Fig. 2

Differences in predicted biological functions and networks in tonsils of pigs infected with the KS06 versus NVSL isolate based on the RNA-seq data by Ingenuity Pathway Analysis. a and b was used to identify a subset of genes known to be regulated by one and two up-stream regulators, respectively, that included genes with significant differential expression (q-value < 0.1) in tonsils when accounting for cell enrichment. All five and 12 differentially expressed genes were expressed more in tonsils of KS06-infected pigs than of NVSL-infected pigs (intensity of red color indicates magnitude). Orange color (z-score ≥ 2) and blue color (z-score ≤ − 2) indicate activation and inhibition of predicted relationships between these genes, potential up-stream regulators, and potential down-stream functions. Inconclusive genes indicated by grey color. c A novel network that includes differentially expressed genes for isolate in tonsils at 42 dpi when accounting for cell enrichment. Dotted lines represent indirect interactions and solid lines are direct interactions. Genes in red (green) were expressed more (less) in tonsils of the KS06-infected pigs than in tonsils of the NVSL-infected pigs. The grey genes were not differentially expressed and white genes were not expressed but predicted by IPA to be involved in the network