title: A comprehensive overview of lncRNA annotation resources.
abstract: Long noncoding RNAs (lncRNAs) are emerging as a class of important regulators participating in various biological functions and disease processes. With the widespread application of next-generation sequencing technologies, large numbers of lncRNAs have been identified, producing plenty of lncRNA annotation resources in different contexts. However, at present, we lack a comprehensive overview of these lncRNA annotation resources. In this study, we reviewed 24 currently available lncRNA annotation resources referring to > 205 000 lncRNAs in over 50 tissues and cell lines. We characterized these annotation resources from different aspects, including exon structure, expression, histone modification and function. We found many distinct properties among these annotation resources. Especially, these resources showed diverse chromatin signatures, remarkable tissue and cell type dependence and functional specificity. Our results suggested the incompleteness and complementarity of current lncRNA annotations and the necessity of integration of multiple resources to comprehensively characterize lncRNAs. Finally, we developed 'LNCat' (lncRNA atlas, freely available at http://biocc.hrbmu.edu.cn/LNCat/), a user-friendly database that provides a genome browser of lncRNA structures, visualization of different resources from multiple angles and download of different combinations of lncRNA annotations, and supports rapid exploration, comparison and integration of lncRNA annotation resources. Overall, our study provides a comprehensive comparison of numerous lncRNA annotations, and can facilitate understanding of lncRNAs in human disease.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Jinyuan
authors.initials: J
authors.lastname: Xu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Bai
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Xinxin
authors.initials: X
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Yanling
authors.initials: Y
authors.lastname: Lv
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
authors.forename: Yonghui
authors.initials: Y
authors.lastname: Gong
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Liu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
authors.forename: Hongying
authors.initials: H
authors.lastname: Zhao
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
authors.forename: Fulong
authors.initials: F
authors.lastname: Yu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Yanyan
authors.initials: Y
authors.lastname: Ping
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
authors.forename: Guanxiong
authors.initials: G
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
authors.forename: Yujia
authors.initials: Y
authors.lastname: Lan
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.|Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang, China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.
authors.forename: Xia
authors.initials: X
authors.lastname: Li
mesh_terms: D002843:Chromatin; D006801:Humans; D058977:Molecular Sequence Annotation; D062085:RNA, Long Noncoding / Q000235:genetics*
chemical_list: D002843:Chromatin; D062085:RNA, Long Noncoding
keywords: annotation resource; database; integration; lncRNA