Screening and biologically functional analysis of differentially expressed genes for neuropathic pain
沈鹏 1柴欣萍 2李昱彤 2梁颖 1陈希文 1黄子怡 1熊凤 1冯珍1
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作者信息
1. 南昌大学第一附属医院康复医学科,江西省南昌市,330000
2. 南昌大学
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摘要
目的:通过生物信息学方法分析正常人与坐骨神经痛患者数据,从而筛选出神经病理性疼痛(neuropathic pain,NP)的潜在差异基因.方法:从基因表达数据库下载芯片数据GSE150408.用R软件的limma包筛选差异表达基因(differentially expressed genes,DEGs),使用clusterProfiler包进行基因本体论(gene ontology,GO)富集分析和京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)通路分析,通过STRING数据库进行DEGs蛋白互作网络分析.结果:共筛选得到424个DEGs,包括233个上调基因和191个下调基因.GO富集分析表明DEGs主要分布在囊泡、分泌性颗粒、第三粒等细胞组分;参与防御反应、免疫调节过程、细胞激活、白细胞激活等生物学过程,同时发挥免疫受体激活、补体激活、MAP激酶磷酸化等分子功能.KEGG通路分析表明DEGs主要集中在癌症中的转录失调等通路;基因集富集分析(gene set enrichment analysis,GSEA)最显著富集的基因集为细胞内吞作用,疱疹病毒感染等.蛋白互作网络中上调蛋白FCGR1A的度值最高,下调蛋白SPTBN2的度值最高,这2个蛋白是关键节点.结论:NP的外周血液具有炎症和免疫特征,AZU1、BPI、FCGR1A、SPTBN2等4个基因是参与NP的关键基因.
Abstract
Objective:To investigate differentially expressed genes(DEGs)for neuropathic pain between sciatica and healthy controls.Method:The microarray dataset GSE150408 were downloaded from gene expression database(gene expression omnibus database,GEO).The DEGs were screened using the limma V3.42.0(linear models for microarray da-ta)package of the R software program(version 3.5.0).GEO terms and Kyoto encyclopedia of genes and ge-nomes(KEGG)pathway enrichment analysis of DEGs were automatically completed and visualized by the clus-terProiler V3.14.0.STRING was searched to identify and predict interactions between genes or proteins,to con-struct the protein to protein interaction.Result:A total of 424 DEGs were screened,including 233 up-regulated genes and 191 down-regulated genes.The result of GO enrichment indicated that for biological process,DEGs were significantly enriched in de-fense response,regulation of immune system process,cell activation,leukocyte activation.Regarding cell com-ponents,DEGs were significantly enriched in vesicles,secretory granules,tertiary granule.For molecular func-tion,DEGs were significantly enriched in immune receptor activation,complement receptor activity and MAP kinase phosphatase activity.The result of KEGG pathway-enrichment indicated that DEGs were mainly enriched in transcriptional misregulation in cancer.Moreover,the GSEA analysis indicated that the most significant en-riched gene sets included endocytosis,Epstein-Barr virus infection.PPI analysis were performed to explore the potential function of the DEGs.It showed that the degree of FCGR1A was the highest in up-regulated proteins and the highest in down-regulated proteins.These two proteins were the key nodes.Conclusion:It showed an inflammatory and immune characteristic in peripheral blood for neuropathic pain.AZU1,BPI,FCGR1A and SPTBN2 were the key genes in neuropathic pain.
维普
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