mirPRo-a novel standalone program for differential expression and variation analysis of miRNAs.
mirPRo-a novel standalone program for differential expression and variation analysis of miRNAs.
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DOI：
10.1038/srep14617
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发表时间：
2015-10-05
影响因子：
4.6
通讯作者：
Liang C
中科院分区：
文献类型：
--
作者：
Shi J;Dong M;Li L;Liu L;Luz-Madrigal A;Tsonis PA;Del Rio-Tsonis K;Liang C
miRNAs参与许多重要的生物学过程，通过靶向mRNA，促进其降解或翻译抑制，从而调控基因表达。许多miRNA测序研究表明，miRNA变异，如isomiR和“臂转换”是生物学相关的。然而，现有的独立工具通常不能提供关于miRNA变异的全面、详细的信息。为了加深我们对miRNA变异性的理解，我们开发了一种新的独立工具“mirPRo”来量化已知的miRNA并预测新的miRNA。与目前使用最广泛的独立程序miRDeep 2相比，mirPRo提供了几个新功能，包括基于基因组注释的读段编目、可选的种子区域检查、miRNA家族表达定量、isomiR鉴定和分类以及“臂转换”检测。我们使用来自小鼠、人类和鸡的三个数据集进行的比较数据分析表明，通过避免序列读数的过度计数以及通过在衔接子修剪、映射和定量中实施不同的方法，mirPRo比miRDeep 2更准确。mirPRo是一个开源的独立程序（https：//sourceforge.net/projects/mirpro/）。
Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many miRNA sequencing studies reveal that miRNA variations such as isomiRs and “arm switching” are biologically relevant. However, existing standalone tools usually do not provide comprehensive, detailed information on miRNA variations. To deepen our understanding of miRNA variability, we developed a new standalone tool called “mirPRo” to quantify known miRNAs and predict novel miRNAs. Compared with the most widely used standalone program, miRDeep2, mirPRo offers several new functions including read cataloging based on genome annotation, optional seed region check, miRNA family expression quantification, isomiR identification and categorization, and “arm switching” detection. Our comparative data analyses using three datasets from mouse, human and chicken demonstrate that mirPRo is more accurate than miRDeep2 by avoiding over-counting of sequence reads and by implementing different approaches in adapter trimming, mapping and quantification. mirPRo is an open-source standalone program (https://sourceforge.net/projects/mirpro/).