06 avril 19381938/04/06 (N1091)-1938/04/06.Appartient à l’ensemble documentaire : Aquit

J. Robinson (4763871)

W. Henderson (4763868)

BMC Research Notes

Abstract Objective We report a method using functional-molecular databases and network modelling to identify hypothetical mRNA–miRNA interaction networks regulating intestinal epithelial barrier function. The model forms a data-analysis component of our cell culture experiments, which produce RNA expression data from Nanostring Technologies nCounter® system. The epithelial tight-junction (TJ) and actin cytoskeleton interact as molecular components of the intestinal epithelial barrier. Upstream regulation of TJ-cytoskeleton interaction is effected by the Rac/Rock/Rho signaling pathway and other associated pathways which may be activated or suppressed by extracellular signaling from growth factors, hormones, and immune receptors. Pathway activations affect epithelial homeostasis, contributing to degradation of the epithelial barrier associated with osmotic dysregulation, inflammation, and tumor development. The complexity underlying miRNA–mRNA interaction networks represents a roadblock for prediction and validation of competing-endogenous RNA network function. Results We developed a network model to identify hypothetical co-regulatory motifs in a miRNA–mRNA interaction network related to epithelial function. A mRNA–miRNA interaction list was generated using KEGG and miRWalk2.0 databases. R-code was developed to quantify and visualize inherent network structures. We identified a sub-network with a high number of shared, targeting miRNAs, of genes associated with cellular proliferation and cancer, including c-MYC and Cyclin D

J. M. Robinson

W. A. Henderson

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Modelling the structure of a ceRNA-theoretical, bipartite microRNA–mRNA interaction network regulating intestinal epithelial cellular pathways using R programming

Additional file 3: Figure S1. High-resolution histograms showing gene and miRNA names associated with their respective target numbers. The reader may use this to identify genes with highest and lowest numbers of targeting miRNAs, and miRNAs targeting the most and least number of genes

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Additional file 2. R-code. An R-programming language script with functional code to perform all analyses described in this article

MOESM2 of Modelling the structure of a ceRNA-theoretical, bipartite microRNA–mRNA interaction network regulating intestinal epithelial cellular pathways using R programming

Additional file 1: Table S1. Citation data for miRWalk2.0-derived experimentally validated miRNA-mRNA interactions

MOESM1 of Modelling the structure of a ceRNA-theoretical, bipartite microRNA–mRNA interaction network regulating intestinal epithelial cellular pathways using R programming

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