论文摘要
Objective: To determine the key gene and pathway in macrophages during the the rupture process of carotid atherosclerotic plaques by bioinformatics analysis methods. Materials and Methods: Dataset GSE41571 in the gene expression omnibus（GEO） database contained macrophages expression data of 5 ruptured carotid plaque samples and 6 stable carotid plaque samples. The study was performed using the GPL 570 platform（affymetrix human genome U133 plus 2.0 arrays）. Since the data was downloaded from public database, no informed consent was required. The GSE41571 dataset was analyzed using GEO2 R（https://www.ncbi.nlm.nih.gov/geo/geo2 r/） analysis tool from GEO. A site corresponding to a plurality of genes was deleted, and an average of log2 fold change（log2 FC） values of a plurality sites corresponding to one gene was taken as the log2 FC value of the gene. Set adjusted P value < 0.05 and |log2 FC| > 1.5 as the threshold for the screening of differentially expressed genes（DEGs）. The obtained DEGs were uploaded to the online tool database for annotation, visualization and integrated discovery（DAVID, https://david.ncifcrf.gov/, version 6.8） for gene ontology（GO） and Kyoto encyclopedia of genes and genomes（KEGG） pathway enrichment analysis. P<0.05 was set as the threshold. Then, the DEGs were submitted to the online tool search tool for the retrieval of interacting genes（STRING, version 10.5, https://string-db.org/） for protein-protein interaction（PPI） analysis and set the confidence score = 0.04. Results: A total of 72 DEGs were identified, including 7 up-regulated DEGs, the three most up-regulated genes were CD38（log2 FC=2.78）, CXCL2（log2 FC=2.11）, PIK3 R6（log2 FC=1.65）; 65 down-regulated DEGs, the three most down-regulated genes were ASPN（log2 FC=-6.54）, COL21 A1（log2 FC=-5.21）, ITGBL1（log2 FC=-5.20）. In the GO enrichment analysis, we obtained 4 significantly enriched biological processes（BPs）, the top three were potassium ion transmembrane transport（P=1.01 E-02）, negative regulation of transforming growth factor beta receptor signaling pathway（P=2.34 E-02）, muscle organ development（P=4.28 E-02）; for the cellular components（CCs） category, we got 9 significantly enriched CCs, the top three were proteinaceous extracellular matrix（P=4.50 E-04）, plasma membrane（P=2.06 E-03）, lamellipodium membrane（P=2.19 E-03）; for the molecular functions（MFs） category, we got 5 significantly enriched MFs, the top three were frizzled binding（P=2.54 E-04）, voltage-gated potassium channel activity（P=1.70 E-02）, heparin binding（P=1.76 E-02）. The significantly enriched KEGG pathway was protein digestion and absorption（P=3.69 E-02）. In PPI analysis, the key gene was ASPN（Degree=4）. Conclusion: In macrophages during carotid atherosclerotic plaques rupture process, protein digestion and absorption was the most important pathway, and ASPN was the key gene. This provides direction for future research.
论文目录
文章来源
类型: 国际会议
作者: Tie Guo
来源: Workshop 2 2019 2019-01-05
年度: 2019
分类: 基础科学,医药卫生科技
专业: 生物学,心血管系统疾病
单位: Haikou Hospital affiliated to Xiangya School of Medicine of Central South University
分类号: R543.4;Q811.4
页码: 163
总页数: 1
文件大小: 7k
下载量: 3