利用生物信息学分析帕金森病人黑质基因表达谱研究

The Bioinformatics Analyses on Expression Profiles of the Substantia Nigra in Parkinson’s Disease

目的:利用生物信息学分析帕金森病人黑质基因表达谱,为进一步帕金森病研究提供研究方向。方法:在Gene Expression Omnibus (GEO)数据库中使用“帕金森病”、“组织”、“表达谱”,并限定组织来源为“智人”,获得2020年3月22日前GEO数据库中的所有生物学样本信息数据。使用GEO2R、DAVID、STRING网站和Cytoscape软件进行数据分析。结果:根据检索条件获得了两个数据集,GSE42966 (对照组3名,帕金森病组6名)和GSE49036 (对照组8名,帕金森病组7个)。分析两个数据集GSE42966和GSE49036中分别存在632和1247个差异表达基因。在这两个数据集的差异基因中共有92个共表达差异基因,其中表达上调基因49个,表达下调基因43个。此外根据KEGG信号通路分析主要集中在细菌侵袭上皮细胞、神经营养蛋白信号通路、轴突导向和MAPK信号通路信号中富集。通过STRING网站构建PPI蛋白网络然后通过Cytoscape软件分析发现其中NTRK3、BDNF、GAB1、PCSK1、CHURC1、GFRA1、SHC4、DOK6、ASPA和ZEB2这十个基因为鉴定帕金森病的主关键基因。结论:通过两个数据集的生物信息学联合分析,找到与帕金森病相关的10个主关键基因,这可能为帕金森病分子通路的研究以及临床上治疗帕金森病提供新思路。

Objective: The expression profiles of substantia nigra in Parkinson’s disease were analyzed by using bioinformatics identifying novel genetic targets. Methods: All biological data before March 22, 2020 related to “Parkinson’s disease”, “tissue”, “Expression profiles” and “homo sapiens” were down-loaded from the Gene Expression Omnibus (GEO) database. Then GEO2R, DAVID, STRING, and Cyto-scape software were used for data analysis. Results: According to the search conditions, two data sets were obtained, GSE42966 (3 in the control group, 6 in the PD group) and GSE49036 (8 in the control group, 7 in the PD group). From these two datasets 632 and 1247, differentially expressed genes were identified, respectively. There were a total of 92 differentially expressed genes in these two datasets, among which 49 genes were up-regulated and 43 genes were down-regulated. In ad-dition, according to the analysis of the KEGG pathway, the signaling pathways are mainly concen-trated in the signals of bacterial invasion of epithelial cells, neurotrophin signaling pathway, axon guidance and MAPK signaling pathway. The PPI network was established through the STRING web-site and then analyzed through Cytoscape software. Ten genes including NTRK3, BDNF, GAB1, PCSK1, CHURC1, GFRA1, SHC4, DOK6, ASPA and ZEB2 were identified as the hub genes for PD. Con-clusions: Through the combined bioinformatics analysis of the two data sets, 10 hub genes related to Parkinson’s disease were identified, which may provide new ideas for the research of molecular pathways of Parkinson’s disease and the clinical treatment of Parkinson’s disease.