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. 2024 Sep 17;5(4):103317.
doi: 10.1016/j.xpro.2024.103317. Online ahead of print.

Protocol to infer and analyze miRNA sponge modules in heterogeneous data using miRSM 2.0

Junpeng Zhang  1 , Xuemei Wei  2 , Chunwen Zhao  2 , Haolin Yang  2
Affiliations

Protocol to infer and analyze miRNA sponge modules in heterogeneous data using miRSM 2.0

Junpeng Zhang et al. STAR Protoc. .

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.

Keywords: Bioinformatics; Cancer; Systems biology.

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

Figures

None
Graphical abstract
Figure 1
Figure 1
The number of miRNA sponge modules specific to each half K562 cell
Figure 2
Figure 2
Heatmap of the similarity between 19 half K562 cells in miRNA sponge modules
Figure 3
Figure 3
The number of statistically co-expressed miRNA sponge modules specific to each half K562 cell
Figure 4
Figure 4
The number of sharing miRNAs existing in all of miRNA sponge modules specific to each half K562 cell
Figure 5
Figure 5
The number of the predicted interactions specific to each half K562 cell (A) The number of the predicted miRNA-mRNA interactions. (B) The number of the predicted miRNA sponge interactions.
See this image and copyright information in PMC

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References

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