Coexpression networks were created to identify the interactions among lncRNAs and the protein-coding genes involved in nanotubular topography-induced biological and molecular pathways. On the basis of Guttman et al18 (link)–20 (link), lncRNAs that participate in special biological pathways are regulated by critical transcription factors (TFs) of those pathways. In order to determine whether the lncRNAs could possess trans-regulating functions, we compared the mRNAs that are coexpressed with lncRNAs with particular TFs regulated mRNAs. To investigate the mutual regulatory relationships among miRNA, lncRNA, and mRNA, we performed miRNA–lncRNA–mRNA coexpression network analysis based on Pearson’s correlation coefficient. Coexpression relationships with more than three shared miRNAs at p<0.05 were selected to build the miRNA–lncRNA–mRNA interaction network. The networks were constructed using the hypergeometric cumulative distribution function in MATLAB 2012b (The MathWorks, Natick, USA). The graphs were generated in Cytoscape 3.01 (Agilent Technologies).