Among them, 265 potential miRNA-mRNA regulatory modules show that tumor suppressor miRNAs antagonize the expression of major oncogenes upregulated in Exp-subpopulation-III cells, such as PIK3CA, MYC, EGFR, and KRAS and oncomiRs antagonize the expression of tumor suppressors upregulated in Exp-subpopulation-I cells, such as CDKN1C, HES7, CDKN2A, and NFKB1 (Figs. 7a and 6a; Additional file 3: Tables S17, S18). This evidence concerns the gene CDKN1C and neoplasm.