The global effect of follicle-stimulating hormone and tumour necrosis factor α on gene expression in cultured bovine ovarian granulosa cells

Table 4 Upstream regulators determined by IPA to be activated or inhibited by TNF α (± FSH) treatment of cultured granulosa cells^†

Gene symbol or molecule	Full gene name	Actual fold change	Activation z-score	P value of overlap
TNF	Tumour necrosis factor		6.52	7.03E-39
IFNG	Interferon gamma		6.75	6.34E-35
IL1B	Interleukin 1, beta		4.76	9.88E-28
Tretinoin	All-trans retinoic acid		4.12	7.15E-25
IFNB1	Interferon beta 1		3.66	8.03E-20
OSM	Oncostatin M		4.29	5.93E-16
CD40	CD40 molecule, TNF receptor superfamily member 5	10.1	3.25	2.36E-13
TGM2	Transglutaminase 2	31.0	3.34	1.05E-12
FN1	Fibronectin 1	3.3	3.05	7.85E-11
ESR1	Estrogen Receptor 1		3.07	1.99E-07
HTT	Huntingtin		3.32	8.34E-07
IL1RN	Interleukin 1 receptor antagonist	5.9	−3.60	8.11E-19

^†Genes >3-fold differentially regulated between TNFα (± FSH) and control (± FSH) were used for this analysis.
The P value of overlap is the calculated statistical significance of overlap between genes from the dataset and genes that are known to be regulated by the upstream regulator using Fisher’s exact test.
The bias-corrected z-score is used to infer the activation states of transcriptional regulators. It is calculated from the proportions of genes which are differentially regulated in an expected direction based on the known interactions between the regulator and the genes present in the Ingenuity database. Those genes with a z-score greater or less than two are considered to be either activated or inhibited respectively.

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