lncRNAdb: a reference database for long noncoding RNAs

By Paulo P. Amaral, Michael B. Clark, Dennis K. Gascoigne, Marcel E. Dinger, John S. Mattick. Nucleic Acids Res., 2010

575 citations recorded by the source corpus.

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/.

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Citations in the corpus

On the classification of long non-coding RNAs (2013, background): “It has been found that as many as 87% coding transcripts have antisense partners the arbitrary threshold in length (such as BC1 and snaR, which are less than or close to 200 nt but included in lncRNAdb 10 ).”
GENCODE: The reference human genome annotation for The ENCODE Project (2012, background): “Forty-two percent (44 out of 96) of the lncRNA database lncRNAdb (Amaral et al. 2011) are represented in GENCODE lncRNAs.”
NONCODE v3.0: integrative annotation of long noncoding RNAs (2011, unknown): “5 (19), FANTOM3 (20), lncRNAdb (21), miRBase v17.”
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. (2011, background): “2006), or with very small sets of experimentally validated ones (Amaral et al. 2010).”
Revealing protein–lncRNA interaction (2015, background): “Other useful resources are the lncRNAdb of functionally annotated lncRNAs [77] and the NRED database of lncRNA expression [78].”
NONCODEv4: exploring the world of long non-coding RNA genes (2013, background): “However, existing lncRNA resources such as lncRNAdb (7), ncRNAdb (8) and Rfam (9) fail to cover most of the newly identified lncRNAs in recent studies.”
Long Noncoding RNA MALAT1 Controls Cell Cycle Progression by Regulating the Expression of Oncogenic Transcription Factor B-MYB (2013, background): “However, the function of less than 2% of the human lncRNAs is clearly elucidated [11,12].”
LNCipedia: a database for annotated human lncRNA transcript sequences and structures (2012, background): “LncRNAdb (10) September 2011 134 Total number of unique transcripts 21 488”
ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data (2012, methodology): “Known functional lncRNAs were downloaded from lncRNAdb database (29).”
Colorectal Carcinoma: A General Overview and Future Perspectives in Colorectal Cancer (2017, methodology): “0 [1,2] and miRCancer: a microRNA-cancer association database [3–5] and the results obtained were corroborated by a literature search in PubMed.”
The functional role of long non-coding RNA in human carcinomas (2011, unknown): “com/ [250]”
Long non-coding RNAs and complex diseases: from experimental results to computational models (2016, background): “A large number of lncRNAs have been recorded in biological databases such as lncRNAdb [39, 47], NONCODE [48–52], PLncDB [53] and LNCipedia [37, 38].”
lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs (2014, background): “By updating lncRNAdb (8), version 2.0 aims to grow its momentum as the most cited and up-to-date reference database of lncRNAs.”
Comparative genomics reveals insights into avian genome evolution and adaptation (2014, methodology): “We aligned the lncRNA candidates against the lncRNAdb database (145) using BLAST (v2.”