Screening of differentially expressed genes in gastric cancer based on GEO database and function and pathway enrichment analysis
10.12122/j.issn.1673-4254.2024.03.23
- VernacularTitle:基于GEO数据库筛选胃癌差异表达基因及其功能和通路富集分析
- Author:
Yihao LIANG
1
;
Yingjun LAI
;
Yanwen YUAN
;
Wei YUAN
;
Xibo ZHANG
;
Bashan ZHANG
;
Zhifeng LU
Author Information
1. 南方医科大学第十附属医院(东莞市人民医院),检验科,广东 东莞 523059
- Keywords:
gastric cancer;
microarray;
bioinformatics analysis;
differentially expressed genes;
molecular markers
- From:
Journal of Southern Medical University
2024;44(3):605-616
- CountryChina
- Language:Chinese
-
Abstract:
Objective To explore the core genes related to the diagnosis and prognosis of gastric cancer(GC)based on Gene Expression Omnibus(GEO)database and screen the molecular targets involved in the occurrence and development of GC.Methods GC microarray data GSE118916,GSE54129 and GSE79973 were downloaded from GEO database,and the differentially expressed genes(DEGs)were screened.Enrichment analysis of the signaling pathways and molecular functions were preformed and protein-protein interaction networks(PPI)were constructed to identify the hub genes,whose expression levels and diagnostic and prognostic values were verifies based on gastric adenocarcinoma data from TCGA.The expression levels of these core genes were also detected in different GC cell lines using qRT-PCR.Results Seventy-seven DEGs were identified,which encodes proteins located mainly in the extracellular matrix and basement membrane with activities of oxidoreductase and extracellular matrix receptor and ligand,involving the biological processes of digestion and hormone metabolism and the signaling pathways in retinol metabolism and gastric acid secretion.Nine hub genes were obtained,among which SPARC,TIMP1,THBS2,COL6A3 and THY1 were significantly up-regulated and TFF1,GKN1,TFF2 and PGC were significantly down-regulated in GC.The abnormal expressions of SPARC,TIMP1,THBS2,COL6A3,TFF2 and THY1 were significantly correlated with the survival time of GC patients.ROC curve analysis showed that aberrant expression of TIMP1,SPARC,THY1 and THBS2 had high diagnostic value for GC.High expressions of SPARC,TIMP1,THBS2 and COL6A3 were detected in GC tissues.In the GC cell lines,qRT-PCR revealed different expression patterns of these hub genes,but their expressions were largely consistent with those found in bioinformatics analyses.Conclusion SPARC,TIMP1,THBS2 and other DEGs are probably involved in GC occurrence and progression and may serve as potential candidate molecular markers for early diagnosis and prognostic evaluation of GC.
