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07:35
Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data
Published on: December 1, 2023
947
CeNet Omnibus: an R/Shiny application to the construction and analysis of competing endogenous RNA network
Xiao Wen1, Lin Gao2, Tuo Song1
1School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China.
BMC Bioinformatics
|February 19, 2021
Summary
CeNet Omnibus is a new R/Shiny application for constructing and analyzing competing endogenous RNA (ceRNA) networks. This comprehensive platform offers user-friendly tools for exploring ceRNA regulation and its role in biological processes.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Competing endogenous RNA (ceRNA) regulation is a key post-transcriptional mechanism influencing physiological and pathological processes.
- ceRNA networks offer a global perspective on ceRNA regulation, aiding in biomarker discovery and gene function prediction.
- A lack of integrated software platforms for ceRNA network construction and analysis has limited research progress.
Purpose of the Study:
- To introduce CeNet Omnibus, a unified R/Shiny application for comprehensive ceRNA network construction and analysis.
- To provide researchers with a user-friendly, customizable platform for exploring ceRNA regulatory mechanisms.
Main Methods:
- Utilizes multiple measurements (PCC, MI, LA) for identifying ceRNA pairs and constructing networks.
- Integrates tools for topological analysis, module detection, gene enrichment, and survival analysis.
- Developed as an R/Shiny application with a web-based interface for intuitive use.
Main Results:
- CeNet Omnibus provides a unified framework for building and analyzing ceRNA networks.
- The platform supports various analysis methods, including topological, module, enrichment, and survival analyses.
- Offers a user-friendly, customizable, and efficient solution for ceRNA network research.
Conclusions:
- CeNet Omnibus is a comprehensive, customizable, and user-friendly platform for ceRNA network analysis.
- Facilitates a deeper understanding of ceRNA networks and their associated biological phenomena.
- An R package and tutorial are available on GitHub for accessibility.
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