Figure 4

Activation of apoptosis pathways in HeV-infected PaKiT03 cells. (A) GO terms enriched in the up-regulated genes/proteins in PaKiT03 cells were analyzed and visualized using REVIGO, where redundant GO terms are removed. The size of the circle represents the number of enriched child GO terms contributing to the parent term. The circle color represents the uncorrected log10 P-value for each parent GO term. Semantic space is the result of multi-dimensional scaling where similar GO terms cluster together. A full list of enriched GO terms, including false discover rate-corrected P-values, are presented in Additional file 5. (B) Top 10 most over-represented KEGG pathways, and the number of significantly differentially expressed genes/proteins contributing to each pathway. The full list of over-represented KEGG pathways is presented in Additional file 6. (C) Expression profile of significantly up-regulated genes/proteins in the PaKiT03 cells which were assigned to the GO term regulation of apoptotic process [GO:0042981] or apoptotic process [GO:0006915]. Gray cells represent proteins where no peptides were observed. Expression values for mRNA are given as log2-fold change, while expression values for proteins are normalized SILAC ratios. Validation of RNAseq differential expression with real-time quantitative PCR (qPCR) for (D) CASP13, (E) TNFRSF10A, (F) TNFRSF11B, (G) CD40 and (H) TNFAIP3/A20 in PaKiT03 cells. Real-time PCR differential expression was calculated based on relative expression to 0 hpi and normalized to GAPDH. Log2-fold change is presented; *P <0.05, **P <0.01. (I) Relative protein expression profile of CD40 in PaKiT03 cells measured by SILAC. (J) Protein expression profile of CD40 and TNFAIP3/A20 in PaKiT03 cells measured by Western blot. β2-tubulin served as the load control.