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Establishing a comprehensive collection of human lncRNA sets is urgent work at present. Using reference lncRNA sets, enrichment analyses will be useful for analyzing lncRNA lists of interest submitted by users. Therefore, we developed a human lncRNA sets database, called LncSEA, which aimed to document a large number of available resources for human lncRNA sets and provide annotation and enrichment analyses for lncRNAs. LncSEA supports &amp;gt;40 000 lncRNA reference sets across 18 categories and 66 sub-categories, and covers over 50 000 lncRNAs. We not only collected lncRNA sets based on downstream regulatory data sources, but also identified a large number of lncRNA sets regulated by upstream transcription factors (TFs) and DNA regulatory elements by integrating TF ChIP-seq, DNase-seq, ATAC-seq and H3K27ac ChIP-seq data. Importantly, LncSEA provides annotation and enrichment analyses of lncRNA sets associated with upstream regulators and downstream targets. In summary, LncSEA is a powerful platform that provides a variety of types of lncRNA sets for users, and supports lncRNA annotations and enrichment analyses. The LncSEA database is freely accessible at http:\/\/bio.liclab.net\/LncSEA\/index.php.<\/jats:p>","DOI":"10.1093\/nar\/gkaa806","type":"journal-article","created":{"date-parts":[[2020,9,30]],"date-time":"2020-09-30T12:36:32Z","timestamp":1601469392000},"page":"D969-D980","source":"Crossref","is-referenced-by-count":109,"title":["LncSEA: a platform for long non-coding RNA related sets and enrichment analysis"],"prefix":"10.1093","volume":"49","author":[{"given":"Jiaxin","family":"Chen","sequence":"first","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Jian","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Yu","family":"Gao","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Yanyu","family":"Li","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Chenchen","family":"Feng","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Chao","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Ziyu","family":"Ning","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Xinyuan","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Jianmei","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Minghong","family":"Feng","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Yuexin","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Ling","family":"Wei","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Qi","family":"Pan","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Yong","family":"Jiang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Fengcui","family":"Qian","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3276-0819","authenticated-orcid":false,"given":"Junwei","family":"Han","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}]},{"given":"Yongsan","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"given":"Qiuyu","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4700-5496","authenticated-orcid":false,"given":"Chunquan","family":"Li","sequence":"additional","affiliation":[{"name":"School of Medical Informatics, Daqing Campus, Harbin Medical University,\u00a0Daqing 163319, China"}]}],"member":"286","published-online":{"date-parts":[[2020,10,12]]},"reference":[{"key":"2021010313133287400_B1","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1186\/s12943-017-0734-4","article-title":"Dysregulated long noncoding RNAs (lncRNAs) in hepatocellular carcinoma: implications for tumorigenesis, disease progression, and liver cancer stem cells","volume":"16","author":"Huo","year":"2017","journal-title":"Mol. 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