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Nucleic Acids Research 2005 33(Database Issue):D112-D115; doi:10.1093/nar/gki041
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Nucleic Acids Research, 2005, Vol. 33, Database issue D112-D115
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

NONCODE: an integrated knowledge database of non-coding RNAs

Changning Liu1,2,3, Baoyan Bai1,3, Geir Skogerbø2, Lun Cai2,3, Wei Deng1, Yong Zhang1,3, Dongbo Bu2, Yi Zhao2 and Runsheng Chen1,2,*

1 Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China, 2 Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing Technology and 3 Graduate School of the Chinese Academy of Science, Beijing 100080, China

* To whom correspondence should be addressed. Tel: +86 10 6488 8543; Fax: +86 10 6487 7837; Email: crs{at}sun5.ibp.ac.cn
Correspondence may also be addressed to Yi Zhao. Tel: +86 10 6256 5533 ext. 5717; Fax: +86 10 6256 7724; Email: biozy{at}ict.ac.cn
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

Received August 11, 2004; Revised and Accepted September 27, 2004

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.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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