Global Gene Expression Profiling in PPAR-γ Agonist-Treated Kidneys in an Orthologous Rat Model of Human Autosomal Recessive Polycystic Kidney Disease

Table 2

(a) Downregulated gene ontology biological process gene sets from genes with greater than 1.25-fold changes in PIO-treated compared with vehicle-treated kidneys. The name of biological process is listed in order of nominal 𝑃 value. (b) Common genes found in cell cycle or cell proliferation gene sets downregulated by PIO treatment. ✓: listed gene in the gene set, —: non-listed gene in the gene set. (c) Upregulated gene ontology biological process gene sets with greater than 1.25-fold changes in PIO-treatmed compared with vehicle-treated kidneys.

(a)

Name of biological process gene sets	Number of genes in the gene set	Nominal 𝑃 value
Carbohydrate METABOLIC PROCESS	16	0.019
Cell proliferation GO 0008283	70	0.024
Organelle organization and biogenesis	34	0.025
Cell cycle GO 0007049	44	0.027
Negative regulation of cell proliferation	28	0.032
Cell cycle process	31	0.037

(b)

Gene symbol	Description	Name of biological process gene sets
		Cell cycle GO 0007049	Negative regulation of cell proliferation	Cell cycle process	Cell proliferation GO 0008283
Brca2	Breast cancer 2	✓	✓	✓	✓
Cdkn2b	Cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)	✓	✓	✓	✓
Chek1	CHK1 checkpoint homolog	✓	✓	✓	—
BUB1B	Cell cycle checkpoint protein kinase Bub1 Fragment	✓	✓	—	✓
PLK1	Pololike kinase 1	✓	✓	—	✓
Cdkn1c	Cyclin-dependent kinase inhibitor 1C	✓	✓	✓	—
Cul5	Cullin 5	✓	✓	✓	✓
Tgfb2	Transforming growth factor, beta 2	✓	—	✓	✓
Bcat1	Branched chain aminotransferase 1	✓	✓	—	✓
PTPRC	Protein tyrosine phosphatase, receptor type, C	✓	✓	—	✓
POLA1	Polymerase (DNA directed), alpha 1	✓	✓	—	✓

(c)

Name of biological process gene sets	Number of genes in the gene set	Nominal 𝑃 value
Neurological System Process	40	0.032