Table 3. Differential pathways between PBMC from M. bovis-infected animals and control animals using GSEA.

Downregulated pathways
KEGG	Path	url KEGG
04010	MAPK signaling pathway	http://www.genome.jp/dbget-bin/www_bget?pathway:bta04010
04142	Lysosome	http://www.genome.jp/dbget-bin/www_bget?pathway:bta04142
04144	Endocytosis	http://www.genome.jp/dbget-bin/www_bget?pathway:bta04144
04145	Phagosome	http://www.genome.jp/dbget-bin/www_bget?pathway:bta04145
04722	Neurotrophin signaling pathway	http://www.genome.jp/dbget-bin/www_bget?pathway:bta04722
04810	Regulation of actin cytoskeleton	http://www.genome.jp/dbget-bin/www_bget?pathway:bta04810
05140	Leishmaniasis	http://www.genome.jp/dbget-bin/www_bget?pathway:bta05140
Upregulated pathways
KEGG	Path	url KEGG
00190	Oxidative phosphorylation	http://www.genome.jp/dbget-bin/www_bget?pathway:bta00190
00230	Purine metabolism	http://www.genome.jp/dbget-bin/www_bget?pathway:bta00230
01100	Metabolic pathways	http://www.genome.jp/dbget-bin/www_bget?pathway:bta01100
03040	Spliceosome	http://www.genome.jp/dbget-bin/www_bget?pathway:bta03040
04660	T cell receptor signaling pathway	http://www.genome.jp/dbget-bin/www_bget?pathway:bta04660
05012	Parkinson’s disease	http://www.genome.jp/dbget-bin/www_bget?pathway:bta05012
05016	Huntington’s disease	http://www.genome.jp/dbget-bin/www_bget?pathway:bta05016
05200	Pathways in cancer	http://www.genome.jp/dbget-bin/www_bget?pathway:bta05200

The differential pathways were assessed with the gseattperm function in the Category Bioconductor package (10,000 permutations). All the pathways shown were significant at a P<0.01, adjusted for multiple comparisons using the false discovery rate method.