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Table 3 Ingenuity Pathway Analysis on individual modules

From: Efficient identification of multiple pathways: RNA-Seq analysis of livers from 56Fe ion irradiated mice

Pathway Analysis
Module #Genes #Molecular Pathways Identified as Enriched (p-value ≤ 0.05) in Each Module
128Sirtuin Signaling Pathway, Mitochondrial Dysfunction, Oxidative Phosphorylation, LXR/RXR Activation, FXR/RXR Activation, NAD Biosynthesis III, Oleate Biosynthesis II, Histamine Degradation
211IL-9 Signaling, Transcriptional Network in Embryonic Stem Cells, Mitotic Roles of Polo-Like Kinase, GM-CSF Signaling, Growth Hormone Signaling, JAK/STAT Signaling, STAT3 Pathway
35No Pathway. 3 genes in this module are not Identified. Specifically, Gm28437, Gm28661, Gm29216. The other two are mir-122 (microRNA 122) and Gm10925 (ATP Synthase F0 subunit 6)
465Acyl-CoA Hydrolysis, Stearate Biosynthesis I, Pregnenolone Biosynthesis, Histidine Degradation VI, Ubiquinol-10-Biosynthesis, Asparagine Biosynthesis I, a-tocopherol Degradation, LSP/IL-1 Mediated Inhibition of RXR Function, FXR/RXR Activation
516Toll-like Receptor Signaling, Heme Degradation, IL-12 Signaling and Production in Macrophages, Acute Phase Response Signaling, Granulocyte Adhesion and Diapedesis, NF-kB Signaling, Agranulocyte Adhesion and Diapedesis, Production of Nitric oxide and ROS in Macrophages
680Nicotine Degradation II, Glutathione-mediated Detoxification, Circadian Rhythm Signaling, LPS/IL-1 Mediated Inhibition of RXR Function, Nicotine Degradation III, Adipogenesis Pathway, PXR/RXR Activation, Melatonin Degradation I
72No Pathway. Two genes (CYP26A1 and CYP26B1) are both part of cytochrome P450 family 26 subfamily A member 1 and subfamily B member 1. They are involved in Pregnenolone Biosynthesis, Histidine Degradation VI, Ubiquinol-10 Biosynthesis and RAR Activation
82No Pathway. Two genes (ANGPTL8 and HES1). HES1 is involved in Notch Signaling, VDR/RXR Activation.
921Unfolded protein response, Protein Ubiquitination Pathway, eNOS Signaling, Glucocorticoid Receptor Signaling, Endoplasmic Reticulum Stress Pathway (6 genes are heat shock proteins)
1089Acute Phase Response Signaling, IL-10 Signaling, IL-6 Signaling, Role of Macrophage, Fibroblasts and Endothelial Cells in Rheumatoid Arthritis, LXR/RXR Activation, B Cell Receptor Signaling, Altered T Cell and B Cell Signaling in Rheumatoid Arthritis, Hepatic Cholestatis
118No Pathway. 4 unidentified genes (Cm23935, Gm24187, Rn 18 s-rs5, Gm155644) and other 4 (Leucyl-tRNA synthetase 2, microRNA 6236, s-rRNA, l-rRNA)
1214No Pathway, basic helix-loop-helix family involved in Circadian Rhythm Signaling, Mir17hg, Small nuclear RNA (Snora57, Snora78) and 10 unidentified genes.
1369Estrogen-mediated S-phase Entry, Cell Cycle Regulation, Chronic Myeloid Leukemia Signaling, a-tocopherol Degradation
1463NRF2-mediated Oxidative Stress Pathway, Endoplasmic Reticulum Stress Pathway, Unfolded Protein Response, Death Receptor Signaling, RhoA Signaling, FXR/RXR Activation.