miRspongeR: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules

Background A 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. Results To 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. Conclusions This package enables researchers to quickly evaluate their new methods, apply existing methods to new datasets, and consequently speed up miRNA sponge research. * ### Abbreviations miRNA : microRNA MRE : miRNA response element ceRNA : Competing endogenous RNA lncRNA : Long non-coding RNA circRNA : Circular RNA miRHomology : miRNA Homology pc : positive correlation sppc : sensitivity partial pearson correlation SC : Sensitivity correlation MI : Mutual information CMI : Conditional mutual information ppc : partial pearson correlation DO : Disease ontology NCG : Network of Cancer Genes GO : Gene Ontology KEGG : Kyoto Encyclopedia of Genes and Genomes Pathway HR : Hazard Ratio BRCA : Breast invasive carcinoma FPKM : Fragments Per Kilobase Million TCGA : The Cancer Genome Atlas KNN : k -nearest neighbours