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Table 2 IPA summary of microarray analysis of liver in riboflavin-deficient chick embryos at e13

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
 IL-8 Signaling 3.85E-05 5.1% 10/197
 JAK/Stat Signaling 2.14E-04 7.2% 6/83
 EIF2 Signaling 4.85E-04 4.1% 9/221
 RANK Signaling in Osteoclasts 6.17E-04 5.9% 6/101
 Proline Biosynthesis I 6.22E-04 50.0% 2/4
Top Upstream Regulators p-value of overlap # Target genes
 E2F1 3.40E-07 19
 MYC 5.14E-07 30
 ATF4 1.60E-06 10
 TCF3 4.20E-06 12
 PPARA 9.09E-06 16
Top Molecular and Cellular Functions p-value # Genes
 Amino Acid Metabolism 1.03E-02 - 1.07E-07 22
 Small Molecule Biochemistry 1.03E-02 - 1.07E-07 58
 Molecular Transport 1.03E-02 - 5.02E-06 59
 Cell Cycle 1.03E-02 - 8.67E-06 38
 Cell Death and Survival 1.03E-02 - 5.35E-05 68
Physiological System Development and Function p-value # Genes
 Endocrine System Development and Function 1.03E-02 - 5.02E-06 7
 Organismal Development 1.03E-02 - 9.26E-06 64
 Cardiovascular System Development and Function 8.81E-03 - 1.41E-05 31
 Organ Morphology 1.03E-02 - 1.41E-05 40
 Digestive System Development and Function 9.14E-03 - 1.74E-05 34
Hepatotoxicity p-value # Genes
 Liver Proliferation 2.04E-02 - 8.34E-05 10
 Liver Steatosis 4.45E-01 - 1.55E-03 11
 Liver Fibrosis 3.91E-01 - 1.72E-03 9
 Hepatocellular Carcinoma 2.28E-01 - 2.89E-03 19
 Liver Hyperplasia/Hyper-proliferation 2.43E-01 - 2.89E-03 76
Top Up-regulated genes log2 Rf+/Rf- Top Down-regulated genes log2 Rf+/Rf-
CHODL 1.41 ANKRD22 −2.74
FAM84A 1.27 OVCH2 −2.42
PROZ 1.24 EIF5B −2.01
TOP1 1.21 ALDH18A1 −1.99
COMT 1.18 CA2 −1.97
F9 1.17 LGALS1 −1.77
RUFY2 1.17 RBP7 −1.75
GATM 1.14 PYCR2 −1.68
F2 1.09 PLIN2 −1.67
GC 1.07 ASNS − 1.38
  1. Ingenuity Pathway Analysis (IPA) of 221 “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 13 (e13). P-values were determined by IPA using Fisher’s Exact Test and represent the likelihood that AR-DE genes are over-represented and associated with a particular biological process or pathway. The percent overlap and ratios were calculated for the number of observed AR genes compared to the number of known genes for that category represented in the Ingenuity® Knowledge Base