lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs.
Bottom Line: 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.
Affiliation: 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.Show MeSH
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Mentions: A switch of focus from the highly studied lncRNAs H19 and XIST can further be noticed by observing the search terms that accompany ‘Long noncoding RNA’ [MeSH] in literature via PubMed, comparing the terms from before the first release of lncRNAdb (August 2010) to those after. It can be observed that the term specific to lncRNAs H19 and XIST are replaced with terms describing functionality or mechanism of action such as ‘function’, ‘cancer’, ‘differentiation’, ‘pathway’, ‘metastasis’, ‘role’ and ‘microRNA’ (Figure 4). The increase of functionally annotated lncRNAs and their annotation within the lncRNAdb can also be seen (Figure 1).
Affiliation: 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.