Long intergenic non-coding RNA expression signature in human breast cancer

Yanfeng Zhang, Erin K. Wagner, Xingyi Guo, Isaac May, Qiuyin Cai, Wei Zheng, Chunyan He, Jirong Long

Research output: Contribution to journalArticlepeer-review

25 Scopus citations


Breast cancer is a complex disease, characterized by gene deregulation. There is less systematic investigation of the capacity of long intergenic non-coding RNAs (lincRNAs) as biomarkers associated with breast cancer pathogenesis or several clinicopathological variables including receptor status and patient survival. We designed a two-stage study, including 1,000 breast tumor RNA-seq data from The Cancer Genome Atlas (TCGA) as the discovery stage, and RNA-seq data of matched tumor and adjacent normal tissue from 50 breast cancer patients as well as 23 normal breast tissue from healthy women as the replication stage. We identified 83 lincRNAs showing the significant expression changes in breast tumors with a false discovery rate (FDR) < 1% in the discovery dataset. Thirty-seven out of the 83 were validated in the replication dataset. Integrative genomic analyses suggested that the aberrant expression of these 37 lincRNAs was probably related with the expression alteration of several transcription factors (TFs). We observed a differential co-expression pattern between lincRNAs and their neighboring genes. We found that the expression levels of one lincRNA (RP5-1198O20 with Ensembl ID ENSG00000230615) were associated with breast cancer survival with P < 0.05. Our study identifies a set of aberrantly expressed lincRNAs in breast cancer.

Original languageEnglish
Article number37821
JournalScientific Reports
StatePublished - Nov 29 2016

ASJC Scopus subject areas

  • General


Dive into the research topics of 'Long intergenic non-coding RNA expression signature in human breast cancer'. Together they form a unique fingerprint.

Cite this