TABLE 3

Top 50 Gene Ontology Biological Process terms enriched in 318- and 936-probe sets through three-way intersection of rosiglitazone, COOH, and SPPARγM-L3 gene signatures

Genes in the three signatures demonstrated fold changes of >1.5 with p values of <0.01. The transcript names and gene symbols for the overlapping genes in the Gene Ontology Biological Process analysis are provided in Supplemental Tables 5 and 6.

Rank	318-Probe Set			936-Probe Set
Rank	Term	Hypergeometric p	Bonferroni-Adjusted p	Term	Hypergeometric p	Bonferroni-Adjusted p
1	Response to osmotic stress	2.58 × 10⁻⁷	4.84 × 10⁻⁴	Energy pathways^{^a}	0.00	0.00
2	Alcohol metabolism^{^a}	2.78 × 10⁻⁷	5.21 × 10⁻⁴	Positive regulation of programmed cell death	1.46 × 10⁻¹²	2.74 × 10⁻⁹
3	Angiogenesis	5.58 × 10⁻⁷	1.05 × 10⁻³	Positive regulation of apoptosis	1.23 × 10⁻¹¹	2.30 × 10⁻⁸
4	Pyruvate metabolism^{^a}	8.95 × 10⁻⁷	1.68 × 10⁻³	Growth	1.16 × 10⁻¹⁰	2.18 × 10⁻⁷
5	Blood vessel development	1.13 × 10⁻⁶	2.11 × 10⁻³	Regulation of cell size	2.12 × 10⁻¹⁰	3.98 × 10⁻⁷
6	Sterol biosynthesis^{^a}	1.33 × 10⁻⁶	2.49 × 10⁻³	Skeletal development	3.43 × 10⁻¹⁰	6.44 × 10⁻⁷
7	Sterol metabolism^{^a}	9.87 × 10⁻⁶	1.85 × 10⁻²	Cell growth	3.94 × 10⁻¹⁰	7.38 × 10⁻⁷
8	Lipid biosynthesis^{^a}	1.62 × 10⁻⁵	3.03 × 10⁻²	Blood vessel development	1.17 × 10⁻⁹	2.19 × 10⁻⁶
9	Cholesterol biosynthesis^{^a}	2.01 × 10⁻⁵	3.77 × 10⁻²	Adipocyte differentiation	1.40 × 10⁻⁹	2.63 × 10⁻⁶
10	Steroid metabolism^{^a}	2.09 × 10⁻⁵	3.92 × 10⁻²	Regulation of development	5.05 × 10⁻⁹	1.10 × 10⁻⁵
11	Fatty acid metabolism^{^a}	2.21 × 10⁻⁵	4.13 × 10⁻²	Induction of apoptosis	1.07 × 10⁻⁸	2.01 × 10⁻⁵
12	Response to hypoxia	3.22 × 10⁻⁵	6.04 × 10⁻²	Induction of programmed cell death	1.15 × 10⁻⁸	2.16 × 10⁻⁵
13	Regulation of angiogenesis	5.34 × 10⁻⁵	1.00 × 10⁻¹	Fatty acid metabolism^{^a}	3.25 × 10⁻⁸	6.10 × 10⁻⁵
14	Response to inorganic substance	6.09 × 10⁻⁵	1.14 × 10⁻¹	Angiogenesis	4.53 × 10⁻⁸	8.50 × 10⁻⁵
15	Acetyl-CoA biosynthesis^{^a}	9.14 × 10⁻⁵	1.71 × 10⁻¹	Mitotic cell cycle	6.27 × 10⁻⁸	1.18 × 10⁻⁴
16	Response to oxidative stress	9.20 × 10⁻⁵	1.72 × 10⁻¹	Regulation of growth	2.22 × 10⁻⁷	4.15 × 10⁻⁴
17	Steroid biosynthesis^{^a}	1.11 × 10⁻⁴	2.08 × 10⁻¹	Antiapoptosis	3.16 × 10⁻⁷	5.93 × 10⁻⁴
18	Glycerolipid metabolism^{^a}	1.23 × 10⁻⁴	2.30 × 10⁻¹	Alcohol metabolism^{^a}	5.65 × 10⁻⁷	1.06 × 10⁻³
19	Defense response to pathogenic fungi	1.25 × 10⁻⁴	2.34 × 10⁻¹	Negative regulation of apoptosis	6.47 × 10⁻⁷	1.21 × 10⁻³
20	Muscle development	1.26 × 10⁻⁴	2.36 × 10⁻¹	Negative regulation of programmed cell death	7.20 × 10⁻⁷	1.35 × 10⁻³
21	Defense response to pathogen	1.46 × 10⁻⁴	2.73 × 10⁻¹	Actin cytoskeleton organization and biogenesis	1.26 × 10⁻⁶	2.37 × 10⁻³
22	Second-messenger-mediated signaling	1.69 × 10⁻⁴	3.16 × 10⁻¹	Regulation of cell growth	1.30 × 10⁻⁶	2.44 × 10⁻³
23	Isoprenoid biosynthesis^{^a}	2.13 × 10⁻⁴	4.00 × 10⁻¹	Lipid transport^{^a}	1.36 × 10⁻⁶	2.54 × 10⁻³
