lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs
By Xiu Cheng Quek, Daniel W. Thomson, Jesper L. V. Maag, Nenad Bartonicek, Bethany Signal, Michael B. Clark, Brian S. Gloss, Marcel E. Dinger. Nucleic Acids Res., 2014
489 citations recorded by the source corpus.
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.
Subfields: Cancer Research, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/3175b7873502610bcf9c3c4299d4c71c07053a02
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Citations in the corpus
- 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.”
- TANRIC: An interactive open platform to explore the function of lncRNAs in cancer (2015, unknown): “Compared with other available lncRNA-focused bioinformatics resources (11,25-34), TANRIC has several unique features (Table 2): (i) It provides extensive, intuitive and interactive analyses on lncRNAs of interest for”
- LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases (2018, background): “0 with other related database (Table 1), including lncRNAdb (15), Lnc2Cancer (14), EVLncRNAs (29), which are now still available to download.”
- CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features (2017, background): “The first function is querying the transcript against well-annotated databases, including Swiss-Prot (24), RNAdb (31) and lncRNAdb (32) by BLAST (33), to identify more evidence.”
- 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].”
- Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers (2015, background): “For example, NONCODE (8), lncRNAdb (9), LNCipedia (10) and LncRNAWiki (11) integrate lncRNA data obtained from different sources.”
- NONCODEV5: a comprehensive annotation database for long non-coding RNAs (2017, unknown): “The data sources of NONCODEv5 include literature published since the last NONCODE update and the latest versions of several public databases (Ensembl (10), RefSeq (11), lncRNAdb (12) and LNCipedia (13)).”
- NONCODE 2016: an informative and valuable data source of long non-coding RNAs (2015, methodology): “NONCODE has collected data from literature published since the last update and includes the latest versions of several public databases (Ensembl (13), RefSeq(14), lncRNAdb (15) and GENCODE (16)).”