Diet Modifies Pioglitazone’s Influence on Hepatic PPARγ-Regulated Mitochondrial Gene Expression

Table 4

Gene set analysis on BETA data from WT Pio-treated vs. Pio-untreated mice on control or HFD (as designated).

Gene set name (# in Hallmark set)	Description	Overlap	value
(a) Induced by Pio in WT mice on control diet
OXIDATIVE_PHOSPHORYLATION [200]	Genes encoding proteins involved in oxidative phosphorylation.	28	7.09^-16
FATTY_ACID_METABOLISM [158]	Genes encoding proteins involved in metabolism of fatty acids.	25	9.9^-16
ADIPOGENESIS [200]	Genes upregulated during adipocyte differentiation (adipogenesis).	20	5.16^-9
MYC_TARGETS_V1 [200]	A subgroup of genes regulated by MYC—version 1 (v1).	19	2.54^-8
(b) Induced by Pio in WT mice on HFD
OXIDATIVE_PHOSPHORYLATION [200]	Genes encoding proteins involved in oxidative phosphorylation.	23	5.46^-16
MYC_TARGETS_V1 [200]	A subgroup of genes regulated by MYC - version 1 (v1).	15	5.89^-8
FATTY_ACID_METABOLISM [158]	Genes encoding proteins involved in metabolism of fatty acids.	13	1.52^-7
(c) Suppressed by Pio in WT mice on control diet
UV_RESPONSE_UP [158]	Genes upregulated in response to ultraviolet (UV) radiation.	23	1.49^-9
UNFOLDED_PROTEIN_RESPONSE [113]	Genes upregulated during unfolded protein response, a cellular stress response related to the endoplasmic reticulum.	17	1.66^-7
E2F_TARGETS [200]	Genes encoding cell cycle related targets of E2F transcription factors.	21	8.05^-7
P53_PATHWAY [200]	Genes involved in p53 pathways and networks.	21	8.05^-7
TNFA_SIGNALING_VIA_NFKB [200]	Genes regulated by NF-kB in response to TNF (GeneID=7124).	21	8.05^-7
(d) Suppressed by Pio in WT mice on HFD
MYC_TARGETS_V1 [200]	A subgroup of genes regulated by MYC—version 1 (v1).	17	4.45 e^-8

Using the Broad Institute platform with the Hallmark gene set platform to identify the top 10 categories with (see text for details).