title: NONCODE: an integrated knowledge database of non-coding RNAs.
abstract: 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.
authors.affiliation: Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
authors.forename: Changning
authors.initials: C
authors.lastname: Liu
authors.forename: Baoyan
authors.initials: B
authors.lastname: Bai
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerbø
authors.forename: Lun
authors.initials: L
authors.lastname: Cai
authors.forename: Wei
authors.initials: W
authors.lastname: Deng
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Dongbo
authors.initials: D
authors.lastname: Bu
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhao
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: D001483:Base Sequence; D030561:Databases, Nucleic Acid; D022661:RNA, Untranslated / Q000737:chemistry* / Q000145:classification; D018511:Systems Integration
chemical_list: D022661:RNA, Untranslated