School of Engineering, Dali University, Dali, 671003, Yunnan, China.
School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia.
BMC Bioinformatics. 2019 May 10;20(1):235. doi: 10.1186/s12859-019-2861-y.
A microRNA (miRNA) sponge is an RNA molecule with multiple tandem miRNA response elements that can sequester miRNAs from their target mRNAs. Despite growing appreciation of the importance of miRNA sponges, our knowledge of their complex functions remains limited. Moreover, there is still a lack of miRNA sponge research tools that help researchers to quickly compare their proposed methods with other methods, apply existing methods to new datasets, or select appropriate methods for assisting in subsequent experimental design.
To fill the gap, we present an R/Bioconductor package, miRspongeR, for simplifying the procedure of identifying and analyzing miRNA sponge interaction networks and modules. It provides seven popular methods and an integrative method to identify miRNA sponge interactions. Moreover, it supports the validation of miRNA sponge interactions and the identification of miRNA sponge modules, as well as functional enrichment and survival analysis of miRNA sponge modules.
This package enables researchers to quickly evaluate their new methods, apply existing methods to new datasets, and consequently speed up miRNA sponge research.
微小 RNA（miRNA）海绵是一种具有多个串联 miRNA 反应元件的 RNA 分子，可将 miRNA 从其靶 mRNA 中隔离出来。尽管人们越来越重视 miRNA 海绵的重要性，但我们对其复杂功能的了解仍然有限。此外，仍然缺乏 miRNA 海绵研究工具，这些工具可以帮助研究人员快速比较他们提出的方法与其他方法，将现有方法应用于新数据集，或选择适当的方法来协助后续的实验设计。
为了填补这一空白，我们提出了一个 R/Bioconductor 包 miRspongeR，用于简化识别和分析 miRNA 海绵相互作用网络和模块的过程。它提供了七种流行的方法和一种综合方法来识别 miRNA 海绵相互作用。此外，它还支持 miRNA 海绵相互作用的验证以及 miRNA 海绵模块的识别，以及 miRNA 海绵模块的功能富集和生存分析。
该软件包使研究人员能够快速评估他们的新方法，将现有方法应用于新数据集，从而加速 miRNA 海绵的研究。
