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基于生物信息学分析肾透明细胞癌预后相关关键基因
- Affiliations：
1College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, Anhui, China
2Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, Lu’an 237012, Anhui, China
- Author bio：
*Tel: 86-13516482068, E-mail: 646923623@qq.com
- Funds：National Technical system of Chinese Medicinal Materials Industry(CARS-21);Natural Science Projects of West Anhui University in China(WXZR201932);Training Program of Innovate and Entrepreneurship of National College students in China(201810376058);Training Program of Innovate and Entrepreneurship of National College students in China(201810376061);Anhui Provincial Natural Science Foundation in China(2017A030311022);Anhui Provincial University Natural Science Project in China(KJ2018A0413);Anhui Provincial University Natural Science Project in China(KJ2017a407);Anhui Provincial Quality of Undergraduate project in China(2018zygc075);Anhui Provincial Quality of Undergraduate project in China(2018jyxm1153);Anhui Provincial Quality of Undergraduate project in China(2018jyxm1155);Teaching and Research Projects of West Anhui University in China(wxxy2018026)
DOI：10.24920/003651
中图分类号：收稿日期：2020-08-02，
网络出版日期：2020-12-25，
纸质出版日期：2021-06-30
- Accepted：
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蒋平, 孙桃桃, 陈存武, 等. 基于生物信息学分析肾透明细胞癌预后相关关键基因[J]. 中国医学科学杂志（英文版）, 2021,36(2):127-134.
Jiang Ping, Sun Taotao, Chen Cunwu, et al. Identification of Prognostic Related Hub Genes in Clear-Cell Renal Cell Carcinoma
via Bioinformatical Analysis[J]. Chinese medical sciences journal, 2021, 36(2): 127-134.蒋平, 孙桃桃, 陈存武, 等. 基于生物信息学分析肾透明细胞癌预后相关关键基因[J]. 中国医学科学杂志（英文版）, 2021,36(2):127-134. DOI： 10.24920/003651.
Jiang Ping, Sun Taotao, Chen Cunwu, et al. Identification of Prognostic Related Hub Genes in Clear-Cell Renal Cell Carcinoma
via Bioinformatical Analysis[J]. Chinese medical sciences journal, 2021, 36(2): 127-134. DOI： 10.24920/003651.
摘要
目的
识别与肾透明细胞癌预后相关的关键基因。
方法
基于生物信息学分析技术对GEO数据库中的62个肾透明细胞癌样本和54个正常肾组织的数据集（GSE12606
GSE36895和GSE66272）进行分析。首先在GEO2R和J Venn网站上获取差异表达基因基因
之后采用GO和KEGG对基因进行功能注释;在使用STRING网站构建PPI网络后
采用Cytoscape软件的MCODE App对核心基因进行筛选;最后利用GEPIA网站分析与生存率有关的核心基因。
结果
我们共发现648个差异表达基因
包括222个上调表达基因和426个下调表达基因。PPI蛋白网络分析共发现28个表达上调的核心基因
其中7个核心基因（
CCNE2
CDK1
CDC6
CCNB2
BUB1
TTK
和
PTTG1
）富集于细胞周期
4个（
CCNE2
CDK1
CCNB2
和
RRM2
）富集于p53信号通路。GEPIA生存率分析发现：
CDK1
CCNB2
RRM2
BUB1
PTTG1
与肾透明细胞癌患者的生存率密切相关。肾透明细胞癌患者
BUB1
CCNB2
PTTG1
和
RRM2
等4个关键基因的表达量高于正常人群（
P
<
0.05）。
结论
BUB1
、
CCNB2
、
PTTG1
、
RRM2
等4个上调差异表达基因可能是肾透明细胞癌患者预后关键预测基因。
Abstract
Objective
To identify new genes that correlate with prognosis of clear-cell renal cell carcinoma (ccRCC)
via
bioinformatics analysis.
Methods
The gene expression profiles of 62 ccRCC and 54 normal kidney tissues were available from the Gene Expression Omnibus database: GSE12606
GSE36895 and GSE66272. The differentially expressed genes were screened with GEO2R and J Venn online tools. Functional annotation including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) was applied to identify the possible function of the hub genes involved in prognosis of ccRCC. In protein protein interaction network (PPI network)
the STRING online tool was used to visualize the network of the differentially expressed genes
and the core gene was selected by MCODE App in Cytoscape software. Finally
GEPIA Survival Plot was performed to assess genes associated with worse survival.
Results
We totally found 648 differentially expressed genes
including 222 up-regulated genes and 426 down-regulated genes. PPI network showed that in 28 up-regulated genes 7 (
CCNE2
CDK1
CDC6
CCNB2
BUB1
TTK
and
PTTG1
) enriched in cell cycle and 4 genes (
CCNE2
CDK1
CCNB2
and
RRM2
) enriched in p53 signaling pathway. GEPIA Survival Plot assay revealed that ccRCC patients carrying
CDK1
CCNB2
RRM2
BUB1
and
PTTG1
had a worse survival. GEPIA Box Plot showed that
BUB1
CCNB2
PTTG1
and
RRM2
were over expressed in the ccRCC tissues in contrast to the normal tissues (
P
<
0.05).
Conclusion
ccRCC patients with the four up-regulated differentially expressed genes including
BUB1
CCNB2
PTTG1
and
RRM2
might manifest a poor prognosis.
关键词
Keywords
references
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