Time to infer miRNA sponge modules

Abstract Inferring competing endogenous RNA (ceRNA) or microRNA (miRNA) sponge modules is a challenging and meaningful task for revealing ceRNA regulation mechanism at the module level. Modules in this context refer to groups of miRNA sponges which have mutual competitions and act as functional units for achieving biological processes. The recent development of computational methods based on heterogeneous data provides a novel way to discern the competitive effects of miRNA sponges on human complex diseases. This article aims to provide a comprehensive perspective of miRNA sponge module discovery methods. We first review the publicly available databases of cancer‐related miRNA sponges, as the miRNA sponges involved in human cancers contribute to the discovery of cancer‐associated modules. Then we review the existing computational methods for inferring miRNA sponge modules. Furthermore, we conduct an assessment on the performance of the module discovery methods with the pan‐cancer dataset, and the comparison study indicates that it is useful to infer biologically meaningful miRNA sponge modules by directly mapping heterogeneous data to the competitive modules. Finally, we discuss the future directions and associated challenges in developing in silico methods to infer miRNA sponge modules. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule‐RNA Interactions Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs