Pathways Activated by Infected and Bystander Chondrocytes in Response to Ross River Virus Infection

Figures

• 

  Figure 1. Transcriptomics of GFP+ (RRV-infected) and GFP− (uninfected bystander) populations relative to mock controls of primary human chondrocyte cells. Gene expression of GFP+ cells (A) and GFP− cells (B) relative to healthy mock controls are shown represented as volcano plots. Differentially expressed genes (DEGs) defined whereby log2 Fold Change (FC) threshold of 0.58 (1.5FC) and False Discovery Rate (FDR) <0.05. The down- and up-regulated DEGs are coloured blue and red, respectively, and non-significant genes are shown in grey.

• 

  Figure 2. Differential gene expression in GFP+ (RRV-infected) and GFP-mock (uninfected bystander) populations. Differentially expressed genes (DEGs) for GFP+ and GFP− cells relative to healthy mock controls were compared and the proportion of genes expressed as a Venn diagram (A). Up- and down-regulated DEGs in each of the four gene profiles (genes in the GFP+ group only, overlapping genes which are present in GFP+ cells, overlapping genes which are present in GFP− cells and genes that are found in the GFP− group only) are shown (B).

• 

  Figure 3. Gene set enrichment analysis of DEGs in GFP+ only and GFP− only populations showing unique genes identified in each population. The top 5 functional annotation gene-set associations for the two gene profiles: GFP+ (A) and GFP− (B) without overlap were identified using Enrichr with Gene Ontology Biological Process (GO2018 BP) and Molecular Function (GO2018 MF), KEGG and Jensen DISEASES databases. Keywords associated with up- and downregulated genes are coloured red and blue, respectively. The grey bar represents the p-values determined by the Enrichr analysis platform.

• 

  Figure 4. Gene-set enrichment analysis of overlapping DEGs in GFP+ and GFP− populations. The top 5 functional annotation for the two gene profiles: overlap-DEGs-GFP+ (A) and overlap-DEGs-GFP− (B) were identified using Enrichr with Gene Ontology Biological Process (GO2018 BP) and Molecular Function (GO2018 MF), KEGG and Jensen DISEASES databases. Keywords associated with up- and down-regulated genes are coloured red and blue, respectively. The grey bar represents the p-values determined by the Enrichr analysis platform.

• 

  Figure 5. Differential gene expression for gene-sets related to joint pathology. The proportion of up- and down regulated differentially expressed genes (DEGs) in each of the four unique/overlapping gene profiles (GFP+ group only, overlapping genes in GFP+ cells, overlapping genes in GFP− cells and GFP− group only) were assessed using functional annotation gene-sets related to joint pathology from the Human Phenotype Ontology (HPO) database: increased inflammatory response (A), abnormal joint morphology (B) and arthritis (C).

• 

  Figure 6. Differential gene expression for gene-sets associated with extracellular matrix (ECM) architecture and remodelling. The proportion of up- and down-regulated differentially expressed genes (DEGs) in each of the four unique/overlapping gene profiles (GFP+ group only, overlapping genes in GFP+ cells, overlapping genes in GFP− cells and GFP− group only) were assessed using functional annotation gene-sets related to extracellular matrix remodelling (ECM) from the Gene Ontology Biological Processes database (GO2018 BP): ECM structural constituents (A), ECM assembly (B) and ECM disassembly (C).