24	Cholesterol metabolism^{^a}	2.39 × 10⁻⁴	4.49 × 10⁻¹	Regulation of cell migration	1.69 × 10⁻⁶	3.16 × 10⁻³
25	Acetyl-CoA metabolism^{^a}	2.70 × 10⁻⁴	5.06 × 10⁻¹	Main pathways of carbohydrate metabolism^{^a}	2.37 × 10⁻⁶	4.45 × 10⁻³
26	Lymphocyte proliferation	3.10 × 10⁻⁴	5.80 × 10⁻¹	Energy derivation by oxidation of organic compounds	3.32 × 10⁻⁶	6.22 × 10⁻³
27	Oxygen and reactive oxygen species metabolism	3.18 × 10⁻⁴	5.96 × 10⁻¹	Tricarboxylic acid cycle^{^a}	3.53 × 10⁻⁶	6.62 × 10⁻³
28	Fatty acid oxidation^{^a}	3.29 × 10⁻⁴	6.17 × 10⁻¹	Actin filament-based process	3.65 × 10⁻⁶	6.83 × 10⁻³
29	Heart development	3.80 × 10⁻⁴	7.11 × 10⁻¹	Bone remodeling	5.61 × 10⁻⁶	1.05 × 10⁻²
30	Triacylglycerol metabolism^{^a}	4.69 × 10⁻⁴	8.79 × 10⁻¹	Ossification	6.05 × 10⁻⁶	1.13 × 10⁻²
31	Response to metal ions	4.69 × 10⁻⁴	8.79 × 10⁻¹	Electron transport^{^a}	6.76 × 10⁻⁶	1.27 × 10⁻²
32	Neuropeptide signaling pathway	5.09 × 10⁻⁴	9.55 × 10⁻¹	Response to radiation	7.60 × 10⁻⁶	1.42 × 10⁻²
33	Defense response to fungi	6.94 × 10⁻⁴	1.30	Cell matrix adhesion	8.32 × 10⁻⁶	1.56 × 10⁻²
34	Response to pathogenic fungi	1.08 × 10⁻³	2.02	Positive regulation of development	1.23 × 10⁻⁵	2.31 × 10⁻²
35	Fatty acid β-oxidation^{^a}	1.12 × 10⁻³	2.10	Extracellular matrix organization and biogenesis	1.72 × 10⁻⁵	3.23 × 10⁻²
36	Xenobiotic metabolism	1.15 × 10⁻³	2.15	Extracellular structure organization and biogenesis	1.86 × 10⁻⁵	3.49 × 10⁻²
37	Excretion	1.15 × 10⁻³	2.15	DNA replication and chromosome cycle	1.90 × 10⁻⁵	3.57 × 10⁻²
38	Response to pathogenic bacteria	1.25 × 10⁻³	2.34	Cholesterol transport^{^a}	2.25 × 10⁻⁵	4.22 × 10⁻²
39	Response to toxin	1.27 × 10⁻³	2.39	Reproductive physiological process	2.93 × 10⁻⁵	5.48 × 10⁻²
40	Acylglycerol metabolism^{^a}	1.31 × 10⁻³	2.45	Steroid metabolism^{^a}	3.02 × 10⁻⁵	5.67 × 10⁻²
41	Negative regulation of apoptosis	1.40 × 10⁻³	2.62	Heart development	3.09 × 10⁻⁵	5.78 × 10⁻²
42	Glycerol ether metabolism^{^a}	1.40 × 10⁻³	2.63	Regulation of cell shape	3.88 × 10⁻⁵	7.27 × 10⁻²
43	Negative regulation of programmed cell death	1.45 × 10⁻³	2.73	Amine metabolism^{^a}	4.37 × 10⁻⁵	8.18 × 10⁻²
44	Neutral lipid metabolism^{^a}	1.62 × 10⁻³	3.03	M phase of mitotic cell cycle	4.54 × 10⁻⁵	8.50 × 10⁻²
45	Hyperosmotic response	1.77 × 10⁻³	3.32	Pregnancy	5.51 × 10⁻⁵	1.03 × 10⁻¹
46	Response to cold	1.77 × 10⁻³	3.32	M phase-specific microtubule process	5.76 × 10⁻⁵	1.08 × 10⁻¹
47	Negative regulation of cell adhesion	1.77 × 10⁻³	3.32	Positive regulation of body size	6.46 × 10⁻⁵	1.21 × 10⁻¹
48	Sulfur metabolism	1.89 × 10⁻³	3.54	Fatty acid β-oxidation^{^a}	7.08 × 10⁻⁵	1.33 × 10⁻¹
49	Isoprenoid metabolism^{^a}	1.98 × 10⁻³	3.70	Pyruvate metabolism^{^a}	7.56 × 10⁻⁵	1.42 × 10⁻¹
50	Insulin receptor signaling pathway^{^a}	1.98 × 10⁻³	3.71	Sterol transport	7.59 × 10⁻⁵	1.42 × 10⁻¹

↵a Direct metabolic pathway.