NONCODEv4: exploring the world of long non-coding RNA genes

By Chao Xie, Jiao Yuan, Ming Li, Guoguang Zhao, Dechao Bu, Weimin Zhu, Wei Wu, Runsheng Chen, Yi Zhao. Nucleic Acids Res., 2013

407 citations recorded by the source corpus.

NONCODE (http://www.bioinfo.org/noncode/) is an integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs). Non-coding RNAs (ncRNAs) have been implied in diseases and identified to play important roles in various biological processes. Since NONCODE version 3.0 was released 2 years ago, discovery of novel ncRNAs has been promoted by high-throughput RNA sequencing (RNA-Seq). In this update of NONCODE, we expand the ncRNA data set by collection of newly identified ncRNAs from literature published in the last 2 years and integration of the latest version of RefSeq and Ensembl. Particularly, the number of long non-coding RNA (lncRNA) has increased sharply from 73 327 to 210 831. Owing to similar alternative splicing pattern to mRNAs, the concept of lncRNA genes was put forward to help systematic understanding of lncRNAs. The 56 018 and 46 475 lncRNA genes were generated from 95 135 and 67 628 lncRNAs for human and mouse, respectively. Additionally, we present expression profile of lncRNA genes by graphs based on public RNA-seq data for human and mouse, as well as predict functions of these lncRNA genes. The improvements brought to the database also include an incorporation of an ID conversion tool from RefSeq or Ensembl ID to NONCODE ID and a service of lncRNA identification. NONCODE is also accessible through http://www.noncode.org/.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/39429671c164492f877d40461bcc8a38c7abcf33

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In Molecular Biology

Citations in the corpus

Revealing protein–lncRNA interaction (2015, background): “Normally used gene-sets from common public repositories might not contain the most updated annotations of lncRNAs, and specialized data sets can provide more recent and exhaustive collections, for example the GENCODE lncRNA catalogue [74], NONCODE [75] or LNCipedia [76].”
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.”
Proteogenomics: concepts, applications, and computational strategies (2014, background): “43); the Pseudogene.org database (http:// pseudogene.org/), the noncoding RNA sequence database NONCODE 44 (used in ref.”
NONCODEV5: a comprehensive annotation database for long non-coding RNAs (2017, background): “According to the definition of lncRNA gene (19), NONCODEv5 collected a total of 354 855 genes.”
NONCODE 2016: an informative and valuable data source of long non-coding RNAs (2015, methodology): “According to the definition of lncRNA genes (18), NONCODE collected 337,880 genes altogether.”
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”