As a proof-of-principle study, we applied this integrative genomic strategy to breast cancer (BC), the most common cancer (besides skin cancer) and one of the leading causes of cancer-related death in women, to uncover the cryptic lncRNA-encoded proteins that may be functionally important and potentially clinically relevant in estrogen receptor α–positive (ER+) BC that accounts for more than two-thirds of all BC cases. Here, ESR1 is linked to skin neoplasm.