Oncotarget

Research Papers:

Transcriptome sequencing identified hub genes for hepatocellular carcinoma by weighted-gene co-expression analysis

Qi Pan, Xianli Long, Liting Song, Dachun Zhao, Xiaoyuan Li, Dewei Li, Min Li, Jinxue Zhou, Xia Tang, Hong Ren and Keyue Ding _

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Oncotarget. 2016; 7:38487-38499. https://doi.org/10.18632/oncotarget.9555

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Abstract

Qi Pan1, Xianli Long1, Liting Song1, Dachun Zhao2, Xiaoyuan Li3, Dewei Li4, Min Li5, Jinxue Zhou6, Xia Tang1, Hong Ren1, Keyue Ding1

1Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China

2Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China

3Department of Medical Oncology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China

4Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China

5Department of Hepatobiliary Surgery, Suining Central Hospital, Suining, Sichuan Province, P. R. China

6Department of Hepatobiliary Surgery, Henan Tumor Hospital, Zhenzhou, Henan Province, P.R. China

Correspondence to:

Keyue Ding, email: [email protected]

Keywords: hepatocellular carcinoma, transcriptome sequencing, weighted gene co-expression network, hub gene

Received: February 26, 2016     Accepted: May 05, 2016     Published: May 23, 2016

ABSTRACT

Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide, and it remains a challenge to understand the genetic mechanisms underlying hepatocarcinogenesis. A global gene network of differential expression profiles in HCC has yet to be fully characterized. In the present study, we performed transcriptome sequencing (mRNA and lncRNA) in liver cancer and cirrhotic tissues of nine HCC patients. We identified differentially expressed genes (DEGs) and constructed a weighted gene co-expression network for the DEGs. In total, 755 DEGs (747 mRNA and eight lncRNA) were identified, and several co-expression modules were significantly associated with HCC clinical traits, including tumor location, tumor grade, and the α-fetoprotein (AFP) level. Of note, we identified 15 hub genes in the module associated with AFP level, and three (SPX, AFP and ADGRE1) of four hub genes were validated in an independent HCC cohort (n=78). Identification of hub genes for HCC clinical traits has implications for further understanding of the molecular genetic basis of HCC.


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