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Protocol to infer and analyze miRNA sponge modules in heterogeneous data using miRSM 2.0
Junpeng Zhang1, Xuemei Wei1, Chunwen Zhao1
1School of Engineering, Dali University, Yunnan 671003, China.
STAR Protocols
|September 18, 2024
Summary
This study introduces miRSM 2.0, an R package for analyzing microRNA (miRNA) sponge modules. It helps researchers understand the role of miRNA sponges in various diseases using heterogeneous data.
Area of Science:
- Computational Biology
- Genomics
- Bioinformatics
Background:
- MicroRNA (miRNA) sponges play a role in physiological and pathological processes.
- These regulatory interactions often occur in modules or clusters.
- Understanding these complex interactions is crucial for disease research.
Purpose of the Study:
- To present a protocol for inferring and analyzing miRNA sponge modules.
- To introduce the R package miRSM 2.0 for this purpose.
- To facilitate the study of miRNA sponges in heterogeneous data.
Main Methods:
- Utilizing the R package miRSM 2.0.
- Identifying gene modules within datasets.
- Inferring miRNA sponge modules at both multi-sample and single-sample levels.
- Performing modular analysis on biological data.
Main Results:
- The protocol enables the identification of miRNA sponge modules.
- Analysis can be performed on heterogeneous data.
- miRSM 2.0 provides a framework for modular analysis of miRNA sponges.
Conclusions:
- miRSM 2.0 offers a computational approach to study miRNA sponge modules.
- This tool can advance the understanding of miRNA sponge roles in diseases.
- The protocol supports the analysis of complex biological data for disease insights.
