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Table 3 IPA summary of microarray analysis of liver in riboflavin-deficient chick embryos at e15

From: Transcriptional profiling of liver in riboflavin-deficient chicken embryos explains impaired lipid utilization, energy depletion, massive hemorrhaging, and delayed feathering

Top Canonical Pathways

p-value

Overlap

Ratio

 EIF2 Signaling

9.53E-08

13.1%

29/221

 Intrinsic Prothrombin Activation Pathway

1.99E-07

34.5%

10/29

 LXR/RXR Activation

2.25E-07

16.5%

20/121

 Tryptophan Degradation III

3.58E-07

37.5%

9/24

 Super-pathway of Cholesterol Biosynthesis

1.62E-06

32.1%

9/28

Top Upstream Regulators

p-value of overlap

# Target genes

 HNF4A

4.81E-14

161

 MYC

5.70E-11

93

 PPARA

1.34E-10

50

 ESR1

5.09E-10

150

 NFE2L2

9.70E-08

105

Top Molecular and Cellular Functions

p-value

# Genes

 Protein Synthesis

2.61E-03 - 8.55E-11

139

 Lipid Metabolism

3.08E-03 - 7.82E-10

173

 Small Molecule Biochemistry

3.33E-03 - 7.82E-10

212

 Amino Acid Metabolism

3.19E-03 - 4.41E-09

47

 Vitamin and Mineral Metabolism

2.18E-03 - 7.36E-09

61

Physiological System Development and Function

p-value

# Genes

 Tissue Morphology

3.00E-03 - 1.44E-06

131

 Organismal Development

3.31E-03 - 1.84E-06

246

 Connective Tissue Development and Function

2.92E-03 - 5.93E-06

158

 Tissue Development

3.31E-03 - 5.93E-06

159

 Digestive System Development and Function

1.85E-03 - 7.57E-06

77

Hepatotoxicity

p-value

# Genes

 Hepatocellular Carcinoma

6.04E-01 - 9.22E-05

64

 Liver Hyperplasia/Hyperproliferation

6.04E-01 - 9.22E-05

313

 Liver Fibrosis

4.36E-01 - 2.50E-04

23

 Liver Proliferation

4.60E-01 - 2.50E-04

24

 Liver Necrosis/Cell Death

4.04E-01 - 1.85E-03

20

Top Up-regulated genes

log2 Rf+/Rf-

Top Down-regulated genes

log2 Rf+/Rf-

 FKERa

3.43

HMGCS1

−3.61

 AHSG

2.57

OVCH2

−2.61

 SPINK5

2.38

ANKRD22

−2.58

 ALB

2.27

HMGCL

−2.40

 SLC13A3

2.21

LGALS1

−2.34

 SERPINC1

2.17

RBP7

−2.09

 ANGPTL3

2.14

ACAT2

−1.99

 PLG

2.10

TPPP

−1.92

 GATM

2.06

EIF5B

−1.78

 NEBL

2.06

RPL22L1

−1.78

  1. Ingenuity Pathway Analysis (IPA) was used for functional analysis of 929 “Analysis Ready” (AR) and differentially expressed (DE; FDR ≤ 0.05) (AR-DE) genes from riboflavin-rescued (Rf+) and riboflavin-deficient (Rf-) chickens on embryonic day 15 (e15)
  2. aNote: FKER was the highest expressed gene found in liver of Rf + embryos at e15 (see Additional file 3, Riboflavin_e15 worksheet). However, this avian-specific gene was not annotated in the Ingenuity® Knowledge Base and therefore rejected by IPA
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BMC Genomics

ISSN: 1471-2164

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