\u00fcrnberg, Erlangen, Germany"}]},{"given":"Beat","family":"Wolf","sequence":"additional","affiliation":[{"name":"University of Applied Sciences and Arts of Western Switzerland, Perolles 80, 1700 Fribourg, Switzerland"}]},{"given":"Maximilian","family":"Fuchs","sequence":"additional","affiliation":[{"name":"Functional Genomics and Systems Biology Group, Department of Bioinformatics, University of W\u00fcrzburg, Germany"}]},{"given":"Jan","family":"Christoph","sequence":"additional","affiliation":[{"name":"Chair of Medical Informatics, Friedrich-Alexander University of Erlangen-N\u00fcrnberg, Erlangen, Germany"}]},{"given":"Ke","family":"Xiao","sequence":"additional","affiliation":[{"name":"Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany"}]},{"given":"Thomas","family":"Thum","sequence":"additional","affiliation":[{"name":"Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany"},{"name":"REBIRTH Excellence Cluster, Hannover Medical School, Hannover, Germany"},{"name":"National Heart and Lung Institute, Imperial College London, London, UK"}]},{"given":"David","family":"Atlan","sequence":"additional","affiliation":[{"name":"Phenosystems SA, 137 Rue de Tubize, 1440 Braine le Ch\u00e2teau, Belgium"}]},{"given":"Hans-Ulrich","family":"Prokosch","sequence":"additional","affiliation":[{"name":"Chair of Medical Informatics, Friedrich-Alexander University of Erlangen-N\u00fcrnberg, Erlangen, Germany"}]},{"given":"Thomas","family":"Dandekar","sequence":"additional","affiliation":[{"name":"Functional Genomics and Systems Biology Group, Department of Bioinformatics, University of W\u00fcrzburg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2019,10,3]]},"reference":[{"key":"2020080709264311100_ref1","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1534\/genetics.112.146704","article-title":"Long noncoding RNAs: past, present, and future","volume":"193","author":"Kung","year":"2013","journal-title":"Genetics"},{"key":"2020080709264311100_ref2","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nrg2521","article-title":"Long non-coding RNAs: insights into functions","volume":"10","author":"Mercer","year":"2009","journal-title":"Nat Rev 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