PT  - JOURNAL ARTICLE
AU  - Junpeng Zhang
AU  - Lin Liu
AU  - Taosheng Xu
AU  - Yong Xie
AU  - Chunwen Zhao
AU  - Jiuyong Li
AU  - Thuc Duy Le
TI  - miRspongeR: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules
AID  - 10.1101/507749
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 507749
4099  - http://biorxiv.org/content/early/2019/03/21/507749.short
4100  - http://biorxiv.org/content/early/2019/03/21/507749.full
AB  - 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.AbbreviationsmiRNAmicroRNAMREmiRNA response elementceRNACompeting endogenous RNAlncRNALong non-coding RNAcircRNACircular RNAmiRHomologymiRNA Homologypcpositive correlationsppcsensitivity partial pearson correlationSCSensitivity correlationMIMutual informationCMIConditional mutual informationppcpartial pearson correlationDODisease ontologyNCGNetwork of Cancer GenesGOGene OntologyKEGGKyoto Encyclopedia of Genes and Genomes PathwayHRHazard RatioBRCABreast invasive carcinomaFPKMFragments Per Kilobase MillionTCGAThe Cancer Genome AtlasKNNk-nearest neighbours