Both genes and lncRNAs can be used as biomarkers of prostate cancer by using high throughput sequencing data

W.-S. Cheng, H. Tao, E.-P. Hu, S. Liu, H.-R. Cai, X.-L. Tao, L. Zhang, J.-J. Mao, D.-L. Yan

Department of Urology, Taizhou Municipal Hospital, Taizhou, Zhejiang, China. dongliangyan123@126.com

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• Oncology

OBJECTIVE: To investigate prostate cancer-related genes and lncRNAs by using a high throughput sequencing dataset.

MATERIALS AND METHODS: RNA-seq data were obtained from the sequencing read archive database, including both benign and malignant tumor samples. After aligning the RNA-seq reads to human genome reference, gene expression profile as well as lncRNA expression profile was obtained. Next, student’s t-test was used to screen both the differentially expressed genes (DEGs) and lncRNAs (DELs) between benign and malignant samples. Finally, goseq was used to conduct the functional annotation of DEGs.

RESULTS: A total of 7112 DEGs were screened, such as ZNF512B, UCKL1, STMN3, GMEB2, and PTK6. The top 10 enriched functions of DEGs were mainly related to organism development, including multi-cellular development, system development and anatomical structure development. Also, we discovered 26 differentially expressed lncRNAs.

CONCLUSIONS: The analysis used in this study is reliable in screening prostate cancer markers including both genes and lncRNAs by using RNA-seq data, which provides new insight into the understanding of molecular mechanism of prostate cancer.

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