Overall, XIST down-regulation may suggest the malignant transformation for female GIST patients, while down-regulation of HYMAI, NEAT1 and FTX, or up-regulation of LRRC75A-AS1 may suggest the malignant transformation for both female and male patient, which may be the promising biomarkers irrespective of small intestinal or gastric origin. The gene discussed is FTX; the disease is gastrointestinal stromal tumor.