Table 3.

Gene set enrichment analysis

Rank	Gene set
1	Microbody
2	Peroxisome
20	Peroxisome organization and biogenesis
7	KEGG propanoate metabolism
3	KEGG peroxisome
12	Reactome peroxisomal lipid metabolism
4	Kegg PPAR signaling pathway
5	Reactome metabolism of lipids and lipoproteins
6	Reactome regulation of lipid metabolism by peroxisome proliferator activated receptor alpha
22	Reactome cholesterol biosynthesis
23	Reactome synthesis of bile acids and bile salts via 7 alpha hydroxycholesterol
8	KEGG valine leucine and isoleucine degradation
7	Kegg propanoate metabolism
9	KEGG fatty acid metabolism
10	Reactome metabolism of vitamins and cofactors
11	KEGG pyruvate metabolism
7	KEGG propanoate metabolism
13	KEGG glycerolipid metabolism
15	Lipid catabolic process
24	Cellular lipid catabolic process
16	Mitochondrion
14	Mitochondrial lumen
17	Mitochondrial matrix
7	KEGG propanoate metabolism
18	Reactome branched chain amino acid catabolism
19	Cofactor metabolic process
21	KEGG biosynthesis of unsaturated fatty acids
25	Vitamin metabolic process

Positive enrichment: chronic C. pneumoniae-treated group vs. chronic control group.

The top 25 C. pneumoniae gene sets whose member genes are predominantly upregulated with respect to the chronic control group. Column 1 indicates the rank of the gene set based on Normalized Enrichment Score (NES). Column 2 lists the gene set name (bold) as provided by MSigDB. Gene set names and ranks that are not in bold are gene sets that are redundant or partially redundant and included within larger bolded gene sets. The NES ranged from 2.64 (for Microbody Peroxisome, the top ranked gene set) to 2.03 (Vitamin Metabolic Process, the 25th-ranked gene set). FDR q range: 0-0.001.