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

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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13104-018-3126-y) contains supplementary material, which is available to authorized users.