Screening and Identification of Potential Biomarkers in Hepatitis B Virus-Related Hepatocellular Carcinoma by Bioinformatics Analysis

Frontiers in Genetics
Xian-Chang ZengXu Lin

Abstract

Hepatocellular carcinoma (HCC) is one of the most lethal cancers globally. Hepatitis B virus (HBV) infection might cause chronic hepatitis and cirrhosis, leading to HCC. To screen prognostic genes and therapeutic targets for HCC by bioinformatics analysis and determine the mechanisms underlying HBV-related HCC, three high-throughput RNA-seq based raw datasets, namely GSE25599, GSE77509, and GSE94660, were obtained from the Gene Expression Omnibus database, and one RNA-seq raw dataset was acquired from The Cancer Genome Atlas (TCGA). Overall, 103 genes were up-regulated and 127 were down-regulated. A protein-protein interaction (PPI) network was established using Cytoscape software, and 12 pivotal genes were selected as hub genes. The 230 differentially expressed genes and 12 hub genes were subjected to functional and pathway enrichment analyses, and the results suggested that cell cycle, nuclear division, mitotic nuclear division, oocyte meiosis, retinol metabolism, and p53 signaling-related pathways play important roles in HBV-related HCC progression. Further, among the 12 hub genes, kinesin family member 11 (KIF11), TPX2 microtubule nucleation factor (TPX2), kinesin family member 20A (KIF20A), and cyclin B2 (CCNB2) were ident...Continue Reading

References

Dec 31, 2002·Toxicology·Xin W WangCurtis C Harris
Jan 15, 2003·BMC Bioinformatics·Gary D Bader, Christopher W V Hogue
Feb 12, 2004·Bioinformatics·M J L de HoonS Miyano
Apr 8, 2004·Neoplasia : an International Journal for Oncology Research·Daniel R RhodesArul M Chinnaiyan
Nov 14, 2006·Nucleic Acids Research·Tanya BarrettRon Edgar
Mar 30, 2007·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Elisa WurmbachJosep M Llovet
Jun 16, 2007·Gastroenterology·Hashem B El-Serag, K Lenhard Rudolph
Oct 22, 2008·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Tatsuya OrimoTadashi Kondo
Jan 15, 2009·International Journal of Cancer. Journal International Du Cancer·Norihisa UemuraTadashi Kondo
Aug 26, 2010·Journal of Thoracic Oncology : Official Publication of the International Association for the Study of Lung Cancer·Jayawant N Mandrekar
Dec 9, 2010·The Oncologist·Alan P VenookLaura Ladrón de Guevara
Nov 8, 2011·The American Journal of Pathology·Isabelle GasnereauJoëlle Sobczak-Thépot
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
Jan 16, 2014·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Jia-Hao JiangJian Zhou
Dec 19, 2014·BMC Systems Biology·Chia-Hao ChinChung-Yen Lin
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
Dec 26, 2015·Nucleic Acids Research·Antonio ColapricoHoutan Noushmehr
Apr 17, 2016·Journal of Hepatology·Massimo Levrero, Jessica Zucman-Rossi
Jan 18, 2017·Hepatology International·Ming WangQin Ning
Mar 30, 2017·International Journal of Molecular Sciences·Yongchen GuoWancai Yang
Sep 1, 2017·Molecular Cancer·Galina KhemlinaRazelle Kurzrock
Sep 14, 2017·Journal of Cancer Research and Therapeutics·Jianliang ChenGuoqiang Li
Jan 13, 2018·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Shan-Ying WuHsiao-Sheng Liu
May 20, 2018·Cancer Research·Liang-Zhi WenWei-Fen Xie
Dec 7, 2018·Journal of Cellular Biochemistry·Dongyang TangCheng Wang
May 28, 2019·Journal of Cellular Physiology·Qiang MaXiaolan Guo

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Datasets Mentioned

BETA
GSE25599
GSE94660
GSE77509
GPL9052
GSE69715
GLP570

Methods Mentioned

BETA
RNA-seq
RNA
-seq

Software Mentioned

Perl
TCGAbiolinks R package
pheatmap
limma R
corrplot
edgeR R package
edgeR R
Molecular Complex Detection
gglpot2
Cytoscape

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