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. 2012 Jan;40(Database issue):D210-5.
doi: 10.1093/nar/gkr1175. Epub 2011 Dec 1.

NONCODE v3.0: integrative annotation of long noncoding RNAs

Dechao Bu  1 , Kuntao Yu, Silong Sun, Chaoyong Xie, Geir Skogerbø, Ruoyu Miao, Hui Xiao, Qi Liao, Haitao Luo, Guoguang Zhao, Haitao Zhao, Zhiyong Liu, Changning Liu, Runsheng Chen, Yi Zhao
Affiliations

NONCODE v3.0: integrative annotation of long noncoding RNAs

Dechao Bu et al. Nucleic Acids Res. 2012 Jan.

Abstract

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.

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Figures

Figure 1.
Figure 1.
Overview of the NONCODE v3.0 Database. Raw data were mainly obtained from three types of sources: GenBank, specialized databases and literature. Sequences from different sources first go through redundancy elimination and are then included in the database. The ncRNAs in NONCODE can be accessed and analyzed by various tools and services, including a variety of search or browse options, a local Genome Browser for visualization, and a BLAST server for sequence-alignment search. ncRNA sequences can be download directly from the website or accessed through the SOAP API or DAS servers. In addition, an on-line submission system is provided for continuous collection of new ncRNAs.
Figure 2.
Figure 2.
Length distribution of human and mouse lncRNAs.
Figure 3.
Figure 3.
Distribution of the lncRNAs on organisms.
See this image and copyright information in PMC

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