Article

Inferring functional miRNA-mRNA regulatory modules in epithelial-mesenchymal transition with a probabilistic topic model

Kunming University of Science and Technology, Kunming, China.
Computers in Biology and Medicine (Impact Factor: 1.24). 01/2012; 42(4):428-37. DOI: 10.1016/j.compbiomed.2011.12.011
Source: PubMed

ABSTRACT

MicroRNAs (miRNAs) play important roles in gene regulatory networks. In this paper, we propose a probabilistic topic model to infer regulatory networks of miRNAs and their target mRNAs for specific biological conditions at the post-transcriptional level, so-called functional miRNA-mRNA regulatory modules (FMRMs). The probabilistic model used in this paper can effectively capture the relationship between miRNAs and mRNAs in specific cellular conditions. Furthermore, the proposed method identifies negatively and positively correlated miRNA-mRNA pairs which are associated with epithelial, mesenchymal, and other condition in EMT (epithelial-mesenchymal transition) data set, respectively. Results on EMT data sets show that the inferred FMRMs can potentially construct the biological chain of 'miRNA→mRNA→condition' at the post-transcriptional level.

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Available from: Junpeng Zhang, Jul 25, 2014
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    • "The discovery of MRMs has demonstrated that using both sequence information and expression profiles can produce more accurate predictions. Attempts have also been made to infer functional miRNA–mRNA regulatory modules (FMRMs), which are regulatory networks of miRNAs and mRNAs for specific biological conditions [19] [20] [21] [22] [23] [24] [25] [26]. The identified FMRMs give insights into biological processes, functional regulatory interactions of many diseases and gene target therapy. "
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