Table 1.

IPA summary of liver transcriptomes in-hatchling chicks--D1FED24h vs. D1FAST24h contrast

Top Canonical Pathways	p-value	Overlap	Ratio
Tryptophan Degradation (Eukaryotic)	1.15E-12	42.9%	9/21
Super-pathway of Cholesterol Biosynthesis	9.65E-10	28.6%	8/28
Cholesterol Biosynthesis I-III	4.48E-09	46.2%	6/13
NAD Biosynthesis II	9.23E-09	40.0%	6/15
Tryptophan Degradation 2-amino-3-carboxymuconate	9.83E-09	62.5%	5/8
Top Upstream Regulators	p-value of overlap	# Target genes
SREBF2	1.08E-15	19
PPARA	9.38E-14	27
SREBF1	2.55E-13	15
PPARG	3.15E-09	24
PPARGC1A	1.07E-08	18
Top Molecular and Cellular Functions	p-value	# Genes
Amino Acid Metabolism	9.80E-03 - 6.26E-11	25
Small Molecule Biochemistry	1.19–02 - 6.26E-11	94
Lipid Metabolism	1.19–02 - 2.16E-08	66
Molecular Transport	1.19–02 - 2.16E-08	68
Vitamin and Mineral Metabolism	5.45E-03 - 7.14E-07	21
Physiological System Development and Function	p-value	# Genes
Connective Tissue Development and Function	1.13E-02 - 3.88E-04	26
Digestive System Development and Function	1.02E-02 - 4.29E-04	17
Hepatic System Development and Function	6.03E-03 - 4.29E-04	17
Organ Morphology	1.13E-02 - 4.29E-04	21
Organismal Development	1.13E-02 - 4.29E-04	19
Top Up-regulated genes	D1FED24h/D1FAST24h	Top Down-regulated genes	D1FED24h/D1FAST24h
THRSPA	4.46	UPP2	−2.70
DIO2	3.24	CYP4A22	−2.01
HKDC1	3.22	HMGCS1	−1.89
ME1	2.75	CYP3A7	−1.73
PLIN2	2.63	TDH	−1.62
FADS2	2.47	FKBP5	−1.62
MSMO1	2.21	ADSL	−1.60
CYP51A1	2.06	ECI2	−1.52
SCD	1.74	CYP2C44	−1.44
BATF3	1.72	LDHB	−1.37

Ingenuity Pathway Analysis (IPA) was used for functional analysis of 259 DEGs (FDR adj. P ≤ 0.05) that were also “Analysis Ready” (AR)-DEGs from the D1FED24h vs. D1FAST24h contrast. The top 10 up-regulated and down-regulated AR-DEGs are presented along with their respective log2 ratio of treatment conditions