[miRNA-mRNA相互作用预测程序的效率]

[Efficiency of the miRNA- mRNA Interaction Prediction Programs].

作者信息

Plotnikova O M, Skoblov M Y

机构信息

Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow oblast, 141700 Russia.

Research Centre for Medical Genetics, Moscow, 115478 Russia.

出版信息

Mol Biol (Mosk). 2018 May-Jun;52(3):543-554. doi: 10.7868/S0026898418030187.

DOI:10.7868/S0026898418030187

PMID:29989587

Abstract

miRNAs play a key role in regulation of gene expression. Nowadays it is known more than 2500 human miRNAs, while a majority of miRNA-mRNA interactions remains unidentified. The recent development of a high-throughput CLASH (crosslinking, ligation and sequencing of hybrids) technique for discerning miRNA-mRNA interactions allowed an experimental analysis of the human miRNA-mRNA interactome. Therefore, it allowed us, for the first time, make an experimental analysis of the human miRNA-mRNA interactome as a whole and an evaluation of the quality of most commonly used miRNA prediction tools (TargetScan, PicTar, PITA, RNA22 and miRanda). To estimate efficiency of the miRNA-mRNA prediction tools, we used next parameters: sensitivity, positive predicted value, predictions in different mRNA regions (3' UTR, CDS, 5' UTR), predictions for different types of interactions (5 classes), predictions of "canonical" and "nocanonical" interactions, similarity with the random generated data. The analysis revealed low efficiency of all prediction programs in comparison with the CLASH data in terms of the all examined parameters.

摘要

微小RNA（miRNAs）在基因表达调控中发挥关键作用。如今已发现超过2500种人类微小RNA，然而大多数微小RNA与信使核糖核酸（mRNA）的相互作用仍未明确。用于识别微小RNA与mRNA相互作用的高通量交联、连接和杂交测序（CLASH）技术的最新发展，使得对人类微小RNA与mRNA相互作用组进行实验分析成为可能。因此，它使我们首次能够对人类微小RNA与mRNA相互作用组进行整体实验分析，并评估最常用的微小RNA预测工具（TargetScan、PicTar、PITA、RNA22和miRanda）的质量。为了评估微小RNA与mRNA预测工具的效率，我们使用了以下参数：敏感性、阳性预测值、在不同mRNA区域（3'非翻译区、编码区、5'非翻译区）的预测、对不同类型相互作用（5类）的预测、“典型”和“非典型”相互作用的预测、与随机生成数据的相似性。分析表明，就所有检查的参数而言，与CLASH数据相比，所有预测程序的效率都很低。