In conclusion, differentially expressed TFs (e.g., HOXA2, HOXB2, HOXC10, and NKX2-1), genes that encode proteins located on the cell surface and in the ECM of DCIS (e.g., FREM2), and TFs of DEGs (e.g., E2F1 and CREB1), as well as high-frequency mutant genes (RWDD4, SDHC, SEPT7, and SFN), may participate in the progression of DCIS. This evidence concerns the gene HOXA2 and ductal breast carcinoma in situ.