School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China.
BMC Bioinformatics. 2021 Feb 18;22(1):75. doi: 10.1186/s12859-021-04012-y.
The competing endogenous RNA (ceRNA) regulation is a newly discovered post-transcriptional regulation mechanism and plays significant roles in physiological and pathological progress. CeRNA networks provide global views to help understand the regulation of ceRNAs. CeRNA networks have been widely used to detect survival biomarkers, select candidate regulators of disease genes, and predict long noncoding RNA functions. However, there is no software platform to provide overall functions from the construction to analysis of ceRNA networks.
To fill this gap, we introduce CeNet Omnibus, an R/Shiny application, which provides a unified framework for the construction and analysis of ceRNA network. CeNet Omnibus enables users to select multiple measurements, such as Pearson correlation coefficient (PCC), mutual information (MI), and liquid association (LA), to identify ceRNA pairs and construct ceRNA networks. Furthermore, CeNet Omnibus provides a one-stop solution to analyze the topological properties of ceRNA networks, detect modules, and perform gene enrichment analysis and survival analysis. CeNet Omnibus intends to cover comprehensiveness, high efficiency, high expandability, and user customizability, and it also offers a web-based user-friendly interface to users to obtain the output intuitionally.
CeNet Omnibus is a comprehensive platform for the construction and analysis of ceRNA networks. It is highly customizable and outputs the results in intuitive and interactive. We expect that CeNet Omnibus will assist researchers to understand the property of ceRNA networks and associated biological phenomena. CeNet Omnibus is an R/Shiny application based on the Shiny framework developed by RStudio. The R package and detailed tutorial are available on our GitHub page with the URL https://github.com/GaoLabXDU/CeNetOmnibus .
竞争内源性 RNA（ceRNA）调控是一种新发现的转录后调控机制，在生理和病理过程中发挥着重要作用。ceRNA 网络提供了全局视角，有助于理解 ceRNAs 的调控。ceRNA 网络已广泛用于检测生存生物标志物、选择疾病基因的候选调节剂、预测长非编码 RNA 的功能。然而，目前尚无软件平台能够提供从 ceRNA 网络的构建到分析的全面功能。
为了填补这一空白，我们引入了 CeNet Omnibus，这是一个 R/Shiny 应用程序，为 ceRNA 网络的构建和分析提供了一个统一的框架。CeNet Omnibus 允许用户选择多种度量标准，如 Pearson 相关系数（PCC）、互信息（MI）和液体关联（LA），以识别 ceRNA 对并构建 ceRNA 网络。此外，CeNet Omnibus 还提供了一站式解决方案，用于分析 ceRNA 网络的拓扑性质、检测模块，并进行基因富集分析和生存分析。CeNet Omnibus 旨在涵盖全面性、高效性、高可扩展性和用户可定制性，并且还提供了基于网络的用户友好界面，使用户能够直观地获得输出。
CeNet Omnibus 是一个用于构建和分析 ceRNA 网络的综合性平台。它具有高度的可定制性，并以直观和交互的方式输出结果。我们希望 CeNet Omnibus 将帮助研究人员理解 ceRNA 网络的性质和相关的生物学现象。CeNet Omnibus 是一个基于 RStudio 的 Shiny 框架开发的 R/Shiny 应用程序。R 包和详细教程可在我们的 GitHub 页面上获得，网址为 https://github.com/GaoLabXDU/CeNetOmnibus 。
