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

Table 2

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

Gene set name (# in Hallmark set)	Description	Overlap	value
(a) Induced by Pio in KO mice on control diet
CHOLESTEROL_HOMEOSTASIS [74]	Genes involved in cholesterol homeostasis.	20	1.04^-18
ESTROGEN_RESPONSE_LATE [200]	Genes defining late response to estrogen.	22	3.64^-12
TNFA_SIGNALING_VIA_NFKB [200]	Genes regulated by NF-κB in response to TNF (GeneID=7124).	21	2.17^-11
MTORC1_SIGNALING [200]	Genes upregulated through activation of mTORC1 complex.	20	1.38^-10
APOPTOSIS [161]	Genes mediating apoptosis by activation of caspases.	18	1.83^-10
ESTROGEN_RESPONSE_EARLY [200]	Genes defining early response to estrogen.	19	7.36^-10
NOTCH_SIGNALING [32]	Genes upregulated by activation of notch signaling.	8	8.45^-8
HYPOXIA [200]	Genes upregulated in response to low oxygen levels (hypoxia).	16	1.98^-7
UV_RESPONSE_UP [158]	Genes upregulated in response to ultraviolet (UV) radiation.	14	3.57^-7
ADIPOGENESIS [200]	Genes upregulated during adipocyte differentiation (adipogenesis).	15	9.91^-7
(b) Induced by Pio in KO mice on HFD
No significantly differentially expressed genes
(c) Suppressed by Pio in KO mice on control diet
XENOBIOTIC_METABOLISM [200]	Genes encoding proteins that process drugs and xenobiotics.	24	2.13^-13
(d) Suppressed by Pio in KO mice on HFD
No significantly differentially expressed genes

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