According to the topological analysis of the lncRNA–mRNA interaction network and our validated results, four pivotal nodes, including one lncRNA (NEAT1) and three mRNAs (PGAP1, FKBP5 and CDON), were identified, and they were previously reported to be associated with human tumors, such as non-small-cell lung cancer, prostate cancer, melanoma, and breast cancer [25–29]. Here, PGAP1 is linked to breast carcinoma.