Gene-level analysis revealed that the CIS, compared to the epithelial cells, expressed the known tumor marker genes [e.g., CXCL1, EFNA1, TM4SF1, ELF3, and keratin cytoskeletal genes (i.e., KRT19, KRT13, KRT18, and KRT8)], indicating their malignant characteristics15–17 (fold difference > 1, permuted Student’s t-test P < 0.0001, Fig. 2d). This evidence concerns the gene EFNA1 and neoplasm.