Fig. 4: Gene Ontology (GO) over-representation analysis of differentially expressed genes (DEG) upregulated upon antigen stimulation before and after vaccination.
Over-representation analysis was performed using DEG identified from samples of two elephants (n = 2). Representative immune-relevant GO terms following reduction of redundant terms (>85% gene overlap) in contrasts comparing unstimulated vs. antigen-stimulated samples pre- and post-vaccination are shown according to their occurrence in the pre-vaccination comparison only, in both pre- and post-vaccination comparisons and post-vaccination comparisons only. DEG with an adjusted p value (padj) ≤0.01 were analysed. Significantly over-represented GO terms were identified using a one-sided Fisher’s exact test (H0: no association), corrected for multiple comparisons with the Benjamini-Hochberg method, and ranked according to the combined score (z-score of the observed and expected means of the DEG and pathways overlap). The cut-off for consideration of GO terms as significant was padj ≤0.05. IFN interferon, IL interleukin, NK natural killer, Th T helper, TNF tumour necrosis factor.
