Figure 5

Comparative transcriptome analysis of unstimulated vs. PPD-B stimulated whole blood from M. bovis AF2122/97 or M. tuberculosis H37Rv infected cattle. (A) The overlap of differentially expressed genes from the comparison of unstimulated whole blood samples and PPD-B stimulated whole blood samples for M. bovis AF2122/97 infected animals at day 14 and day 42 (blue) and M. tuberculosis H37Rv infected animals at day 14 and day 42 (purple) (−1 > log₂FC < 1, FDR < 0.05). (B) The relative expression of Interferon stimulated genes (R-HSA-877300) from the comparison of unstimulated whole blood samples and PPD-B stimulated whole blood samples for M. bovis AF2122/97 infected animals at day 14 and day 42 and M. tuberculosis H37Rv infected animals at day 14 and day 42. Genes that pass multiple hypothesis testing are denoted with an asterisk (Benjamini-Hochberg, FDR < 0.05) (*). (C) Pathway enrichment analysis results for 658 genes that are significantly differentially expressed (−1 > log₂FC < 1, FDR < 0.05) in PPD-B stimulated whole blood samples from both M. bovis AF2122/97- and M. tuberculosis H37Rv- infected animals at both 14 and 42 days post infection in comparison to unstimulated whole blood samples. The graph depicts the association of each pathway with the differentially expressed gene list based on the SIGORA successes metric (circle size) and the number of genes annotated within the pathway (“#genes in pathway”) while the colour bar depicts the significance of the association (Bonferroni < 0.05). (D) The relative expression (transcripts per million, TPM, “log(TPM +1)”) and the relative change in expression (log₂ fold change (“Log₂FC”)) of 658 genes that are significantly differentially expressed (−1 > log₂FC < 1, FDR < 0.05) in PPD-B stimulated whole blood samples from both M. bovis AF2122/97- and M. tuberculosis H37Rv- infected animals at both 14 and 42 days post infection in comparison to unstimulated whole blood samples. The genes are associated with pathways related to TNF signalling (R-HSA-5668541, R-HSA-5676594, R-HSA-5357786, R-HSA-5669034), Antigen processing-Cross presentation (R-HSA-1236975) and Chemokines and complement activation (R-HSA-380108, R-HSA-173736). Genes that pass multiple hypothesis testing are denoted with an asterisk (Benjamini-Hochberg, FDR < 0.05) (*).