Identification of significant gene and pathways involved in HBV-related hepatocellular carcinoma by bioinformatics analysis

PeerJ
Shucai XieYijun Yang

Abstract

Hepatocellular carcinoma (HCC) is a common malignant tumor affecting the digestive system and causes serious financial burden worldwide. Hepatitis B virus (HBV) is the main causative agent of HCC in China. The present study aimed to investigate the potential mechanisms underlying HBV-related HCC and to identify core biomarkers by integrated bioinformatics analyses. In the present study, HBV-related HCC GSE19665, GSE55092, GSE94660 and GSE121248 expression profiles were downloaded from the Gene Expression Omnibus database. These databases contain data for 299 samples, including 145 HBV-related HCC tissues and 154 non-cancerous tissues (from patients with chronic hepatitis B). The differentially expressed genes (DEGs) from each dataset were integrated and analyzed using the RobustRankAggreg (RRA) method and R software, and the integrated DEGs were identified. Subsequently, the gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed using the DAVID online tool, and the protein-protein interaction (PPI) network was constructed using STRING and visualized using Cytoscape software. Finally, hub genes were identified, and the cBioPortal online platform was used to ana...Continue Reading

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Citations

Jun 21, 2020·Cancers·Nguyen Minh Tuan, Chang Hoon Lee
Dec 4, 2020·Cancer Control : Journal of the Moffitt Cancer Center·Liping ZhuangZongguo Yang
Oct 30, 2020·Cancer Management and Research·Feng WangWei-Bing Zhou
Nov 14, 2020·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jie YangChen Wang

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Datasets Mentioned

BETA
GSE19665
GSE55092
GSE94660
GSE121248
GPL16791

Methods Mentioned

BETA
chips
chip

Software Mentioned

DAVID
R
RobustRankAggreg
Biological Networks Gene Oncology tool ( BiNGO )
BiNGO
limma R
cBioPortal
limma R package
Search Tool for the Retrieval of Interacting Genes ( STRING )
STRING

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