NONCODEV5: a comprehensive annotation database for long non-coding RNAs

By Shuangsang Fang, Lili Zhang, Jincheng Guo, Yiwei Niu, Yang Wu, Hui Li, Lianhe Zhao, Xiyuan Li, Xueyi Teng, XianHui Sun and 4 more. Nucleic Acids Res., 2017

439 citations recorded by the source corpus.

Abstract NONCODE (http://www.bioinfo.org/noncode/) is a systematic database that is dedicated to presenting the most complete collection and annotation of non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs). Since NONCODE 2016 was released two years ago, the amount of novel identified ncRNAs has been enlarged by the reduced cost of next-generation sequencing, which has produced an explosion of newly identified data. The third-generation sequencing revolution has also offered longer and more accurate annotations. Moreover, accumulating evidence confirmed by biological experiments has provided more comprehensive knowledge of lncRNA functions. The ncRNA data set was expanded by collecting newly identified ncRNAs from literature published over the past two years and integration of the latest versions of RefSeq and Ensembl. Additionally, pig was included in the database for the first time, bringing the total number of species to 17. The number of lncRNAs in NONCODEv5 increased from 527 336 to 548 640. NONCODEv5 also introduced three important new features: (i) human lncRNA–disease relationships and single nucleotide polymorphism-lncRNA–disease relationships were constructed; (ii) human exosome lncRNA expression profiles were displayed; (iii) the RNA secondary structures of NONCODE human transcripts were predicted. NONCODEv5 is also accessible through http://www.noncode.org/.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f791ad82d7772192f2a895cf7adf3b52b3ba26f0

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In Molecular Biology

1. Pieter Mestdagh
2. Jo Vandesompele
3. Lennart Martens
4. Pieter-Jan Volders
5. Xiaoxi Zeng

Citations in the corpus

• LNCipedia 5: towards a reference set of human long non-coding RNAs (2018, background): “Notable examples are LncRNAWiki, a wiki-based resource that combines computational and manual curation (7,8) and NONCODE, a lncRNA annotation database covering 17 species of which human and mouse have the highest number of annotations (9).”
• HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine (2020, background): “With more and diverse data becoming available, further studies based on these data will be required for analyzing the gene regulation networks under the herb/ingredient perturbation (51,52), and identifying new types of diseaserelevant genes (53,54).”
• LncRNA2Target v2.0: a comprehensive database for target genes of lncRNAs in human and mouse (2018, background): “Many important databases such as lncRNADisease (16), lncRNASNP2 (17), LncRNAWiki (18), MNDR (19), EVLncRNAs (20), NONCODE (21), LncRNA2Function (22) and TF2LncRNA (23) were developed for collecting the sequence information and functional characteristics of lncRNAs (16–23).”
• GENCODE 2021 (2020, neutral): “miTranscriptome (28), NONCODE (29), FANTOM CAT (30)).”