NONCODE v3.0: integrative annotation of long noncoding RNAs

By Dechao Bu, Kuntao Yu, Silong Sun, Chao Xie, G. Skogerbø, Ruoyu Miao, Hui Xiao, Q. Liao, Haitao Luo, Guoguang Zhao and 5 more. Nucleic Acids Res., 2011

408 citations recorded by the source corpus.

Facilitated by the rapid progress of high-throughput sequencing technology, a large number of long noncoding RNAs (lncRNAs) have been identified in mammalian transcriptomes over the past few years. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. Notably, a growing number of lncRNAs have been implicated in disease etiology. With the increasing number of published lncRNA studies, the experimental data on lncRNAs (e.g. expression profiles, molecular features and biological functions) have accumulated rapidly. In order to enable a systematic compilation and integration of this information, we have updated the NONCODE database (http://www.noncode.org) to version 3.0 to include the first integrated collection of expression and functional lncRNA data obtained from re-annotated microarray studies in a single database. NONCODE has a user-friendly interface with a variety of search or browse options, a local Genome Browser for visualization and a BLAST server for sequence-alignment search. In addition, NONCODE provides a platform for the ongoing collation of ncRNAs reported in the literature. All data in NONCODE are open to users, and can be downloaded through the website or obtained through the SOAP API and DAS services.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/dc6b2d7e1139c3a8882f7a6f033ffc2566b69272

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Citations in the corpus

NONCODEV5: a comprehensive annotation database for long non-coding RNAs (2017, methodology): “The data sources for NONCODEv5 include the previous versions of NONCODE (18–20), public literature and lncRNA databases.”
LNCipedia: a database for annotated human lncRNA transcript sequences and structures (2012, background): “The NONCODE database (12) contains a larger collection of human long non-coding RNAs (33 829) obtained from different sources and by different experimental procedures (13).”
DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs (2012, background): “3 database (24), supporting a unified set of non-coding transcripts derived from all acknowledged relevant databases and the available literature.”
On the classification of long non-coding RNAs (2013, background): “0 50 (a database of literature documented lncRNAs).”
lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs (2014, background): “…investigated at lnCeDB (12). lncRNAdb remains the only expertly curated reference database of biologically investigated lncRNAs and accord-* Nucleic Acids Research, 2015, Vol. 43, Database issue D169 ingly serves as a source for other integrative databases, such as RNAcentral (13) and NONCODE (14).”