Identification of genes associated with gastric cancer prognosis from TCGA datasets
- VernacularTitle:基于癌基因组图谱挖掘胃癌预后相关基因
- Author:
Xiaoyi ZHANG
;
Xiaoyue WANG
- Keywords:
the cancer genome atlas;
somatic mutation;
gene expression;
prognosis
- From:
Basic & Clinical Medicine
2017;37(7):1042-1046
- CountryChina
- Language:Chinese
-
Abstract:
Objective To identify genes associated with prognosis or differentiated type in gastric cancer from fre quently mutated genes or highly-expressed genes,using large-scale genomic data from The Cancer Genome Atlas.Methods The somatic mutation data,RNAseqV2 data and clinical information were downloaded from the TCGA website.The frequency of deleterious somatic mutations for each gene was counted to select the frequently mutated genes.DESeq2 was used to analyze the gene expression data.Then survival analysis was performed on genes highlyexpressed in the tumor tissue.Kaplan-Meier curves were generated by R-survival package,and significance was evaluated by log-rank test.Results The frequency for pathogenic mutations in PIK3CA and APC was significantly discordant between different grades of gastric cancer.2 040 genes were up-regulated in tumor tissue,while 2 357 genes were down-regulated.Among the up-regulated genes,7 genes were associated with poor prognosis of gastric cancer and one was associated with better prognosis.Conclusions Genes associated with differentiation types or prognosis in gastric cancer are identified.The result may clue us future research on potential prognostic markers in clinical treatment.
