mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts.
mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts.
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DOI：
10.1038/nmeth.1247
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发表时间：
2008-09
期刊：
影响因子：
48
通讯作者：
Ambros, Victor
中科院分区：
文献类型：
--
作者：
Hammell, Molly;Long, Dang;Zhang, Liang;Lee, Andrew;Carmack, C. Steven;Han, Min;Ding, Ye;Ambros, Victor
动物microRNA的靶标预测受到可用于评估预测的microRNA：靶标相互作用的准确性的少量经验证的靶标的阻碍。最近，通过RNA诱导沉默复合物（RISC）组分AIN-1和AIN-2的免疫沉淀（IP）鉴定了3404个microRNA相关mRNA转录物的数据集。该数据集的分析揭示了功能性microRNA靶相互作用的定义特征的富集，包括靶序列的结构可及性、microRNA：靶杂交的总自由能以及与microRNA的5'种子区的碱基配对的拓扑结构。这些丰富的特征形成了定量microRNA靶标预测方法mirrandom（通过加权IP数据集参数的microRNA靶标）的基础，该方法优化了对验证的microRNA：靶标相互作用的灵敏度和对AIN-IP数据集的特异性。镜像方法可以捕获所有已知的保守的microRNA：mRNA靶关系在C。以低于目前标准方法的假阳性率。
Target prediction for animal microRNAs has been hindered by the small number of verified targets available for evaluating the accuracy of predicted microRNA:target interactions. Recently, a dataset of 3404 microRNA-associated mRNA transcripts was identified by immuno-precipitation (IP) of the RNA-induced silencing complex (RISC) components, AIN-1 and AIN-2. Analysis of this dataset reveals enrichment for defining characteristics of functional microRNA target interactions, including structural accessibility of target sequences, the total free energy of microRNA:target hybridization, and the topology of base-pairing to the 5’ seed region of the microRNA. These enriched characteristics form the basis for a quantitative microRNA target prediction method, mirWIP (microRNA targets by Weighting IP dataset parameters), that optimizes sensitivity to verified microRNA:target interactions and specificity to the AIN-IP dataset. The mirWIP method can capture all of the known conserved microRNA:mRNA target relationships in C. elegans at a lower false positive rate than the current standard methods.
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