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Published on: April 14, 2010
Candidate genes in gastric cancer identified by constructing a weighted gene co-expression network
Jian Chen1,2, Xiuwen Wang1, Bing Hu2
1Department of Chemotherapy, Qilu Hospital, Shandong University, Jinan, Shandong, China.
Background:
Gastric cancer (GC) is one of the most common cancers with high mortality globally. However, the molecular mechanisms of GC are unclear, and the prognosis of GC is poor. Therefore, it is important to explore the underlying mechanisms and screen for novel prognostic markers and treatment targets.
Methods:
The genetic and clinical data of GC patients in The Cancer Genome Atlas (TCGA) was analyzed by weighted gene co-expression network analysis (WGCNA). Modules with clinical significance and preservation were distinguished, and gene ontology and pathway enrichment analysis were performed. Hub genes of these modules were validated in the TCGA dataset and another independent dataset from the Gene Expression Omnibus (GEO) database by t-test. Furthermore, the significance of these genes was confirmed via survival analysis.
Results:
We found a preserved module consisting of 506 genes was associated with clinical traits including pathologic T stage and histologic grade. PDGFRB, COL8A1, EFEMP2, FBN1, EMILIN1, FSTL1 and KIRREL were identified as candidate genes in the module. Their expression levels were correlated with pathologic T stage and histologic grade, also affected overall survival of GC patients.
Conclusion:
These candidate genes may be involved in proliferation and differentiation of GC cells. They may serve as novel prognostic markers and treatment targets. Moreover, most of them were first reported in GC and deserved further research.
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