Table 2.

Gene set enrichment analysis

Rank	Gene set
2	Reactome integration of energy metabolism
4	KEGG oxidative phosphorylation
5	KEGG parkinsons disease
7	Mitochondrial part
8	Mitochondrian
10	Mitochondrial membrane
11	Mitochondrial envelope
17	Mitochondrial membrane part
9	KEGG citrate cycle tca cycle
12	KEGG alzheimers disease
13	Organelle inner membrane
16	Mitochondrial inner membrane
14	KEGG huntingtons disease
15	Reactome pyruvate metabolism and TCA cycle
18	Reactome citric acid cycle
19	KEGG cardiac muscle contraction
20	Reactome diabetes pathways
1	Reactome glucose regulation of insulin secretion
3	Reactome electron transport chain
6	Reactome regulation of insulin secretion
21	Reactome glucose metabolism
22	Energy derivation by oxidation of organic compounds
23	Cellular respiration
24	Regulation of heart contraction
25	KEGG PPAR signaling pathway

Negative enrichment: chronic P. gingivalis-treated group vs. chronic control group.

The top 25 P. gingivalis gene sets whose member genes are predominantly downregulated 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 -3.24 (for REACTOME Integration of Energy Metabolism, the top ranked gene set) to -2.33 (KEGG PPAR Signaling Pathway, the 25th-ranked gene set). FDR q < 1 × 10^-30.