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

Quek XC, Thomson DW, Maag JL, Bartonicek N, Signal B, Clark MB, Gloss BS, Dinger ME - Nucleic Acids Res. (2014)

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.

View Article: PubMed Central - PubMed

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.

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Related in: MedlinePlus

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).
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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).

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).


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

Quek XC, Thomson DW, Maag JL, Bartonicek N, Signal B, Clark MB, Gloss BS, Dinger ME - Nucleic Acids Res. (2014)

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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384040&req=5

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).
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).

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.

View Article: PubMed Central - PubMed

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
Related in: MedlinePlus