LncBook


36330950	LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations. [PMID: 36330950] Li Z, Liu L, Feng C, Qin Y, Xiao J, Zhang Z, Ma L. Abstract LncBook, a comprehensive resource of human long non-coding RNAs (lncRNAs), has been used in a wide range of lncRNA studies across various biological contexts. Here, we present LncBook 2.0 (https://ngdc.cncb.ac.cn/lncbook), with significant updates and enhancements as follows: (i) incorporation of 119 722 new transcripts, 9632 new genes, and gene structure update of 21 305 lncRNAs; (ii) characterization of conservation features of human lncRNA genes across 40 vertebrates; (iii) integration of lncRNA-encoded small proteins; (iv) enrichment of expression and DNA methylation profiles with more biological contexts and (v) identification of lncRNA-protein interactions and improved prediction of lncRNA-miRNA interactions. Collectively, LncBook 2.0 accommodates a high-quality collection of 95 243 lncRNA genes and 323 950 transcripts and incorporates their abundant annotations at different omics levels, thereby enabling users to decipher functional significance of lncRNAs in different biological contexts. Nucleic Acids Res. 2022:() \| 34 Citations (from Europe PMC, 2025-03-15)
30329098	LncBook: a curated knowledgebase of human long non-coding RNAs. [PMID: 30329098] Ma L, Cao J, Liu L, Du Q, Li Z, Zou D, Bajic VB, Zhang Z. Abstract Long non-coding RNAs (lncRNAs) have significant functions in a wide range of important biological processes. Although the number of known human lncRNAs has dramatically increased, they are poorly annotated, posing great challenges for better understanding their functional significance and elucidating their complex functioning molecular mechanisms. Here, we present LncBook (http://bigd.big.ac.cn/lncbook), a curated knowledgebase of human lncRNAs that features a comprehensive collection of human lncRNAs and systematic curation of lncRNAs by multi-omics data integration, functional annotation and disease association. In the present version, LncBook houses a large number of 270 044 lncRNAs and includes 1867 featured lncRNAs with 3762 lncRNA-function associations. It also integrates an abundance of multi-omics data from expression, methylation, genome variation and lncRNA-miRNA interaction. Also, LncBook incorporates 3772 experimentally validated lncRNA-disease associations and further identifies a total of 97 998 lncRNAs that are putatively disease-associated. Collectively, LncBook is dedicated to the integration and curation of human lncRNAs as well as their associated data and thus bears great promise to serve as a valuable knowledgebase for worldwide research communities. Nucleic Acids Res. 2019:47(D1) \| 121 Citations (from Europe PMC, 2025-03-15)

LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations. [PMID: 36330950]

Li Z, Liu L, Feng C, Qin Y, Xiao J, Zhang Z, Ma L.

LncBook, a comprehensive resource of human long non-coding RNAs (lncRNAs), has been used in a wide range of lncRNA studies across various biological contexts. Here, we present LncBook 2.0 (https://ngdc.cncb.ac.cn/lncbook), with significant updates and enhancements as follows: (i) incorporation of 119 722 new transcripts, 9632 new genes, and gene structure update of 21 305 lncRNAs; (ii) characterization of conservation features of human lncRNA genes across 40 vertebrates; (iii) integration of lncRNA-encoded small proteins; (iv) enrichment of expression and DNA methylation profiles with more biological contexts and (v) identification of lncRNA-protein interactions and improved prediction of lncRNA-miRNA interactions. Collectively, LncBook 2.0 accommodates a high-quality collection of 95 243 lncRNA genes and 323 950 transcripts and incorporates their abundant annotations at different omics levels, thereby enabling users to decipher functional significance of lncRNAs in different biological contexts.

Nucleic Acids Res. 2022:() | 34 Citations (from Europe PMC, 2025-03-15)

LncBook: a curated knowledgebase of human long non-coding RNAs. [PMID: 30329098]

Ma L, Cao J, Liu L, Du Q, Li Z, Zou D, Bajic VB, Zhang Z.

Abstract

Long non-coding RNAs (lncRNAs) have significant functions in a wide range of important biological processes. Although the number of known human lncRNAs has dramatically increased, they are poorly annotated, posing great challenges for better understanding their functional significance and elucidating their complex functioning molecular mechanisms. Here, we present LncBook (http://bigd.big.ac.cn/lncbook), a curated knowledgebase of human lncRNAs that features a comprehensive collection of human lncRNAs and systematic curation of lncRNAs by multi-omics data integration, functional annotation and disease association. In the present version, LncBook houses a large number of 270 044 lncRNAs and includes 1867 featured lncRNAs with 3762 lncRNA-function associations. It also integrates an abundance of multi-omics data from expression, methylation, genome variation and lncRNA-miRNA interaction. Also, LncBook incorporates 3772 experimentally validated lncRNA-disease associations and further identifies a total of 97 998 lncRNAs that are putatively disease-associated. Collectively, LncBook is dedicated to the integration and curation of human lncRNAs as well as their associated data and thus bears great promise to serve as a valuable knowledgebase for worldwide research communities.

Nucleic Acids Res. 2019:47(D1) | 121 Citations (from Europe PMC, 2025-03-15)

URL:	http://bigd.big.ac.cn/lncbook
Full name:	a comprehensive database of human long non-coding RNAs
Description:	LncBook is devoted to the integration and multi-omics annotation of human lncRNAs. It provides a comprehensive and high-quality list of human lncRNAs, enriches these lncRNAs with essential multi-omics signatures, and identifies featured lncRNAs in diseases and diverse biological contexts. LncBook 2.0 accommodates a high-quality collection of 95 243 lncRNA genes and 323 950 transcripts and incorporates their abundant annotations at different omics levels.
Year founded:	2019
Last update:	2024/09/13
Version:	v2.0
Accessibility:	Accessible
Country/Region:	China

Data type:	RNA
Data object:	Animal
Database category:	Gene genome and annotation
Major species:	Homo sapiens
Keywords:	multi-omics annotation conservation lncRNA-protein interaction small protein featured gene lncRNA gene expression DNA methylation miRNA-lncRNA interactions

University/Institution:	Beijing Institute of Genomics, Chinese Academy of Sciences
Address:	No. 1 Beichen West Road, Chaoyang District, Beijing, China
City:	Beijing
Province/State:	Beijing
Country/Region:	China
Contact name (PI/Team):	Lina Ma
Contact email (PI/Helpdesk):	malina@big.ac.cn

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Database Commons a catalog of worldwide biological databases