基于GEO数据挖掘分析恶性胸膜间皮瘤相关枢纽基因及其通路

楚雄师范学院学报 ›› 2023, Vol. 38 ›› Issue (3): 62-69.

基于GEO数据挖掘分析恶性胸膜间皮瘤相关枢纽基因及其通路

王心萌^1,2, 李淑芳^1,2, 李彬^1,2, 周崇熙^1,2, 余敏³, 邱璐^4,*

1.大理大学基础医学院,云南大理 671000;
2.云南省高校临床生物化学检验重点实验室,云南大理 671000;
3.云南大学生命科学学院,云南昆明 650091;
4.楚雄师范学院资源与环境科学院,云南楚雄 675000

收稿日期:2022-09-27 出版日期:2023-05-20 发布日期:2023-08-07
通讯作者: * 邱璐（1964–）,女,教授,硕士生导师,研究方向为分子与分子光谱。E-mail：qiulu@163.com
作者简介:王心萌（2000–）,女,硕士研究生,研究方向为病理学与病理生理学。E-mail：1363215344@qq.com,Tel： 17863916323
基金资助:
国家自然科学基金（No. 82160516,No. 11864002）; 云南省应用基础研究面上项目（No. 202101AT070006）; 云南省教育厅科研基金（No. 2022Y808）; 云南省大学生创新创业计划项目（No. 202110679042）

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

摘要/Abstract

摘要： 基于GEO数据挖掘分析恶性胸膜间皮瘤（MPM）相关枢纽基因及其信号通路。从GEO数据库下载GSE51024数据集矩阵数据,应用R软件limma包筛选差异表达基因（DEGs）,应用ggplot 2和pheatmap包对差异基因进行可视化展示,应用 DAVID 在线数据库对DEGs进行GO分析和 KEGG通路分析,运用STRING和Cytoscape软件构建DEGs的蛋白质-蛋白质相互作用网络并筛选出枢纽基因。通过 GEPIA 数据库对枢纽基因的表达进行验证,Kaplan-Meier 法分析各枢纽基因的预后价值。获得了1259个DEGs,包括351个上调基因及908个下调基因。GO分析和KEGG 通路富集分析表明,DEGs主要参与PI3K-Akt信号通路、IL-17信号通路、补体系统、细胞外基质受体相互作用、细胞周期、蛋白质消化和吸收、白细胞跨内皮迁移以及病毒蛋白与细胞因子和细胞因子受体的相互作用、细胞黏附分子。利用Cytoscape筛选出与MPM相关的10个枢纽基因,分别是KIF20A、DLGAP5、NCAPG、CCNB1、KIF23、KIF11、BUB1B、MAD2L1、CCNB2、TTK。枢纽基因高表达的MPM患者OS均显著低于低表达的患者,表明这些基因的高表达患者预后不良。本研究获得的10个枢纽基因可能是MPM潜在的诊断和预后标志物。

关键词: GEO数据库, 恶性胸膜间皮瘤, 生物信息学, 差异表达基因

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

中图分类号:

R734.3

王心萌, 李淑芳, 李彬, 周崇熙, 余敏, 邱璐. 基于GEO数据挖掘分析恶性胸膜间皮瘤相关枢纽基因及其通路[J]. 楚雄师范学院学报, 2023, 38(3): 62-69.

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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