Table 2.
List of pathways involved in nonalcoholic fatty liver disease selected from significant Q-values independently on whether they represent the effect of gene/s or metabolite/s only
| Pathway name | Pathway source | Q-joint |
| Adipogenesis | Wikipathways | 2.00E-17 |
| Non-alcoholic fatty liver disease (NAFLD) - homo sapiens (human) | KEGG | 2.33E-17 |
| Metabolism | Reactome | 3.72E-17 |
| AGE-RAGE pathway | Wikipathways | 4.22E-17 |
| Vitamin B12 Metabolism | Wikipathways | 5.24E-17 |
| Hepatitis B - homo sapiens (human) | KEGG | 1.79E-16 |
| Folate metabolism | Wikipathways | 1.29E-15 |
| Selenium micronutrient network | Wikipathways | 3.87E-15 |
| TNF signaling pathway - homo sapiens (human) | KEGG | 5.77E-15 |
| JAK-STAT-core | Signalink | 1.99E-14 |
| Adipocytokine signaling pathway - homo sapiens (human) | KEGG | 7.07E-14 |
| Nuclear receptors meta-pathway | Wikipathways | 1.26E-13 |
| IL1 and megakaryocytes in obesity | Wikipathways | 2.73E-13 |
| AGE-RAGE signaling pathway in diabetic complications - homo sapiens (human) | KEGG | 3.79E-13 |
| Spinal cord injury | Wikipathways | 5.44E-13 |
| Malaria - homo sapiens (human) | KEGG | 7.09E-13 |
| Metabolism of lipids and lipoproteins | Reactome | 7.09E-13 |
| SLC-mediated transmembrane transport | Reactome | 1.23E-12 |
| Pathways in cancer - homo sapiens (human) | KEGG | 1.41E-12 |
| Inflammatory bowel disease (IBD) - homo sapiens (human) | KEGG | 2.25E-12 |
| Lung fibrosis | Wikipathways | 2.63E-12 |
| Integrated pancreatic cancer pathway | Wikipathways | 3.10E-12 |
| PI3K-Akt signaling pathway - homo sapiens (human) | KEGG | 3.28E-12 |
| Chagas disease (American trypanosomiasis) - homo sapiens (human) | KEGG | 4.67E-12 |
| HIF-1 signaling pathway - homo sapiens (human) | KEGG | 4.67E-12 |
| AMPK signaling pathway - homo sapiens (human) | KEGG | 9.56E-12 |
| Transmembrane transport of small molecules | Reactome | 9.66E-12 |
| Central carbon metabolism in cancer - homo sapiens (human) | KEGG | 1.41E-11 |
| Jak-STAT signaling pathway - homo sapiens (human) | KEGG | 5.75E-11 |
| DNA damage response (only ATM dependent) | Wikipathways | 7.27E-11 |
| Cytokine-cytokine receptor interaction - homo sapiens (human) | KEGG | 1.01E-10 |
| Longevity regulating pathway - homo sapiens (human) | KEGG | 1.02E-10 |
| Toll-like receptor signaling pathway | Wikipathways | 2.12E-10 |
| Toll-like receptor signaling pathway - homo sapiens (human) | KEGG | 3.94E-10 |
| Toxoplasmosis - homo sapiens (human) | KEGG | 4.73E-10 |
| ABC transporters - homo sapiens (human) | KEGG | 5.94E-10 |
| Transport of glucose and other sugars bile salts and organic acids metal ions and amine compounds | Wikipathways | 8.40E-10 |
| Leukotriene biosynthesis | HumanCyc | 8.71E-10 |
| Insulin resistance - homo sapiens (human) | KEGG | 1.14E-09 |
| Transport of glucose and other sugars bile salts and organic acids metal ions and amine compounds | Reactome | 1.91E-09 |
| Sudden infant death syndrome (SIDS) susceptibility pathways | Wikipathways | 2.12E-09 |
| Cytokines and inflammatory response | Wikipathways | 2.17E-09 |
| AP-1 transcription factor network | PID | 2.22E-09 |
| FoxO signaling pathway - homo sapiens (human) | KEGG | 3.05E-09 |
| Leptin signaling pathway | Wikipathways | 3.57E-09 |
| Transport of inorganic cations-anions and amino acids-oligopeptides | Wikipathways | 4.27E-09 |
