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

From: Transcriptome profiling of granulosa cells from bovine ovarian follicles during atresia

  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 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
  1. †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.
  2. †† 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).
  3. Gene symbols which are underlined indicate those genes which interact with a minimum of 4 other molecules within the dataset.