Zhang Jing, Storey Kenneth B
Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada.
Institute of Biochemistry, Departments of Biology and Chemistry, Carleton University, Ottawa, Canada.
PeerJ. 2018 Jan 12;6:e4262. doi: 10.7717/peerj.4262. eCollection 2018.
With the continuous discovery of microRNA's (miRNA) association with a wide range of biological and cellular processes, expression profile-based functional characterization of such post-transcriptional regulation is crucial for revealing its significance behind particular phenotypes. Profound advancement in bioinformatics has been made to enable in depth investigation of miRNA's role in regulating cellular and molecular events, resulting in a huge quantity of software packages covering different aspects of miRNA functional analysis. Therefore, an all-in-one software solution is in demand for a comprehensive yet highly efficient workflow. Here we present RBiomirGS, an R package for a miRNA gene set (GS) analysis.
The package utilizes multiple databases for target mRNA mapping, estimates miRNA effect on the target mRNAs through miRNA expression profile and conducts a logistic regression-based GS enrichment. Additionally, human ortholog Entrez ID conversion functionality is included for target mRNAs.
By incorporating all the core steps into one package, RBiomirGS eliminates the need for switching between different software packages. The modular structure of RBiomirGS enables various access points to the analysis, with which users can choose the most relevant functionalities for their workflow.
With RBiomirGS, users are able to assess the functional significance of the miRNA expression profile under the corresponding experimental condition by minimal input and intervention. Accordingly, RBiomirGS encompasses an all-in-one solution for miRNA GS analysis. RBiomirGS is available on GitHub (http://github.com/jzhangc/RBiomirGS). More information including instruction and examples can be found on website (http://kenstoreylab.com/?page_id=2865).
随着微小RNA（miRNA）与广泛的生物学和细胞过程之间关联的不断发现，基于表达谱对这种转录后调控进行功能表征对于揭示其在特定表型背后的意义至关重要。生物信息学已取得了重大进展，能够深入研究miRNA在调节细胞和分子事件中的作用，从而产生了大量涵盖miRNA功能分析不同方面的软件包。因此，需要一种一体化的软件解决方案来实现全面且高效的工作流程。在此，我们展示了RBiomirGS，一个用于miRNA基因集（GS）分析的R包。
该包利用多个数据库进行靶标mRNA映射，通过miRNA表达谱估计miRNA对靶标mRNA的影响，并进行基于逻辑回归的GS富集。此外，还包括针对靶标mRNA的人类直系同源Entrez ID转换功能。
通过将所有核心步骤整合到一个包中，RBiomirGS消除了在不同软件包之间切换的需求。RBiomirGS的模块化结构提供了各种分析接入点，用户可以据此为其工作流程选择最相关的功能。
借助RBiomirGS，用户能够通过最少的输入和干预来评估在相应实验条件下miRNA表达谱的功能意义。因此，RBiomirGS为miRNA GS分析提供了一体化解决方案。RBiomirGS可在GitHub（http://github.com/jzhangc/RBiomirGS）上获取。更多信息，包括使用说明和示例，可在网站（http://kenstoreylab.com/?page_id=2865）上找到。