| Oncostatin M signaling pathway | Wikipathways | 5.72E-09 |
| Focal adhesion-PI3K-Akt-mTOR-signaling pathway | Wikipathways | 6.53E-09 |
| Amino acid and oligopeptide SLC transporters | Reactome | 1.10E-08 |
| Apoptosis | Wikipathways | 1.41E-08 |
| Apoptotic signaling pathway | Wikipathways | 1.41E-08 |
| Photodynamic therapy-induced NF-kB survival signaling | Wikipathways | 1.84E-08 |
| JAK STAT molecularvariation 1 | INOH | 2.04E-08 |
| MAPK signaling pathway | Wikipathways | 2.04E-08 |
| Aryl hydrocarbon receptor | Wikipathways | 2.35E-08 |
| Transport of inorganic cations/anions and amino acids/oligopeptides | Reactome | 2.40E-08 |
| tRNA aminoacylation | Wikipathways | 3.03E-08 |
| gamma-glutamyl cycle | HumanCyc | 3.61E-08 |
| Glucose homeostasis | Wikipathways | 4.08E-08 |
| Validated transcriptional targets of AP1 family members Fra1 and Fra2 | PID | 4.13E-08 |
| Hepatitis C and hepatocellular carcinoma | Wikipathways | 4.26E-08 |
| Calcineurin-regulated NFAT-dependent transcription in lymphocytes | PID | 4.29E-08 |
| Prostate cancer - homo sapiens (human) | KEGG | 4.29E-08 |
| Tuberculosis - homo sapiens (human) | KEGG | 4.45E-08 |
| Apoptosis - homo sapiens (human) | KEGG | 4.54E-08 |
| tRNA charging | HumanCyc | 5.96E-08 |
| Transcription factor regulation in adipogenesis | Wikipathways | 6.27E-08 |
| Sterol regulatory element-binding proteins (SREBP) signalling | Wikipathways | 6.27E-08 |
| Integrated lung cancer pathway | Wikipathways | 6.43E-08 |
| TNF related weak inducer of apoptosis (TWEAK) signaling pathway | Wikipathways | 8.14E-08 |
| mRNA protein and metabolite inducation pathway by cyclosporin A | Wikipathways | 8.47E-08 |
| PPAR signaling pathway | Wikipathways | 9.54E-08 |
| Immune system | Reactome | 9.57E-08 |
| Regulation of lipid metabolism by peroxisome proliferator-activated receptor alpha (PPARalpha) | Wikipathways | 1.13E-07 |
| AMP-activated protein kinase (AMPK) signaling | Wikipathways | 1.34E-07 |
| Photodynamic therapy-induced NFE2L2 (NRF2) survival signaling | Wikipathways | 1.52E-07 |
| Leptin insulin overlap | Wikipathways | 1.65E-07 |
| Class I MHC mediated antigen processing and presentation | Wikipathways | 1.73E-07 |
| Caspase cascade in apoptosis | PID | 1.99E-07 |
| Overview of nanoparticle effects | Wikipathways | 2.17E-07 |
| Alpha6Beta4Integrin | NetPath | 2.29E-07 |
| VEGFA-VEGFR2 signaling pathway | Wikipathways | 2.30E-07 |
| HIV-1 Nef: Negative effector of Fas and TNF-alpha | PID | 2.65E-07 |
| Innate immune system | Reactome | 2.69E-07 |
| Na+/Cl- dependent neurotransmitter transporters | Reactome | 3.10E-07 |
| Colorectal cancer - homo sapiens (human) | KEGG | 3.42E-07 |
| Regulation of toll-like receptor signaling pathway | Wikipathways | 3.64E-07 |
| stress induction of hsp regulation | BioCarta | 3.64E-07 |
| Amino acid transport across the plasma membrane | Reactome | 3.72E-07 |
| Programmed cell death | Reactome | 3.85E-07 |
| Apoptosis modulation and signaling | Wikipathways | 4.42E-07 |
| SREBF and miR33 in cholesterol and lipid homeostasis | Wikipathways | 4.84E-07 |
| JAK STAT pathway and regulation | INOH | 5.42E-07 |
OMICs-integrative analysis was performed using the IMPaLA (Integrated Molecular Pathway Level Analysis, http://impala.molgen.mpg.de)[67] platform. A joined adjusted P-value (Q-value) was calculated to control for multiple testing by false discovery rate.