Of the numerous lncRNAs and novel transcripts up-regulated at the early neoplasia stage, the previously identified novel transcript (transcript 13741) whose transcription was specific to breast tissue and highly correlated with ER + breast cancers [11] was the highest ranking differentially up-regulated transcript in early neoplasias relative to normal within our sequencing dataset (paired SAMseq; Table S11 in Additional file 1; see Materials and methods). Here, ESR1 is linked to breast cancer.