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Background: Accumulating evidence indicates long non-coding RNAs (lncRNAs) have shown promise as cancer biomarkers,and little lncRNAs and their function associated with breast cancer (BC) were discovered.Method: We re-annotated and filtered the lncRNA profile of 616 BC and 113 normal samples,applied DESeq2 to discover the differential expressed lncRNAs (DELs),and then provided a framework for discovering differential co-expressed lncRNA-lncRNAs (DCLLs).