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MicroRNAs are a family of small, non-coding RNAs that regulate gene expression in a sequence-specific manner. We propose a computational method to predict miRNA regulatory modules or groups of miRNAs and target genes that are believed to participate cooperatively in post-transcriptional gene regulation. We tested our method with the human genes and miRNAs, predicting 431 miRNA regulatory modules. The validations of predicted modules with the literature and Gene Ontology show that the genes in the modules appear to be closely related in specific biological processes, such as gene regulation involved in various cancers.