miRSM: an R package to infer and analyse miRNA sponge modules in heterogeneous data
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(Published version)
Date
2021
Authors
Zhang, J.
Liu, L.
Xu, T.
Zhang, W.
Zhao, C.
Li, S.
Li, J.
Rao, N.
Le, T.D.
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Journal article
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RNA Biology, 2021; 18(12):2308-2320
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In molecular biology, microRNA (miRNA) sponges are RNA transcripts which compete with other RNA transcripts for binding with miRNAs. Research has shown that miRNA sponges have a fundamental impact on tissue development and disease progression. Generally, to achieve a specific biological function, miRNA sponges tend to form modules or communities in a biological system. Until now, however, there is still a lack of tools to aid researchers to infer and analyse miRNA sponge modules from heterogeneous data. To fill this gap, we develop an R/Bioconductor package, <i>miRSM</i>, for facilitating the procedure of inferring and analysing miRNA sponge modules. <i>miRSM</i> provides a collection of 50 co-expression analysis methods to identify gene co-expression modules (which are candidate miRNA sponge modules), four module discovery methods to infer miRNA sponge modules and seven modular analysis methods for investigating miRNA sponge modules. <i>miRSM</i> will enable researchers to quickly apply new datasets to infer and analyse miRNA sponge modules, and will consequently accelerate the research on miRNA sponges.
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Data source: , https://doi.org/10.1080/15476286.2021.1905341
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Copyright 2021 Informa UK Limited, trading as Taylor & Francis Group
Access Condition Notes: Accepted manuscript available after 1 July 2022