Protocol to infer and analyze miRNA sponge modules in heterogeneous data using miRSM 2.0
Year: 2024
Type: article
Abstract: MicroRNA (miRNA) sponges synergistically modulate physiological and pathological processes in the form of modules or clusters. Here, we present a protocol for inferring and analyzing miRNA sponge modules in heterogeneous data using the R package miRSM 2.0. We describe steps for identifying gene modules, inferring miRNA sponge modules at multi-sample and single-sample levels, and performing modular analysis. From the perspective of computational biology, miRSM 2.0 has the potential to advance our understanding of the role of miRNA sponges in diseases. For complete details on the use and execution of this protocol, please refer to Zhang et al. 1 , 2 , 3 • Instructions for identifying gene modules from single or paired gene expression data • Steps for predicting miRNA sponge modules between the same or different RNA types • Procedures for inferring miRNA sponge modules at single sample resolution • Guidance on performing five types of modular analysis to explore miRNA sponge modules Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. MicroRNA (miRNA) sponges synergistically modulate physiological and pathological processes in the form of modules or clusters. Here, we present a protocol for inferring and analyzing miRNA sponge modules in heterogeneous data using the R package miRSM 2.0. We describe steps for identifying gene modules, inferring miRNA sponge modules at multi-sample and single-sample levels, and performing modular analysis. From the perspective of computational biology, miRSM 2.0 has the potential to advance our understanding of the role of miRNA sponges in diseases.
Source: STAR Protocols
Institution: Dali University
Language: English
Subfield: Cancer Research
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $1,500
OpenAlex ID: W4402564264