ArticleBMC bioinformatics2019
miRspongeR: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- UCA1 lncRNA regulates γ-globin expression by modulating the miR-148b/BCL11A axis.Life science alliance · 2026Article
- Review
- Modeling ncRNA Synergistic Regulation in Cancer.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Modelling cell type-specific lncRNA regulatory network in autism with Cycle.BMC bioinformatics · 2024Article
- spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.Bioinformatics (Oxford, England) · 2023Article
- Noncoding RNAs in Vascular Cell Biology and Restenosis.Biology · 2022Review
- Comparisons of the immunological landscape of COVID-19 patients based on sex and disease severity by multi-omics analysis.Chemico-biological interactions · 2022Article
- miRspongeR 2.0: an enhanced R package for exploring miRNA sponge regulation.Bioinformatics advances · 2022Article
- Prognostic Roles of ceRNA Network-Based Signatures in Gastrointestinal Cancers.Frontiers in oncology · 2022Review
- ceRNAshiny: An Interactive R/Shiny App for Identification and Analysis of ceRNA Regulation.Frontiers in molecular biosciences · 2022Article
- Prognostic Implications and Immune Infiltration Characteristics of Chromosomal Instability-Related Dysregulated CeRNA in Lung Adenocarcinoma.Frontiers in molecular biosciences · 2022Article
- Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data.BMC bioinformatics · 2021Article
- miRSM: an R package to infer and analyse miRNA sponge modules in heterogeneous data.RNA biology · 2021Article
- miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale.Nucleic acids research · 2021Article
- MicroRNA as a Potential Biomarker and Treatment Strategy for Ischemia-Reperfusion Injury.International journal of genomics · 2021Review
- ceRNAs in Cancer: Mechanism and Functions in a Comprehensive Regulatory Network.Journal of oncology · 2021Review
- Illuminating lncRNA Function Through Target Prediction.Methods in molecular biology (Clifton, N.J.) · 2021Article
- An Overview of the Computational Models Dealing with the Regulatory ceRNA Mechanism and ceRNA Deregulation in Cancer.Methods in molecular biology (Clifton, N.J.) · 2021Review
- The Role of MicroRNAs in Acute Respiratory Distress Syndrome and Sepsis, From Targets to Therapies: A Narrative Review.Anesthesia and analgesia · 2020Review
- Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundA microRNA (miRNA) sponge is an RNA molecule with multiple tandem miRNA response elements that can sequester miRNAs from their target mRNAs. Despite growing appreciation of the importance of miRNA sponges, our knowledge of their complex functions remains limited. Moreover, there is still a lack of miRNA sponge research tools that help researchers to quickly compare their proposed methods with other methods, apply existing methods to new datasets, or select appropriate methods for assisting in subsequent experimental design.
resultsTo fill the gap, we present an R/Bioconductor package, miRspongeR, for simplifying the procedure of identifying and analyzing miRNA sponge interaction networks and modules. It provides seven popular methods and an integrative method to identify miRNA sponge interactions. Moreover, it supports the validation of miRNA sponge interactions and the identification of miRNA sponge modules, as well as functional enrichment and survival analysis of miRNA sponge modules.
conclusionsThis package enables researchers to quickly evaluate their new methods, apply existing methods to new datasets, and consequently speed up miRNA sponge research.
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Registered trials
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