NONCODE: an integrated knowledge database of non-coding RNAs

By Changning Liu, Baoyan Bai, G. Skogerbø, Lun Cai, W. Deng, Yong Zhang, Dongbo Bu, Yi Zhao, Runsheng Chen. Nucleic Acids Res., 2004

315 citations recorded by the source corpus.

NONCODE is an integrated knowledge database dedicated to non-coding RNAs (ncRNAs), that is to say, RNAs that function without being translated into proteins. All ncRNAs in NONCODE were filtered automatically from literature and GenBank, and were later manually curated. The distinctive features of NONCODE are as follows: (i) the ncRNAs in NONCODE include almost all the types of ncRNAs, except transfer RNAs and ribosomal RNAs. (ii) All ncRNA sequences and their related information (e.g. function, cellular role, cellular location, chromosomal information, etc.) in NONCODE have been confirmed manually by consulting relevant literature: more than 80% of the entries are based on experimental data. (iii) Based on the cellular process and function, which a given ncRNA is involved in, we introduced a novel classification system, labeled process function class, to integrate existing classification systems. (iv) In addition, some 1100 ncRNAs have been grouped into nine other classes according to whether they are specific to gender or tissue or associated with tumors and diseases, etc. (v) NONCODE provides a user-friendly interface, a visualization platform and a convenient search option, allowing efficient recovery of sequence, regulatory elements in the flanking sequences, secondary structure, related publications and other information. The first release of NONCODE (v1.0) contains 5339 non-redundant sequences from 861 organisms, including eukaryotes, eubacteria, archaebacteria, virus and viroids. Access is free for all users through a web interface at http://noncode.bioinfo.org.cn.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/38fa2b8e2de9e7151f0e72ce743d3f844a957a23

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Citations in the corpus

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).”
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs (2013, background): “For instance, in predicting miRNA target sites, Ribosome binding site RBSfinder [17] Rho-independent terminator TransTermHP [18] UTR Motifs UTRsite [1] PatSearch [22] 48 UTRsite motifs AU-rich element ARED [ INFERNAL [24] 209 Rfam cis -reg families Long stem einverted [30] Known functional RNAs fRNA”
Long non-coding RNAs and complex diseases: from experimental results to computational models (2016, methodology): “The lncRNA sequences and annotation information in it are collected from three databases: GENCODE (version 19; 23 898 human lncRNA transcripts) [11, 12], NONCODE (version 4.0; 95 135 human lncRNA transcripts) [48–52] and LNCipedia (version 2.1; 32 181 human lncRNA transcripts) [37, 38].”
RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure (2008, methodology): “Furthermore, the growth of RNA databases, such as NONCODE [9], Rfam [10], RNaseP [11] and RNAdb [12] has increased two to three fold annually.”
Genome-wide computational identification and manual annotation of human long noncoding RNA genes. (2010, background): “Existing ncRNA databases classify ncRNAs in different ways (Liu et al. 2005; Dinger et al. 2009) not including the proximity to known genes.”
Bioinformatic discovery of microRNA precursors from human ESTs and introns (2006, methodology): “Because many non-miRNA ncRNAs distribute in introns, we masked them by means of RepeatMasker[26], whereby the library is replaced with the ncRNA sequences downloaded from NONCODE [27].”
The functional role of long non-coding RNA in human carcinomas (2011, unknown): “org/ [249]”
Non-coding RNA. (2006, background): “The number of known functional ncRNA genes has risen dramatically in recent years and over 800 ncRNAs (excluding tRNAs, rRNAs and snRNAs) have been catalogued in mammals, at least some of which are alternatively spliced (115,116).”