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林景峰,高强,刘甘露,马华萍,胡文悦,韩振蕴.基于多组全基因组表达谱的阳虚人群关键候选基因集和通路筛选及生物信息学分析[J].湖南中医药大学学报英文版,2021,41(3):425-430.[Click to copy
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| 基于多组全基因组表达谱的阳虚人群关键候选基因集和通路筛选及生物信息学分析 |
| 林景峰,高强,刘甘露,马华萍,胡文悦,韩振蕴 |
| (北京中医药大学, 北京 100029;北京中医药大学深圳医院(龙岗), 广东 深圳 518100) |
| 摘要: |
| 目的 基于多组全基因组表达谱筛选阳虚人群关键候选基因集和通路，探讨不同阳虚人群与对照组差异基因的异同，提出阳虚与基因表达关系的可能结论。方法 查找GEO基因表达数据库及PubMed、Embase、CNKI、万方、维普等中英文文献数据库，筛选出其中存在阳虚人群及其对照组的基因表达谱数据或基因表达谱分析结果。应用R语言和生物信息学方法筛选差异表达基因，并进行GO、KEGG和GSEA富集分析，利用韦恩图展现不同阳虚人群的差异表达基因结果的关系，并分析差异基因、富集结果与阳虚之间的关系。结果 共得到2个数据集（GSE87474、GSE56116）和4个基因表达谱分析结果，数据集GSE56116中存在350个差异表达基因，数据集GSE87474中存在138个差异表达基因。4个基因表达谱进行去重与合并后，形成3个差异基因集，分别报道了190个、66个和21个差异表达基因。对差异表达基因结果取交集，未发现重合的基因。对其中差异表达基因相关的基因集和通路取交集分析，寻找到8个共同的基因集和通路。这些通路的功能集中在免疫功能、细胞质囊泡等方面。结论 阳虚人群与非阳虚人群的差异基因集和通路主要与能量代谢、细胞质囊泡及免疫调节相关。不同阳虚人群间关键候选基因集和通路存在一定的相似性，但其作用的具体基因存在差异。中医的阳虚概念更可能与一系列基因集和通路存在紧密的联系，而不是单一的基因。 |
| 关键词: 阳虚 全基因组表达 基因集 通路 生物信息学 |
| DOI：10.3969/j.issn.1674-070X.2021.03.020 |
| Received:September 18, 2020 |
| 基金项目:国家重点研发计划项目（2019YFC1710103）。 |
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| Bioinformatics Analysis Along with Screening on Key Candidate Gene Sets and Pathways in Yang Deficiency Population Based on Genome-wide Expression Profile |
| LIN Jingfeng,GAO Qiang,LIU Ganlu,MA Huaping,HU Wenyue,HAN Zhenyun |
| (Beijing University of Chinese Medicine, Beijing 100029, China;Shenzhen Hospital of Beijing University of Chinese Medicine(Long Gang), Shenzhen, Guangdong 518100, China) |
| Abstract: |
| Objective To screen the key candidate gene sets and pathways in the Yang deficiency population based on multiple genome-wide expression profile sets. To explore the differences and similarities between the different genes in the Yang deficiency syndrome population and the control group, and to propose a possible hypothesis on the relationship between Yang deficiency and gene expression. Methods Searching for GEO gene expression database and PubMed, Embase, CNKI, Wanfang, Viper databases in language of Chinese and English, and screened out gene expression profile data sets or gene expression profile analysis results of Yang deficiency group and its control group. Differentially expressed genes were screened by R software and bioinformatics methods, and gene ontology (GO) analysis, kyoto encyclopedia of genes and genomes (KEGG) and gene set enrichment analysis (GSEA) were carried out. The Venn diagram was used to show the relationship between the results of differentially expressed genes in different people with Yang deficiency, and the relationship between the results of differentially expressed genes, enrichment and Yang deficiency was analyzed. Results Two data sets (GSE87474, GSE56116) and four gene expression profiles were obtained. There were 350 differentially expressed genes in the data set GSE56116 and 138 differentially expressed genes in the data set GSE87474. Four gene expression profiles were selected and combined to form three differentially expressed gene sets. 190, 66 and 21 differentially expressed genes were reported respectively. The results of differentially expressed genes were overlapped and no coincidence genes were found. The gene sets and pathways related to differentially expressed genes were analyzed and 8 common gene sets and pathways were found. The functions of these pathways were concentrated in immune function, cytosolic vesicles and so on. Conclusion The different gene sets and pathways between Yang deficiency and non-Yang deficiency populations are mainly related to energy metabolism, cytoplasmic vesicles and immune regulation. The key candidate gene sets and pathways have some similarities among different Yang deficiency populations, but the expressions of specific genes are different. The concept of Yang deficiency in Chinese medicine is more likely to be related to a series of gene sets and pathways rather than a single gene. |
| Key words: Yang deficiency genome-wide expression gene set pathway bioinformatics |
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