Fig. 1

Two different sets of microarray and next-generation sequencing data were downloaded and analyzed for identifying differentially expressed mRNAs (DEGs), miRNAs (DE miRNAs), and lncRNAs (DE-lncRNAs) in CRC and normal tissues. Next, DEGs were imported to RRA to find the most significant DEGs across all datasets and obtain distinct lists as Group A and Group B. DEGs in the Group B were then used for WGCNA to determine key modules related to each stage of CRC, separately. By combining DEGs in the Group A and B, stage-specific DEGs were found and investigated for protein-protein interaction (PPI) network and functional enrichment analysis. Furthermore, by setting two different cut-off criteria and selecting common DEGs, conserved hub genes across all stages were also obtained. By using DE-miRNAs and DE-lncRNAs as well as conserved hub genes, mRNA-miRNA-lncRNA regulatory network was constructed to find potential therapeutic targets. Ultimately, a comprehensive downstream analysis was performed to identify potential prognostic and diagnostic biomarkers, through different approaches