A GIST-specific circRNA-miRNA-mRNA regulatory network analysis demonstrated that the specific KIT-related regulatory networks involved the three circRNAs, the circRNA host genes and three miRNAs (miR-142-5p, miR-144-3p and miR-485-3p), which may be key regulators of GISTs that could serve as molecular biomarkers and potential therapeutic targets for this malignant disease.