Analysis of Hub Genes and Pathways Associated with Malignant Pleural Mesothelioma Based on GEO Data Mining

Journal of Chuxiong Normal University ›› 2023, Vol. 38 ›› Issue (3): 62-69.

• Bioscience • Previous Articles Next Articles

Analysis of Hub Genes and Pathways Associated with Malignant Pleural Mesothelioma Based on GEO Data Mining

WANG Xinmeng^1,2, LI Shufang^1,2, LI Bin^1,2, ZHOU Chongxi^1,2, YU Min^3,*, QIU Lu⁴

1. College of Basic Medical Sciences, Dali University, Dali, Yunnan Province 671000;
2. Key Laboratory of Clinical Biochemistry of Yunnan Province, Dali University, Dali, Yunnan Province 671000;
3. College of Life Sciences, Yunnan University, Kunming, Yunnan Province 650091;
4. Department of Chemistry and Life Sciences, Chuxiong Normal College, Chuxiong, Yunnan Province 675000

Received:2022-09-27 Online:2023-05-20 Published:2023-08-07

Abstract

Abstract: This paper aims at identifying the differentially expressed genes and pathways involved in malignant pleural mesothelioma (MPM) by bioinformatics analysis. The matrix data of GSE51024 dataset was downloaded from the GEO database, the limma package of R software was applied to screen the differentially expressed genes and the ggplot2 and pheatmap packages were used for visual display. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes were performed using DAVID online database. STRING database and Cytoscape software were used to construct protein interaction networks of differentially expressed genes and screen out hub genes involved in MPM. Hub genes were confirmed by Gene Expression Profiling Interactive Analysis (GEPIA), and the prognostic value of each hub gene was tested by the Kaplan-Meier analysis. 1259 differentially expressed genes were obtained, including 351 up-regulated genes and 908 down-regulated genes. GO analysis and KEGG pathway enrichment analysis showed that differentially expressed genes were significantly enriched in PI3K-Akt signaling pathway, IL-17 signaling pathway, ECM-receptor interaction, cell cycle, complement and coagulation cascades, protein digestion and absorption, leukocyte transendothelial migration, viral protein interaction with cytokine and cytokine receptor, cell adhesion molecules, etc. 10 pivotal genes related to MPM were identified by Cytoscape. The overall survival (OS) of MPM patients with high expression of these hub genes was significantly lower than that of patients with low expression, indicating that patients with high expression of these hub genes had a poor prognosis. The 10 hub genes are potential biomarkers of MPM.

Key words: GEO database, malignant pleural mesothelioma, bioinformatics, differentially expressed genes

CLC Number:

R734.3

WANG Xinmeng, LI Shufang, LI Bin, ZHOU Chongxi, YU Min, QIU Lu. Analysis of Hub Genes and Pathways Associated with Malignant Pleural Mesothelioma Based on GEO Data Mining[J]. Journal of Chuxiong Normal University, 2023, 38(3): 62-69.

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Analysis of Hub Genes and Pathways Associated with Malignant Pleural Mesothelioma Based on GEO Data Mining

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