Identification of hub genes and potential molecular mechanisms in gastric cancer by integrated bioinformatics analysis

PeerJ
Ling CaoPing Wang

Abstract

Gastric cancer (GC) is the fourth most common cause of cancer-related deaths in the world. In the current study, we aim to identify the hub genes and uncover the molecular mechanisms of GC. The expression profiles of the genes and the miRNAs were extracted from the Gene Expression Omnibus database. The identification of the differentially expressed genes (DEGs), including miRNAs, was performed by the GEO2R. Database for Annotation, Visualization and Integrated Discovery was used to perform GO and KEGG pathway enrichment analysis. The protein-protein interaction (PPI) network and miRNA-gene network were constructed using Cytoscape software. The hub genes were identified by the Molecular Complex Detection (MCODE) plugin, the CytoHubba plugin and miRNA-gene network. Then, the identified genes were verified by Kaplan-Meier plotter database and quantitative real-time PCR (qRT-PCR) in GC tissue samples. A total of three mRNA expression profiles (GSE13911, GSE79973 and GSE19826) were downloaded from the Gene Expression Omnibus (GEO) database, including 69, 20 and 27cases separately. A total of 120 overlapped upregulated genes and 246 downregulated genes were identified. The majority of the DEGs were enriched in extracellular matrix or...Continue Reading

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Citations

Jan 16, 2020·The Journal of International Medical Research·Wenfei LiZhanqiu Wang
Apr 27, 2020·Journal of Orthopaedic Surgery and Research·Hai-Ping ZhangFa-Rui Sun
Oct 30, 2020·Cancer Management and Research·Shengnan WangJianjun Dong
Dec 19, 2020·Journal of Oncology·Jun-Fu WangJun-Qiang Chen
Apr 20, 2021·ACS Biomaterials Science & Engineering·Yimin QiuJingjie Yeo
Jun 12, 2020·Journal of Ethnopharmacology·Bihan WuPintong Huang
Aug 29, 2021·Cell & Bioscience·Xiaoxia DongLi Shen
Aug 31, 2021·Frontiers in Oncology·Tabatha Gutierrez PrietoVera Luiza Capelozzi
Sep 4, 2021·Therapeutics and Clinical Risk Management·Ya-Fei QinHao Wang
Nov 13, 2021·Immunity, Inflammation and Disease·Junsong ZhuQunwei Qu

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Datasets Mentioned

BETA
GSE79973
GSE19826
GSE13911

Methods Mentioned

BETA
PCR

Software Mentioned

CytoHubba
MCODE
Search Tool for the Retrieval
Molecular Complex Detection ( MCODE )
GEO2R
miRTarBase
DAVID
R
Cytoscape
TargetScan

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