Bioinformatics Methods for Modeling microRNA Regulatory Networks in Cancer

MicroRNAs (miRNAs) play important roles in the physiology and development of cancers. The increase of multidimensional molecular profiles of tumor patients generated by high-throughput sequencing technologies has enabled computational analysis of miRNA regulatory networks in cancer. In this chapter, we first summarized currently widely used computational methods for identifying miRNA-gene interactions. In addition, crosstalk among miRNAs and competitive endogenous RNAs (ceRNAs) represent novel layers of gene regulation mediated by miRNAs, which also play important roles in cancer. We next reviewed computational methods for modeling miRNA-miRNA crosstalk and ceRNA-ceRNA interactions in cancer. These methods integrate multi-omics data and range from genomics to phenomics. MiRNA-miRNA networks are generally constructed based on genomic sequences, transcriptomes, miRNA-gene regulation, and functional pathways. Moreover, five types of computational methods for identifying ceRNA-ceRNA interactions are summarized in this chapter. Among these methods, two types of global ceRNA regulation and three types of context-specific methods are included. The application of these computational methods focused on miRNA regulation in cancer provides valuable functional insights into the underlying mechanism of cancer, as well as future precision medicine.