Table 1.

Gene set enrichment analysis

Rank	Gene set
1	Basal cell carcinoma
3	Nucleachromosome part
5	Regulation of gene expression epigenetic
6	KEGG melanogenesis
8	DNA replication
2	DNA dependent DNA replication
11	Regulation of DNA replication
9	Proteinaceous extracellular matrix
4	Extracellular matrix part
7	Basement membrane
13	Extracellular matrix
10	KEGG hedgehog signaling pathway
12	Reactome cell extracellular matrix interactions
14	Reactome E2F mediated regulation of DNA replication
15	Reactome apoptotic execution phase
16	Collagen
17	Reactome inactivation of APC via direct inhibition of the AP complex
19	Reactome smooth muscle contraction
20	Reactome conversion from APC CDC20 to APC CD1 in late anaphase
21	Reactome signaling by PDGF
22	KEGG lysosome
23	Microtubule cytoskeleton
24	Cell division
18	Cytokinesis
25	Reactome class B2 secretin family receptors

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

The top 25 P. gingivalis 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 2.32 (for Basal Cell Carcinoma, the top ranked gene set) to 1.66 (REACTOME Class B2 Secretin Family Receptors, the 25th-ranked gene set). FDR q range: 0.001-0.186.