lnCeDB: database of human long noncoding RNA acting as competing endogenous RNA.
lnCeDB: database of human long noncoding RNA acting as competing endogenous RNA.
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DOI：
10.1371/journal.pone.0098965
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Chakrabarti J
中科院分区：
文献类型：
--
作者：
Das S;Ghosal S;Sen R;Chakrabarti J
长链非编码RNA （lncRNA）通过干扰microRNA （miRNA）通路影响转录后调控，作为竞争内源性RNA （ceRNA）。这些lncRNAs具有miRNA响应元件（MRE），控制内源性miRNA可与其靶mrna结合，从而减少对这些mrna的抑制。ln Ce DB提供了一个人类lncrna的数据库（来自GENCODE 19版本），这些lncrna可能作为cerna。从TargetScan和StarBase分别收集了人类mirna的推定mRNA靶点和AGO剪切区域的靶点。人类mirna的lncRNA靶点（GENCODE 11以下）从miRCode数据库下载。其余GENCODE 19 lncrna上的miRNA靶标通过我们的算法预测，以寻找种子匹配的靶点。这些假设的miRNA-lncRNA相互作用被映射到lncrna内的Ago相互作用区域。为了找出lncRNA-mRNA对实际上是ceRNA的可能性，我们采取了两种方法。首先，ceRNA评分是根据配对间共享的MREs数与单个候选基因的MREs总数之比计算出来的。其次，每个ceRNA对的p值通过超几何测试确定，使用ceRNA对之间共享mirna的数量与与单个rna相互作用的mirna数量进行比较。通常，在被共同miRNA靶向的一对rna中，应该存在表达相关性，即一个ceRNA水平的升高会导致另一个ceRNA水平的升高。接近等摩尔浓度的竞争rna与更深刻的ceRNA效应有关。在lnCeDB中，人们不仅可以浏览具有共同靶向mirna的lncRNA-mRNA对，还可以比较这对对在22个人体组织中的表达，以估计这对对实际上是cerna的可能性。可用性：可从http://gyanxet-beta.com/lncedb/免费下载。
Long noncoding RNA (lncRNA) influences post-transcriptional regulation by interfering with the microRNA (miRNA) pathways, acting as competing endogenous RNA (ceRNA). These lncRNAs have miRNA responsive elements (MRE) in them, and control endogenous miRNAs available for binding with their target mRNAs, thus reducing the repression of these mRNAs. ln Ce DB provides a database of human lncRNAs (from GENCODE 19 version) that can potentially act as ceRNAs. The putative mRNA targets of human miRNAs and the targets mapped to AGO clipped regions are collected from TargetScan and StarBase respectively. The lncRNA targets of human miRNAs (up to GENCODE 11) are downloaded from miRCode database. miRNA targets on the rest of the GENCODE 19 lncRNAs are predicted by our algorithm for finding seed-matched target sites. These putative miRNA-lncRNA interactions are mapped to the Ago interacting regions within lncRNAs. To find out the likelihood of an lncRNA-mRNA pair for actually being ceRNA we take recourse to two methods. First, a ceRNA score is calculated from the ratio of the number of shared MREs between the pair with the total number of MREs of the individual candidate gene. Second, the P-value for each ceRNA pair is determined by hypergeometric test using the number of shared miRNAs between the ceRNA pair against the number of miRNAs interacting with the individual RNAs. Typically, in a pair of RNAs being targeted by common miRNA(s), there should be a correlation of expression so that the increase in level of one ceRNA results in the increased level of the other ceRNA. Near-equimolar concentration of the competing RNAs is associated with more profound ceRNA effect. In lnCeDB one can not only browse for lncRNA-mRNA pairs having common targeting miRNAs, but also compare the expression of the pair in 22 human tissues to estimate the chances of the pair for actually being ceRNAs. Availability: Downloadable freely from http://gyanxet-beta.com/lncedb/.
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