Integrative Approaches for microRNA Target Prediction: Combining Sequence Information and the Paired mRNA and miRNA Expression Profiles

Gene regulation is a key factor in gaining a full understanding of molecular biology. microRNA (miRNA), a novel class of non-coding RNA, has recently been found to be one crucial class of post-transactional regulators, and play important roles in cancer. One essential step to understand the regulatory effect of miRNAs is the reliable prediction of their target mRNAs. Typically, the predictions are solely based on the sequence information, which unavoidably have high false detection rates. Recently, some novel approaches are developed to predict miRNA targets by integrating the typical algorithm with the paired expression profiles of miRNA and mRNA. Here we review and discuss these integrative approaches and propose a new algorithm called HCTarget. Applying HCtarget to the expression data in multiple myeloma, we predict target genes for ten specific miRNAs. The experimental verification and a loss of function study validate our predictions. Therefore, the integrative approach is a reliable and effective way to predict miRNA targets, and could improve our comprehensive understanding of gene regulation.