Genomic profiling of Nipah virus using NGS driven RNA-Seq expression data

Abstract

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.

Keywords: NGS RNA-Seq; Nipah virus; Phylogenetic gene tree; Protein-protein interaction network; limma.

Figure 1

The schematic diagram of the work flow of the study of genomic profiling of Nipah virus

Figure 2

Association among zoonotic viruses including Nipah virus using gene-gene interaction network tree for top 20 up regulated DE genes

Figure 3

Association among zoonotic viruses including Nipah virus using gene-gene interaction network tree for top 20 down regulated DE genes

Figure 4

Gene tree for genomic classification of top up regulated seven functional DE genes: (g1) EPST1; (g3) MX1; (g4) IFIT3; (g5) RSAD2; (g6) OAS1; (g7) OASL; (g9) CMPK2

Figure 5

Protein-protein interaction network for top up regulated seven functional DE genes (red color node is the target gene node): (g1) EPST1; (g3) MX1; (g4) IFIT3; (g5) RSAD2; (g6) OAS1; (g7) OASL; (g9) CMPK2

Figure 6

Protein-protein interaction network and phylogenetic gene tree for top down regulated two functional DE genes. (a) PPI network of SLFN13 (b) PPI network of SPAC977.17 (C) phylogenic gene tree of SLFN13