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

• Published in: BMC bioinformatics Vol. 20; no. 1; p. 235
• Main Authors: Zhang, Junpeng, Liu, Lin, Xu, Taosheng, Xie, Yong, Zhao, Chunwen, Li, Jiuyong, Le, Thuc Duy
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 10.05.2019; BioMed Central; BMC
• Subjects: Acids; Algorithms; Analysis; Binding proteins; Binding sites; Bioinformatics; Breast cancer; Carcinoma; Cell cycle; ceRNA; Computational biology; Datasets; Design of experiments; Experimental design; Gene expression; Gene Regulatory Networks - genetics; Genomes; Human breast invasive carcinoma; Humans; Hypotheses; Identification; Identification and classification; Messenger RNA; Methods; MicroRNA; MicroRNAs; MicroRNAs - genetics; miRNA; miRNA sponge; miRNA sponge interaction networks; miRNA sponge modules; Modules; Physiological aspects; Pipelines; Regulatory sequences; Ribonucleic acid; RNA; Software; Studies; Survival analysis; Transcription (Genetics); China; miRNA sponge modules; Human breast invasive carcinoma; ceRNA; miRNA sponge; miRNA; miRNA sponge interaction networks
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-019-2861-y

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. 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. This package enables researchers to quickly evaluate their new methods, apply existing methods to new datasets, and consequently speed up miRNA sponge research.