Table 3.

IPA summary of RNA-Seq analysis of abdominal fat in HG and LG cockerels (7 wk)

Top Canonical Pathways	p-value	Overlap	Ratio
Axonal Guidance Signaling	1.07E-11	20.3%	88/434
Acute Phase Response Signaling	4.80E-11	27.2%	46/169
Role of Tissue Factor in Cancer	4.05E-10	30.9%	34/110
Coagulation System	4.13E-09	48.6%	17/35
Complement System	1.20E-08	45.9%	17/37
Top Upstream Regulators	p-value of overlap		#Target Genes
ESR1	6.70E-29		234
TP53	1.48E-24		230
CTNNB1	4.21E-19		132
ESR2	1.14E-17		83
SMARCA4	3.03E-13		105
Top Molecular and Cellular Functions	p-value		# Genes
Cellular Movement	7.08E-08 – 5.98E-43		538
Cellular Growth and Proliferation	7.49E-08 - 3.56E-37		866
Cell Morphology	1.37E-07 - 5.49E-35		606
Cell Death and Survival	1.31E-07 - 2.52E-30		706
Cellular Assembly and Organization	3.03E-08 - 2.15E-29		452
Physiological System Development and Function	p-value		# Genes
Organismal Development	1.40E-07 - 1.18E-29		701
Tissue Development	1.53E-07 - 9.90E-28		801
Cardiovascular System	1.47E-07 - 5.03E-27		373
Embryonic Development	5.07E-08 – 7.56E-25		476
Organismal Survival	8.82E-09 - 1.54E-24		530
Top Up-regulated Genes	Log2 Ratio	Top Down-regulated Genes	Log2 Ratio
MYL1	7.55	GC	−8.52
SCD	7.02	FGB	−8.34
ACTN2	6.15	PLG	−8.23
CASQ2	5.91	AHSG	−8.18
TNNC2	5.72	FGA	−8.14
MYH3	5.58	HRG	−7.73
RIPPLY3	5.03	FGG	−7.62
TNNI2	4.44	ALB	−7.40
SMOC1	4.13	APOH	−6.93
ABHD3	4.08	KNG1	−6.63

Ingenuity Pathway Analysis (IPA) was used for functional annotation and mapping of 2026 “Analysis Ready” DE genes identified by RNA-Seq analysis of abdominal fat in four HG and four LG cockerels at 7 wk. These tissue samples were from the same HG and LG birds used for microarray analysis at this age