Research Article

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

Table 3

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

Gene set name (# in Hallmark set)DescriptionOverlap value

(a) Induced by Pio in WT mice on control diet
OXIDATIVE_PHOSPHORYLATION [200]Genes encoding proteins involved in oxidative phosphorylation.482.55-35
MYC_TARGETS_V1 [200]A subgroup of genes regulated by MYC - version 1 (v1).402.33-26
ADIPOGENESIS [200]Genes upregulated during adipocyte differentiation (adipogenesis).313.41-17
ESTROGEN_RESPONSE_LATE [200]Genes defining late response to estrogen.245.47-11
FATTY_ACID_METABOLISM [158]Genes encoding proteins involved in metabolism of fatty acids.211.34-10
MTORC1_SIGNALING [200]Genes upregulated through activation of mTORC1 complex.232.45-10
GLYCOLYSIS [200]Genes encoding proteins involved in glycolysis and gluconeogenesis.218.17-9
UNFOLDED_PROTEIN_RESPONSE [113]Genes upregulated during unfolded protein response.168.78-9
ESTROGEN_RESPONSE_EARLY [200]Genes defining early response to estrogen.192-7
DNA_REPAIR [150]Genes involved in DNA repair.164.31-7
(b) Induced by Pio in WT mice on HFD
OXIDATIVE_PHOSPHORYLATION [200]Genes encoding proteins involved in oxidative phosphorylation.312.38-24
MYC_TARGETS_V1 [200]A subgroup of genes regulated by MYC—version 1 (v1).251.66-17
ADIPOGENESIS [200]Genes upregulated during adipocyte differentiation (adipogenesis).202.72-12
ESTROGEN_RESPONSE_LATE [200]Genes defining late response to estrogen.151.22-7
(c, d) Suppressed by Pio in WT mice on control or HFD
 No overlaps found.
(e, f, g, h) Induced or suppressed by Pio or HFD in KO mice in presence or absence of HFD or Pio
 No overlaps found.

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