Journal Article

Integrated analysis of co‐expression and ceRNA network identifies five lncRNAs as prognostic markers for breast cancer

Yao, Yan, Liu, Ruijuan, Sun, Changgang, Wei, Junyu, Zhou, Chao, Qi, Lingyu, Zhang, Tingting, Feng, Fubin

2019

Overview

Long non‐coding RNAs (lncRNAs), which competitively bind miRNAs to regulate target mRNA expression in the competing endogenous RNAs (ceRNAs) network, have attracted increasing attention in breast cancer research. We aim to find more effective therapeutic targets and prognostic markers for breast cancer. LncRNA, mRNA and miRNA expression profiles of breast cancer were downloaded from TCGA database. We screened the top 5000 lncRNAs, top 5000 mRNAs and all miRNAs to perform weighted gene co‐expression network analysis. The correlation between modules and clinical information of breast cancer was identified by Pearson's correlation coefficient. Based on the most relevant modules, we constructed a ceRNA network of breast cancer. Additionally, the standard Kaplan‐Meier univariate curve analysis was adopted to identify the prognosis of lncRNAs. Ultimately, a total of 23 and 5 modules were generated in the lncRNAs/mRNAs and miRNAs co‐expression network, respectively. According to the Green module of lncRNAs/mRNAs and Blue module of miRNAs, our constructed ceRNA network consisted of 52 lncRNAs, 17miRNAs and 79 mRNAs. Through survival analysis, 5 lncRNAs (AL117190.1, COL4A2‐AS1, LINC00184, MEG3 and MIR22HG) were identified as crucial prognostic factors for patients with breast cancer. Taken together, we have identified five novel lncRNAs related to prognosis of breast cancer. Our study has contributed to the deeper understanding of the molecular mechanism of breast cancer and provided novel insights into the use of breast cancer drugs and prognosis.

• Publisher: John Wiley & Sons, Inc,John Wiley and Sons Inc
• Subject: Bioinformatics / Biomarkers / Biomarkers, Tumor - genetics / Breast cancer / Cancer therapies / ceRNA network / Data analysis / DNA methylation / Drug development / Female / Gene expression / Gene Expression Profiling - methods / Gene Expression Regulation, Neoplastic / Gene Regulatory Networks / Genes / Humans / Hypotheses / Kaplan-Meier Estimate / Medical prognosis / MicroRNAs / MicroRNAs - genetics / miRNA / Original / overall survival / Prognosis / RNA, Long Noncoding - genetics / RNA, Messenger - genetics / Software / Studies / Survival analysis / The Cancer Genomes Atlas / Therapeutic applications / Tumors / weighted gene co‐expression network analysis