lncRNAdb


25332394	lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. [PMID: 25332394] Quek XC, Thomson DW, Maag JL, Bartonicek N, Signal B, Clark MB, Gloss BS, Dinger ME. Abstract Despite the prevalence of long noncoding RNA (lncRNA) genes in eukaryotic genomes, only a small proportion have been examined for biological function. lncRNAdb, available at http://lncrnadb.org, provides users with a comprehensive, manually curated reference database of 287 eukaryotic lncRNAs that have been described independently in the scientific literature. In addition to capturing a great proportion of the recent literature describing functions for individual lncRNAs, lncRNAdb now offers an improved user interface enabling greater accessibility to sequence information, expression data and the literature. The new features in lncRNAdb include the integration of Illumina Body Atlas expression profiles, nucleotide sequence information, a BLAST search tool and easy export of content via direct download or a REST API. lncRNAdb is now endorsed by RNAcentral and is in compliance with the International Nucleotide Sequence Database Collaboration. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. Nucleic Acids Res. 2015:43(Database issue) \| 313 Citations (from Europe PMC, 2025-03-15)
21112873	lncRNAdb: a reference database for long noncoding RNAs. [PMID: 21112873] Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS. Abstract Large numbers of long RNAs with little or no protein-coding potential [long noncoding RNAs (lncRNAs)] are being identified in eukaryotes. In parallel, increasing data describing the expression profiles, molecular features and functions of individual lncRNAs in a variety of systems are accumulating. To enable the systematic compilation and updating of this information, we have developed a database (lncRNAdb) containing a comprehensive list of lncRNAs that have been shown to have, or to be associated with, biological functions in eukaryotes, as well as messenger RNAs that have regulatory roles. Each entry contains referenced information about the RNA, including sequences, structural information, genomic context, expression, subcellular localization, conservation, functional evidence and other relevant information. lncRNAdb can be searched by querying published RNA names and aliases, sequences, species and associated protein-coding genes, as well as terms contained in the annotations, such as the tissues in which the transcripts are expressed and associated diseases. In addition, lncRNAdb is linked to the UCSC Genome Browser for visualization and Noncoding RNA Expression Database (NRED) for expression information from a variety of sources. lncRNAdb provides a platform for the ongoing collation of the literature pertaining to lncRNAs and their association with other genomic elements. lncRNAdb can be accessed at: http://www.lncrnadb.org/. Nucleic Acids Res. 2011:39(Database issue) \| 358 Citations (from Europe PMC, 2025-03-15)

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. [PMID: 25332394]

Quek XC, Thomson DW, Maag JL, Bartonicek N, Signal B, Clark MB, Gloss BS, Dinger ME.

Despite the prevalence of long noncoding RNA (lncRNA) genes in eukaryotic genomes, only a small proportion have been examined for biological function. lncRNAdb, available at http://lncrnadb.org, provides users with a comprehensive, manually curated reference database of 287 eukaryotic lncRNAs that have been described independently in the scientific literature. In addition to capturing a great proportion of the recent literature describing functions for individual lncRNAs, lncRNAdb now offers an improved user interface enabling greater accessibility to sequence information, expression data and the literature. The new features in lncRNAdb include the integration of Illumina Body Atlas expression profiles, nucleotide sequence information, a BLAST search tool and easy export of content via direct download or a REST API. lncRNAdb is now endorsed by RNAcentral and is in compliance with the International Nucleotide Sequence Database Collaboration. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2015:43(Database issue) | 313 Citations (from Europe PMC, 2025-03-15)

lncRNAdb: a reference database for long noncoding RNAs. [PMID: 21112873]

Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS.

Abstract

Large numbers of long RNAs with little or no protein-coding potential [long noncoding RNAs (lncRNAs)] are being identified in eukaryotes. In parallel, increasing data describing the expression profiles, molecular features and functions of individual lncRNAs in a variety of systems are accumulating. To enable the systematic compilation and updating of this information, we have developed a database (lncRNAdb) containing a comprehensive list of lncRNAs that have been shown to have, or to be associated with, biological functions in eukaryotes, as well as messenger RNAs that have regulatory roles. Each entry contains referenced information about the RNA, including sequences, structural information, genomic context, expression, subcellular localization, conservation, functional evidence and other relevant information. lncRNAdb can be searched by querying published RNA names and aliases, sequences, species and associated protein-coding genes, as well as terms contained in the annotations, such as the tissues in which the transcripts are expressed and associated diseases. In addition, lncRNAdb is linked to the UCSC Genome Browser for visualization and Noncoding RNA Expression Database (NRED) for expression information from a variety of sources. lncRNAdb provides a platform for the ongoing collation of the literature pertaining to lncRNAs and their association with other genomic elements. lncRNAdb can be accessed at: http://www.lncrnadb.org/.

Nucleic Acids Res. 2011:39(Database issue) | 358 Citations (from Europe PMC, 2025-03-15)

URL:	http://lncrnadb.org/
Full name:	reference database for functional long noncoding RNAs
Description:	lncRNAdb provides users with a comprehensive, manually curated reference database of 287 eukaryotic lncRNAs that have been described independently in the scientific literature. lncRNAdb is now endorsed by RNAcentral and is in compliance with the International Nucleotide Sequence Database Collaboration.
Year founded:	2011
Last update:	2015-11-23
Version:	v2.0
Accessibility:	Unaccessible
Country/Region:	Australia

Data type:	RNA
Data object:	Animal Plant
Database category:	Gene genome and annotation Literature
Major species:	Bos taurus Danio rerio Drosophila melanogaster Homo sapiens Mus musculus Pan troglodytes Rattus norvegicus Xenopus laevis Arabidopsis thaliana
Keywords:	lncRNA functional annotation

University/Institution:	Garvan Institute of Medical Research
Address:	384 Victoria Street,Sydney,NSW 2010,Australia
City:	Sydney
Province/State:	NSW
Country/Region:	Australia
Contact name (PI/Team):	Marcel E. Dinger
Contact email (PI/Helpdesk):	m.dinger@garvan.org.au

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Database Commons a catalog of worldwide biological databases