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

Nia, Anna M.; Chen, Tianlong; Barnette, Brooke L.; Khanipov, Kamil; Ullrich, Robert L.; Bhavnani, Suresh K.; Emmett, Mark R.

doi:10.1186/s12859-020-3446-5

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
1	28	Sirtuin Signaling Pathway, Mitochondrial Dysfunction, Oxidative Phosphorylation, LXR/RXR Activation, FXR/RXR Activation, NAD Biosynthesis III, Oleate Biosynthesis II, Histamine Degradation
2	11	IL-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
3	5	No 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)
4	65	Acyl-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
5	16	Toll-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
6	80	Nicotine 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
7	2	No 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
8	2	No Pathway. Two genes (ANGPTL8 and HES1). HES1 is involved in Notch Signaling, VDR/RXR Activation.
9	21	Unfolded protein response, Protein Ubiquitination Pathway, eNOS Signaling, Glucocorticoid Receptor Signaling, Endoplasmic Reticulum Stress Pathway (6 genes are heat shock proteins)
10	89	Acute 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
11	8	No Pathway. 4 unidentified genes (Cm23935, Gm24187, Rn 18 s-rs5, Gm155644) and other 4 (Leucyl-tRNA synthetase 2, microRNA 6236, s-rRNA, l-rRNA)
12	14	No Pathway, basic helix-loop-helix family involved in Circadian Rhythm Signaling, Mir17hg, Small nuclear RNA (Snora57, Snora78) and 10 unidentified genes.
13	69	Estrogen-mediated S-phase Entry, Cell Cycle Regulation, Chronic Myeloid Leukemia Signaling, a-tocopherol Degradation
14	63	NRF2-mediated Oxidative Stress Pathway, Endoplasmic Reticulum Stress Pathway, Unfolded Protein Response, Death Receptor Signaling, RhoA Signaling, FXR/RXR Activation.

Back to article page