Table 4.

IPA summary of liver transcriptomes in samples from broiler chickens fed diets containing high and low lysine concentrations.

Top Canonical Pathways	p-Value	Overlap	Ratio
Sperm Motility	1.06 × 10−5	3.6%	8/225
Nitric Oxide Signaling in the Cardiovascular System	1.65 × 10−5	5.2%	6/115
Cellular Effects of Sildenafil (Viagra)	3.73 × 10−4	3.8%	5/131
Axonal Guidance signaling	2.39 × 10−3	1.6%	8/501
IL-15 Production	2.49 × 10−3	3.3%	4/121
Top Upstream Regulators	p-value of overlap	Predicted activation
TGFB1	3.63 × 10−8	Activated
ROCK2	5.12 × 10−7	-
PPARGC1A	2.24 × 10−6	-
IGFBP2	2.69 × 10−6	Activated
KLF4	2.73 × 10−6	Activated
Top Molecular and Cellular Functions	p-value	# Genes
Cellular Movement	3.87 × 10−3–9.67 × 10−7	39
Cellular Assembly and Organization	3.30 × 10−3–1.39 × 10−6	31
Cellular Function and Maintenance	3.30 × 10−3–1.39 × 10−6	37
Cellular Development	3.49 × 10−3–8.20 × 10−6	42
Cellular Growth and Proliferation	3.49 × 10−3–8.20 × 10−6	33
Physiological System Development and Function	p-value range	# Genes
Organismal Development	3.80 × 10−3–2.28 × 10−7	58
Tissue Development and Function	3.80 × 10−3–1.12 × 10−6	47
Respiratory System Development and Function	6.94 × 10−3–1.85 × 10−6	15
Cardiovascular System Development and Function	3.80 × 10−3–6.23 × 10−6	43
Tissue Development	3.80 × 10−3–6.50 × 10−6	33
Top Up-regulated genes	Low vs High lysine	Top Down-regulated genes	Low vs High lysine
ANO6	8.426	LRRC75B	−7.410
ADAMTS2	8.185	ANKRD22	−7.359
SEMA3C	7.651	ANGPTL4	−3.017
PRKAR2B	7.599	ADAMTS20	−2.87
UPK1B	7.567	MAGI2	−2.43
CYBRD1	7.489	KIF21A	−2.33
ADTRP	7.370	CCDC77	−2.30
ROR2	7.319	ABCC4	−2.20
ITGB6	7.267	CACNA1C	−2.01
PDE1C	7.267	LRP6	−1.56

Ingenuity pathway analysis (IPA) was used for functional analysis of DEGs found in the low lysine vs. high lysine contrast. The top 10 upregulated and downregulated DEGs are presented, along with their respective log2 ratio of treatment conditions.