Transcriptome profiling of granulosa cells from bovine ovarian follicles during atresia

BMC Genomics

Table 5 The most variable genes in small healthy follicles mapping to networks and pathways in IPA

	Genes mapped from dataset
	Symbol	Biological process
Network 1 †(Score = 42)	PLSCR1, PLSCR4, heparanase, CTSL1, ATP2B1	apoptosis
	UHRF1	cell cycle regulation, mitosis
	TIMP1,	matrix degradation
	EGFR , JUNB , FOSL2	differentiation/maturation of granulosa cell through AP-1
	CYP19A1 , CYP11A1, INHBA , BAMBI	steroidogenesis, regulation of gonadotropin secretion/granulosa cell proliferation
	SOD3	stress response
	ADM	regulation of blood supply
	CLDN11	maintenance of epithelial integrity
	VARS	growth metabolism
	AHNAK	actin cytoskeleton organisation, cell polarization
Network 2 †(Score = 42)	CCNB1 , ESPL1, H1FX, H2AFX, BUB1,NCAPG, NCAPG2, SEPT4, S100A4, G3BP1	cell cycle regulation, mitosis
	PSMD4, PSMD13, UBQLN1, PDIA4, HSP70	protein recycling and folding
	PEG3	apoptosis
	PRC1	cell migration
Canonical pathways	Cell Cycle: G2/M DNA Damage Checkpoint Regulation, Mitotic roles of Polo-Like Kinases		P value††
			Fisher’s	B-H FDR
1	CCNB1,CCNB2,CDK1,GADD45A, RPRM, TOP2A, YWHAG	cell cycle regulation, mitosis	3.2 × 10^-4	5.8 × 10^-2
2	CCNB1,CCNB2,CDK1,GADD45A, RPRM, TOP2A, YWHAG	cell cycle regulation, mitosis	3.9 × 10^-4	5.8 × 10^-2
3	ATM Signalling
	JUN, SMC2, GADD45A, H2AFX, CCNB2, CDK1, CCNB1	response to DNA damage	8.2 × 10^-4	8 × 10^-2

†The network score is based on the hypergeometric distribution and is calculated with the right-tailed Fisher’s Exact Test. The score is the negative log of this P value.
†† Significance of association of genes with canonical pathways was determined by a right tailed Fisher’s Exact Test and the Benjamini-Hochberg False Discovery Rate (B-H FDR) for multiple comparisons. The variability of expression was determined by a frequency distribution of the coefficients of variation for probe sets across the arrays in the small healthy follicle group. The cut-off chosen was a coefficient of variation of > 46.8% (n = 10 arrays, n = 682 probe sets).
Gene symbols which are underlined indicate those genes which interact with a minimum of 4 other molecules within the dataset.

ISSN: 1471-2164