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Table 1 Ingenuity Pathway Analysis (IPA) of the liver transcriptome in the E vs. H contrast

From: Transcriptional profiling of liver during the critical embryo-to-hatchling transition period in the chicken (Gallus gallus)

Top Canonical Pathways

p-value

Overlap

Ratio

 Super-pathway of Cholesterol Biosynthesis

1.00E-12

73.9%

17/23

 Cholesterol Biosynthesis I-III

1.29E-08

90.0%

9/10

 LXR/RXR Activation

1.24E-07

33.3%

24/72

 FXR/RXR Activation

1.14E-07

31.6%

25/79

 Triacylglycerol Biosynthesis

1.29E-06

43.8%

14/32

Top Upstream Regulators

p-value of overlap

# Target genes

 PPARA

1.00E-26

94

 SREBF1

5.15E-17

51

 TP53

8.71E-16

186

 SREBF2

2.88E-14

28

 FOXO1

4.25E-12

74

Top Molecular and Cellular Functions

p-value

# Genes

 Amino Acid Metabolism

1.97E-03 - 6.58E-14

72

 Small Molecule Biochemistry

1.97E-03 - 6.58E-14

358

 Lipid Metabolism

1.97E-03 - 2.36E-13

284

 Molecular Transport

1.82E-03 - 2.36E-13

231

 Vitamin and Mineral Metabolism

1.13E-03 - 3.43E-12

88

Physiological System Development and Function

p-value

# Genes

 Tissue Morphology

1.50E-03 - 1.28E-06

186

 Organismal Development

1.87E-03 - 1.63E-06

373

 Organ Morphology

1.16E-03 - 4.30E-06

123

 Renal and Urological System Development and Function

1.13E-03 - 4.30E-06

66

 Embryonic Development

1.87E-03 - 1.19E-05

195

Toxicity Functions

p-value

# Genes

Ratio

 LXR/RXR Activation

1.67E-07

32.9%

24/73

 FXR/RXR Activation

2.14E-07

31.6%

25/79

 Cholesterol Biosynthesis

2.69E-07

66.7%

10/15

 LPS/IL-1 Mediated Inhibition of RXR Function

2.95E-05

22.1%

32/145

 Liver Necrosis/Cell Death

5.92E-05

19.3%

42/218

Top Up-regulated genes

log2 Ratio (E/H)

Top Down-regulated genes

log2 Ratio (E/H)

 MOGAT1

5.44

THRSPA

−7.15

 DIO3

5.01

SLCO1A2

−5.82

 PPM1K

4.65

ELOVL5

−5.60

 PDK4

3.95

CDO1

−5.23

 SLC13A3

3.82

FASN

−5.08

 ITGBL1

3.66

SQLE

−4.92

 TTLL2

3.64

DIO2

−4.84

 ALKAL2

3.18

NSDHL

− 4.74

 RET

3.16

CYP7A1

−4.73

 ASCL1

3.11

AFMID

−4.44

  1. Ingenuity Pathway Analysis (IPA) provided a functional analysis of 1272 “Analysis Ready” (AR) and differentially expressed genes (AR-DEGs) in the embryo vs. hatchling contrast. The P-values were derived by IPA from Fisher’s Exact Test, which indicates the likelihood of over-representation of AR-DEGs in particular canonical pathways and biological processes. The top 10 up-regulated genes in embryo (E) liver have positive E/H ratios, whereas the 10 down-regulated genes possess negative log2 ratios (E/H) which indicates higher expression in hatchling (H) liver
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BMC Genomics

ISSN: 1471-2164

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