Imputed microRNA regulation based on weighted ranked expression and putative microRNA targets (IMRE) is a method to predict microRNA regulation from genome-wide gene expression. A false discovery rate (FDR) for each microRNA is calculated using the expression of the microRNA putative targets to analyze the regulation between different conditions. FDR is calculated to identify the differences of gene expression. The dataset used in this research is the microarray gene expression of 596 patients with prostate cancer. This dataset includes three different phenotypes: PSA (Prostate-Specific Antigen recurrence), Systemic (Systemic Disease Progression) and NED (No Evidence of Disease). We used the IMRE and ANOVA methods to analyze the dataset and identified several microRNA candidates that can be used to predict PSA recurrence and systemic disease progression in prostate cancer patients.