Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, PR China.
Nucleic Acids Res. 2012 Jan;40(Database issue):D210-5. doi: 10.1093/nar/gkr1175. Epub 2011 Dec 1.
Facilitated by the rapid progress of high-throughput sequencing technology, a large number of long noncoding RNAs (lncRNAs) have been identified in mammalian transcriptomes over the past few years. LncRNAs have been shown to play key roles in various biological processes such as imprinting control, circuitry controlling pluripotency and differentiation, immune responses and chromosome dynamics. Notably, a growing number of lncRNAs have been implicated in disease etiology. With the increasing number of published lncRNA studies, the experimental data on lncRNAs (e.g. expression profiles, molecular features and biological functions) have accumulated rapidly. In order to enable a systematic compilation and integration of this information, we have updated the NONCODE database (http://www.noncode.org) to version 3.0 to include the first integrated collection of expression and functional lncRNA data obtained from re-annotated microarray studies in a single database. NONCODE has a user-friendly interface with a variety of search or browse options, a local Genome Browser for visualization and a BLAST server for sequence-alignment search. In addition, NONCODE provides a platform for the ongoing collation of ncRNAs reported in the literature. All data in NONCODE are open to users, and can be downloaded through the website or obtained through the SOAP API and DAS services.
在高通量测序技术的快速发展的推动下，过去几年中在哺乳动物转录组中已经鉴定出了大量的长非编码 RNA（lncRNA）。lncRNA 已被证明在各种生物学过程中发挥关键作用，如印记控制、多能性和分化的电路控制、免疫反应和染色体动力学。值得注意的是，越来越多的 lncRNA 被牵连到疾病的发病机制中。随着越来越多的 lncRNA 研究的发表，lncRNA 的实验数据（例如表达谱、分子特征和生物学功能）迅速积累。为了能够对这些信息进行系统地编纂和整合，我们将 NONCODE 数据库（http://www.noncode.org）更新到了 3.0 版本，以包含从重新注释的微阵列研究中获得的第一个综合表达和功能 lncRNA 数据集合。NONCODE 具有用户友好的界面，提供了多种搜索或浏览选项，本地基因组浏览器用于可视化，BLAST 服务器用于序列比对搜索。此外，NONCODE 为正在整理文献中报道的 ncRNA 提供了一个平台。NONCODE 中的所有数据都对用户开放，可以通过网站下载，也可以通过 SOAP API 和 DAS 服务获得。
