CHUK and Hirschsprung disease: This study identified a potential TF–miRNA–mRNA network, including the key regulons of two TFs (TP53 and TWIST1), four miRNAs (has-miR-107, has-miR-10b-5p, has-miR-659-3p, and has-miR-371a-5p), and four mRNAs (PIM3, CHUK, F2RL1, and CA1), that can help enrich the connotation of HSCR pathogenesis and diagnosis and provide new horizons for treatment.