Chinese Journal of Tissue Engineering Research ›› 2022, Vol. 26 ›› Issue (23): 3706-3713.doi: 10.12307/2022.671
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Yang Wei1, Yuan Puwei2, Du Longlong2, Li Xuefeng2, Gao Qimeng2, Han Qingmin3
Received:
2021-08-07
Accepted:
2021-09-08
Online:
2022-08-18
Published:
2022-02-23
Contact:
Han Qingmin, MD, Chief physician, Professor, Doctoral supervisor, the Third Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong Province, China
About author:
Yang Wei, MD candidate, Attending physician, the Third Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong Province, China
Supported by:
CLC Number:
Yang Wei, Yuan Puwei, Du Longlong, Li Xuefeng, Gao Qimeng, Han Qingmin. Bioinformatics analysis of gene expression profile of peripheral blood lymphocytes in patients with osteoarthritis[J]. Chinese Journal of Tissue Engineering Research, 2022, 26(23): 3706-3713.
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2.3 差异表达基因的GO功能和KEGG通路富集分析 对筛选得到的所有差异表达基因进行GO和KEGG富集分析,共富集到88条,其中在满足P.adj < 0.05 & q value < 0.05条件下,生物学过程共有24条,CC共有3条,MF共有4条,KEGG共有24条。BP主要富集在“淋巴细胞介导的免疫”“体液免疫反应”“抗原受体介导的信号通路”“B细胞受体信号通路”“免疫球蛋白介导的免疫反应”和“吞噬作用的正调控”等24条生物学过程上;CC富集在“质膜外侧”“MHC Ⅱ类蛋白质复合物”“MHC蛋白复合物”等细胞成分中;MF富集在“信号适配器活动”“SH3/SH2 适配器活动”“MHC 蛋白复合物结合”“核孔结构成分”等分子功能中;KEGG富集在造血细胞谱系、哮喘、炎症性肠病、同种异体排斥、利什曼病、移植物抗宿主病、1型糖尿病、Th1和Th2细胞分化、Th17细胞分化、破骨细胞分化和TNF信号通路等通路上。具体见表2和图5。"
2.4 PPI网络分析及模块分析结果 将筛选到的差异表达基因导入STRING在线平台,其结果导入Cytoscape-v 3.8.2中,得到PPI网络图,共有66个节点,105条互作关系,见图6;经MCODE筛选出4个集簇,展示得分均较低。然后使用cytohubba插件采用MCC、Degree和MNC算法筛选出连结度最高的前10个基因,再联合centiscape插件中度(Degree)、中介中心性(Betweenness)、特征向量(Eigenvector)和紧密度(Closeness)等参数以及对应的P值和log2FC值筛选核心基因,之后将Degree法和MCC法以及Degree法和MNC法筛选的前10基因分别取交集,最后两个交集中共同有8个差异基因为:TNF(肿瘤坏死因子)、CD19、TFRC(转铁蛋白受体)、PAX5(配对框5)、MAP2K7(丝裂原活化蛋白激酶激酶7)、CD24、MS4A1(跨膜4域A1)和BLNK(B细胞连接器),见图7和表3。"
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