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Recognizing the modular organization of biological networks has greatly advanced our understanding of complex cellular systems. However, little is known about the modules that exist in miRNA-gene regulation systems, and even less is known about these modules’ role in specific biological processes and key regulation assemblies. Identifying functional miRNA-gene regulatory modules is a challenging task for several reasons. (i) One gene can be regulated by multiple miRNAs, and one miRNA can regulate a large number of genes. (ii) The miRNA–mRNA target relationships differ among tissues and conditions. (iii) Although miRNAs physically interact with mRNAs, ultimately miRNA regulation affects the quantities of proteins in cells rather than the quantities of mRNAs. (iv) The genomic data are generally noisy and incomplete.
(Zhang et al., 2011) A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. Bioinformatics.