title: NONCODEv4: exploring the world of long non-coding RNA genes.
abstract: 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/.
authors.affiliation: Bioinformatics Research Group, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China, University of Chinese Academy of Sciences, Beijing 100049, China, Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China and Taicang Institute of Life Sciences Information, Suzhou 215400, China.
authors.forename: Chaoyong
authors.initials: C
authors.lastname: Xie
authors.forename: Jiao
authors.initials: J
authors.lastname: Yuan
authors.forename: Hui
authors.initials: H
authors.lastname: Li
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.forename: Guoguang
authors.initials: G
authors.lastname: Zhao
authors.forename: Dechao
authors.initials: D
authors.lastname: Bu
authors.forename: Weimin
authors.initials: W
authors.lastname: Zhu
authors.forename: Wei
authors.initials: W
authors.lastname: Wu
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhao
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D015870:Gene Expression; D006801:Humans; D020407:Internet; D051379:Mice; D058977:Molecular Sequence Annotation; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism
chemical_list: D062085:RNA, Long Noncoding