Table 5.

Gene set enrichment analysis

Rank	Gene set
1	KEGG lysosome
2	Reactome signaling in immune system
10	Reactome innate immunity signaling
24	Cell surface interactions at the vascular wall
3	KEGG natural killer cell mediated cytotoxicity
4	KEGG systemic lupus erythematosus
6	KEGG B cell receptor signaling pathway
7	Leishmania infection
8	KEGG toll like receptor signaling pathway
9	Immune system process
5	Immune response
11	Reactome toll receptor cascades
13	Reactome S phase
15	Reactome synthesis of DNA
14	KEGG FC gamma R mediated phagocytosis
16	Reactome host interactions of HIV factors
17	Reactome M G1 transition
12	DNA replication pre initiation
18	KEGG T cell receptor signaling pathway
19	Defense response
20	KEGG nod like receptor signaling pathway
21	KEGG hematopoietic cell lineage
22	Reactome G1 S transition
12	DNA replication pre initiation
23	KEGG chemokine signaling pathway
25	Reactome cell cycle checkpoints

Positive enrichment: Western diet group vs. chronic control group.

The top 25 Western diet 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 2.97 (for KEGG Lysosome, the top ranked gene set) to 2.42 (REACTOME Cell Cycle Checkpoints, the 25th-ranked gene set). FDR q < 1 × 10^-30.