miRsponge

miRsponge is a software tool for identifying miRNA sponge modules and interactions in breast cancer. It is an in silico method that utilizes module-level analysis to infer module-conserved and module-specific miRNA sponge interactions.

The significance of miRNA sponge acting as a decoy for sequestering miRNAs from their endogenous target mRNAs has been increasingly recognized as an important tool for long-term loss-of-function studies both in vivo and in silico. Although several in silico methods have been developed for studying miRNA sponge interactions or networks in cancer, the module-level properties of miRNA sponges in cancer remain largely unknown.

To address this issue, miRsponge has been proposed as an effective technique to generate hypotheses for in vivo methods for studying the biological functions and regulatory mechanisms of miRNA sponges in breast cancer. The software tool applies module-level analysis to infer both module-conserved and module-specific miRNA sponge interactions.

The software tool has been validated by applying it to the breast invasive carcinoma (BRCA) dataset provided by The Cancer Genome Altas (TCGA) and making functional validation of the computational results. The research concluded that most miRNA sponge interactions are module-conserved across two modules, while a minority of miRNA sponge interactions are module-specific, existing only in a single module. Through functional annotation and differential expression analysis, the researchers also found that the modules discovered using miRsponge are functional miRNA sponge modules associated with BRCA.

Moreover, the module-specific miRNA sponge interactions among miRNA sponge modules may be involved in the progression and development of BRCA. Experimental results show that miRsponge is comparable to the benchmark methods in recovering experimentally confirmed miRNA sponge interactions and that miRsponge outperforms the benchmark methods in identifying interactions related to breast cancer.