Network Properties for Ranking Predicted miRNA Targets in Breast Cancer

Leibniz-Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Beutenbergstrasse 11A, 07745 Jena, Germany.
Advances in Bioinformatics 01/2009; 2009(3-4):182689. DOI: 10.1155/2009/182689
Source: PubMed


MicroRNAs control the expression of their target genes by translational repression and transcriptional cleavage. They are involved in various biological processes including development and progression of cancer. To uncover the biological role of miRNAs it is important to identify their target genes. The small number of experimentally validated target genes makes computer prediction methods very important. However, state-of-the-art prediction tools result in a great number of putative targets with an unpredictable number of false positives. In this paper, we propose and evaluate two approaches for ranking the biological relevance of putative targets of miRNAs which are associated with breast cancer.

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    ABSTRACT: MicroRNAs (miRNAs) are small non-coding endogenous regulatory RNAs that fine-tune gene expression in a wide range of biological processes and diseases. miRNAs exert their function by targeting mRNAs to trigger their degradation or inhibit protein translation. The proteins encoded by the genes targeted by miRNAs may act as key components of cellular networks, thus the use of biological molecular network information for the purposes of elucidating the role of miRNAs in molecular disease mechanism is a key objective in systems biomedicine. The crosstalk layer between miRNA-target networks and functional protein is rich sources of information to explore the function of miRNAs at the system level. Characterizing the influence of miRNAs in the context of the target (protein interactors of the target) is in the early stages with potential to help better understand how miRNAs function within the cellular networks. In this article, the latest research on the cross-talk between miRNAs and protein networks, particularly physical protein interactions and gene regulatory networks is summarized. This article also covers recent research on understanding the biology of miRNAs at the system level and defines principles of miRNA regulation of protein and gene regulatory networks. The second part of the article highlights the promise of considering the protein context of the miRNA target when searching for functional miRNA-target interactions. Some of the applications of integrating protein networks with miRNA-targets that have clinical and functional utility are described. WIREs Syst Biol Med 2014, 6:189-199. doi: 10.1002/wsbm.1251 For further resources related to this article, please visit the WIREs website. Conflict of interest: The author is a genomic analyst at GenomeDx Biosciences, Vancouver, Canada.
    Wiley Interdisciplinary Reviews Systems Biology and Medicine 03/2014; 6(2):189-99. DOI:10.1002/wsbm.1251 · 3.21 Impact Factor