Hassan Md Zakiul, Ahmed Md Shakil, Khan Md Marufuzzaman, Uddin Mohammad Ahsan, Chowdhury Fahmida, Kamruzzaman Md
Infectious Diseases Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka, Bangladesh.
Department of Public Health, The University of Tennessee, Knoxville, Tennessee, USA.
Bioinformation. 2019 Dec 31;15(12):853-862. doi: 10.6026/97320630015853. eCollection 2019.
Nipah virus (NiV) is an ssRNA, enveloped paramyxovirus in the genus Henipaveridae with a case fatality rate >70%. We analyzed the NGS RNA-Seq gene expression data of NiV to detect differentially expressed genes (DEGs) using the statistical R package limma. We used the Cytoscape, Ensembl, and STRING tools to construct the gene-gene interaction tree, phylogenetic gene tree and protein-protein interaction networks towards functional annotation. We identified 2707 DEGs (p-value <0.05) among 54359 NiV genes. The top-up and down-regulated DEGs were EPST1, MX1, IFIT3, RSAD2, OAS1, OASL, CMPK2 and SLFN13, SPAC977.17 using log2FC criteria with optimum threshold 1.0. The top 20 up-regulated gene-gene interaction trees showed no significant association between Nipah and Tularemia virus. Similarly, the top 20 down-regulated genes of neither Ebola nor Tularemia virus showed an association with the Nipah virus. Hence, we document the top-up and down-regulated DEGs for further consideration as biomarkers and candidates for vaccine or drug design against Nipah virus to combat infection.
尼帕病毒（NiV）是一种单链RNA包膜副粘病毒，属于亨尼帕病毒科，病死率>70%。我们使用统计R包limma分析了NiV的NGS RNA-Seq基因表达数据，以检测差异表达基因（DEG）。我们使用Cytoscape、Ensembl和STRING工具构建基因-基因相互作用树、系统发育基因树和蛋白质-蛋白质相互作用网络，以进行功能注释。我们在54359个NiV基因中鉴定出2707个DEG（p值<0.05）。使用log2FC标准和最佳阈值1.0，上调和下调的前几位DEG分别是EPST1、MX1、IFIT3、RSAD2、OAS1、OASL、CMPK2和SLFN13、SPAC977.17。上调的前20个基因-基因相互作用树显示尼帕病毒与土拉菌病病毒之间无显著关联。同样，埃博拉病毒和土拉菌病病毒下调的前20个基因均与尼帕病毒无关联。因此，我们记录了上调和下调的DEG，以供进一步考虑作为生物标志物以及针对尼帕病毒感染的疫苗或药物设计的候选物。
