LNCipedia: a database for annotated human lncRNA transcript sequences and structures.
LNCipedia: a database for annotated human lncRNA transcript sequences and structures.
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DOI：
10.1093/nar/gks915
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发表时间：
2013-01
影响因子：
14.9
通讯作者：
Mestdagh P
中科院分区：
文献类型：
--
作者：
Volders PJ;Helsens K;Wang X;Menten B;Martens L;Gevaert K;Vandesompele J;Mestdagh P
在这里，我们提出LNCipedia (http://www.lncipedia.org)，一个新的人类长链非编码RNA （lncRNA）转录物和基因数据库。LncRNAs构成了一个庞大而多样的非编码RNA基因类别。尽管一些lncrna已被功能注释，但大多数lncrna仍有待鉴定。不同的高通量方法来鉴定新的lncRNA（包括RNA测序和染色质状态图的注释）已经应用于各种研究，导致多个不相关的lncRNA数据集。LNCipedia提供来自不同来源的21488个带注释的人类lncRNA转录本。除了基本的转录本信息和基因结构外，数据库中的每个条目还确定了一些统计信息，如二级结构信息、蛋白质编码电位和microRNA结合位点。我们的分析表明，与microrna非常相似，许多lncrna具有重要的二级结构，这与它们与蛋白质或蛋白质复合物的假定关联一致。有关特定lncrna的可用文献被链接起来，用户或作者可以通过web界面提交文章。蛋白质编码电位的评估采用两种不同的预测算法：编码电位计算器和hmm。此外，我们还集成了一种新的策略，通过自动重新分析PRIDE数据库中大量公开可用的质谱数据来检测潜在的编码lncrna。LNCipedia是公开的，允许用户根据不同的搜索标准查询和下载lncRNA序列和结构。该数据库可作为启动小型和大规模lncRNA研究的资源。作为一个例子，LNCipedia的内容被用来开发一个定制的微阵列，用于分析所有可用的lncrna的表达。
Here, we present LNCipedia (http://www.lncipedia.org), a novel database for human long non-coding RNA (lncRNA) transcripts and genes. LncRNAs constitute a large and diverse class of non-coding RNA genes. Although several lncRNAs have been functionally annotated, the majority remains to be characterized. Different high-throughput methods to identify new lncRNAs (including RNA sequencing and annotation of chromatin-state maps) have been applied in various studies resulting in multiple unrelated lncRNA data sets. LNCipedia offers 21 488 annotated human lncRNA transcripts obtained from different sources. In addition to basic transcript information and gene structure, several statistics are determined for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites. Our analyses suggest that, much like microRNAs, many lncRNAs have a significant secondary structure, in-line with their presumed association with proteins or protein complexes. Available literature on specific lncRNAs is linked, and users or authors can submit articles through a web interface. Protein coding potential is assessed by two different prediction algorithms: Coding Potential Calculator and HMMER. In addition, a novel strategy has been integrated for detecting potentially coding lncRNAs by automatically re-analysing the large body of publicly available mass spectrometry data in the PRIDE database. LNCipedia is publicly available and allows users to query and download lncRNA sequences and structures based on different search criteria. The database may serve as a resource to initiate small- and large-scale lncRNA studies. As an example, the LNCipedia content was used to develop a custom microarray for expression profiling of all available lncRNAs.
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影响因子：
64.8
作者：
通讯作者：
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影响因子：
1.8
作者：
HOFACKER, IL;FONTANA, W;SCHUSTER, P
通讯作者：
SCHUSTER, P
影响因子：
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作者：
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通讯作者：
Rinn, John L.
影响因子：
46.9
作者：
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通讯作者：
Goodsaid, Federico M.
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3.4
作者：
Vaudel, Marc;Burkhart, Julia M.;Zahedi, Rene P.
通讯作者：
Zahedi, Rene P.