lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

Xiu Cheng Quek; Daniel W Thomson; Jesper L V Maag; Nenad Bartonicek; Bethany Signal; Michael B Clark; Brian S Gloss; Marcel E Dinger

doi:10.1093/nar/gku988

lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

Nucleic Acids Res. 2015 Jan;43(Database issue):D168-73. doi: 10.1093/nar/gku988. Epub 2014 Oct 20.

Authors

Xiu Cheng Quek¹, Daniel W Thomson², Jesper L V Maag¹, Nenad Bartonicek², Bethany Signal², Michael B Clark³, Brian S Gloss⁴, Marcel E Dinger⁵

Affiliations

¹ Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia.
² Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia.
³ Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, UK.
⁴ Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia b.gloss@garvan.org.au.
⁵ Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW 2010, Australia St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2052, Australia m.dinger@garvan.org.au.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Conserved Sequence
Databases, Nucleic Acid*
Gene Expression
Humans
Internet
Proteins / genetics
RNA, Long Noncoding / chemistry
RNA, Long Noncoding / metabolism
RNA, Long Noncoding / physiology*
Sequence Alignment

Substances

Proteins
RNA, Long Noncoding