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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