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

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

Xiu Cheng Quek  1 , Daniel W Thomson  2 , Jesper L V Maag  1 , Nenad Bartonicek  2 , Bethany Signal  2 , Michael B Clark  3 , Brian S Gloss  4 , Marcel E Dinger  5
Affiliations

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

Xiu Cheng Quek et al. Nucleic Acids Res. 2015 Jan.

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.

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Figures

Figure 1.
Figure 1.
Coverage of the literature by lncRNAdb v2.0. Cumulative totals of all publications matching the search term ‘long noncoding RNA’ [MeSH] were extracted from PubMed from 1992–2013 (green) and the proportion incorporated into lncRNAdb as ascribing functional annotation to lncRNAs is shown (blue). Cumulative totals of the number of lncRNAs found in lncRNAdb described in literature (red).
Figure 2.
Figure 2.
The lncRNAdb v2.0 user interface. A screenshot of an example profile highlighting new features.
Figure 3.
Figure 3.
Heatmap showing the number of references within PubMed with the term ‘RNA, long noncoding’ [MeSH] for each given year. The top 10 most studied lncRNAs are named and color scale is logarithmic. Nomenclature information of all noncoding RNA from was obtained from HGNC. Entries without search results were removed. The remaining entries were visualized with a heatmap constructed using R Package ‘gplots’ (v.2.14.1).
Figure 4.
Figure 4.
Word cloud collating the top 500 terms within abstracts found in PubMed, following a search with the term ‘long noncoding RNA’ [MeSH]. Terms appearing more frequent in publications before years 2011 are labeled green terms more frequent after in publications after year 2012 are labeled blue. The sizes of the words represent the difference in frequencies of the word appearing in the two sets of abstracts. Word frequencies are normalized against the number of publications in each set. Text preprocessing was conducted by an in-house script (available at http://lncrnadb.org/help) and the word cloud was created with R package ‘tm’ (v.0.6) and ‘wordcloud’ (v.2.5).
See this image and copyright information in PMC

References

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