Table 1. Pathways significantly associated with NASH diagnosis.
| Pathway | Source | No. of genesin pathway | No. of SNPsin pathway | p(DS) | O.R. | q(O.R.) | Significantin HCC |
| Viral Messenger RNA Synthesis | Reactome | 65 | 46 | 0.000 | >10 | 2.51E-06 | |
| Recycling of eIF2:GDP | Reactome | 8 | 5 | 0.000 | 2.58 | 6.11E-03 | |
| mRNA Splicing - Major Pathway | Reactome | 106 | 79 | 0.002 | >10 | 2.63E-07 | |
| Elongation of Intron-Containing Transcripts and co-transcriptional mRNA splicing | Reactome | 44 | 37 | 0.002 | >10 | 1.11E-05 | |
| Cell cycle | KEGG | 82 | 64 | 0.003 | >10 | 8.51E-09 | |
| Terpenoid biosynthesis | KEGG | 6 | 6 | 0.003 | 4.73 | 4.22E-04 | |
| p53 signaling pathway | BioCarta | 13 | 12 | 0.004 | >10 | 3.33E-05 | |
| Leading Strand Synthesis | Reactome | 9 | 6 | 0.004 | 4.50 | 2.05E-03 | |
| inhibition of matrix metalloproteinases | BioCarta | 8 | 7 | 0.006 | 7.30 | 2.65E-04 | |
| Ethanol is oxidized by NAD+ to form acetaldehyde, NADH, and H+ | Reactome | 6 | 6 | 0.007 | 1.88 | 2.04E-03 | |
| cell cycle: g2/m checkpoint | BioCarta | 23 | 18 | 0.009 | >10 | 1.42E-06 | |
| regulation of transcriptional activity by pml | BioCarta | 12 | 10 | 0.010 | >10 | 1.25E-05 | |
| Cholesterol biosynthesis | Reactome | 8 | 8 | 0.012 | >10 | 4.52E-05 | |
| regulation of eif2 | BioCarta | 11 | 9 | 0.013 | 9.83 | 1.44E-04 | |
| Telomere C-strand (Lagging Strand) Synthesis | Reactome | 9 | 6 | 0.014 | 4.50 | 2.05E-03 | |
| Folding of actin by CCT/TriC | Reactome | 10 | 9 | 0.015 | 4.31 | 5.98E-03 | |
| Toll Like Receptor 4 (TLR4) Cascade | Reactome | 6 | 6 | 0.016 | 3.39 | 1.58E-03 | |
| Lagging Strand Synthesis | Reactome | 9 | 6 | 0.016 | 4.50 | 2.05E-03 | |
| RNA Polymerase III Transcription Termination | Reactome | 16 | 12 | 0.016 | >10 | 1.53E-05 | |
| Mitochondrial tRNA aminoacylation | Reactome | 21 | 18 | 0.017 | >10 | 1.16E-05 | |
| Direct p53 effectors | NCI-Nature | 139 | 117 | 0.022 | >10 | 8.51E-09 | |
| Pyrimidine biosynthesis (interconversion) | Reactome | 11 | 7 | 0.022 | 3.50 | 1.29E-02 | |
| Biosynthesis of steroids | KEGG | 23 | 21 | 0.023 | >10 | 8.69E-05 | |
| DNA strand elongation | Reactome | 9 | 6 | 0.023 | 4.50 | 2.05E-03 | |
| Regulation of CDC42 activity | NCI-Nature | 30 | 21 | 0.024 | >10 | 1.18E-06 | |
| mitochondrial fatty acid beta-oxidation of unsaturated fatty acids | Reactome | 6 | 5 | 0.028 | 2.00 | 4.20E-03 | |
| Processing of Capped Intron-Containing Pre-mRNA | Reactome | 35 | 30 | 0.028 | >10 | 4.06E-05 | |
| Aurora B signaling | NCI-Nature | 42 | 36 | 0.028 | >10 | 8.69E-06 | |
| eukaryotic protein translation | BioCarta | 20 | 13 | 0.029 | 8.75 | 2.05E-03 | |
| O-Glycan biosynthesis | KEGG | 30 | 26 | 0.029 | >10 | 6.89E-08 | |
| the prc2 complex sets long-term gene silencing through modification of histone tails | BioCarta | 14 | 11 | 0.031 | >10 | 7.00E-05 | |
| Bile acid biosynthesis | KEGG | 31 | 29 | 0.032 | >10 | 1.95E-05 | |
| Regulation of retinoblastoma protein | NCI-Nature | 65 | 57 | 0.033 | >10 | 1.42E-07 | |
| E2F transcription factor network | NCI-Nature | 72 | 57 | 0.033 | >10 | 4.11E-07 | |
| Gamma-carboxylation, transport, and amino-terminal cleavage of proteins | Reactome | 8 | 6 | 0.034 | 2.62 | 9.75E-03 | yes |
| Trafficking of AMPA receptors | Reactome | 5 | 5 | 0.034 | 1.14 | 3.41E-01 | |
| Phosphorylation of CD3 and TCR zeta chains | Reactome | 8 | 5 | 0.034 | 4.30 | 2.02E-04 | |
| Antigen processing and presentation | KEGG | 64 | 38 | 0.037 | >10 | 1.22E-05 | yes |
| Hemostasis | Reactome | 5 | 5 | 0.040 | >10 | 2.92E-08 | |
| Prostate cancer | KEGG | 80 | 67 | 0.040 | 3.10 | 1.28E-03 | |
| deregulation of cdk5 in alzheimers disease | BioCarta | 7 | 7 | 0.040 | 3.72 | 1.94E-03 | |
| Processive synthesis on the C-strand of the telomere | Reactome | 6 | 5 | 0.043 | 2.57 | 7.36E-03 | |
| Electron Transport Chain | Reactome | 66 | 48 | 0.043 | >10 | 4.67E-06 | |
| BARD1 signaling events | NCI-Nature | 29 | 27 | 0.044 | >10 | 1.59E-05 | |
| cyclins and cell cycle regulation | BioCarta | 23 | 20 | 0.045 | >10 | 2.84E-05 | |
| 1- and 2-Methylnaphthalene degradation | KEGG | 13 | 12 | 0.046 | 3.70 | 2.15E-03 | |
| Aminoacyl-tRNA biosynthesis | KEGG | 39 | 33 | 0.048 | >10 | 6.02E-06 | |
| trefoil factors initiate mucosal healing | BioCarta | 37 | 31 | 0.048 | >10 | 2.37E-06 | |
| Nectin adhesion pathway | NCI-Nature | 28 | 28 | 0.049 | >10 | 8.58E-07 |
Note: Pathway-length based resampled p-values, denoted as p(DS), are given for significant pathways (p<0.05), along with odds ratios and associated FDRs for a logistic regression model. The pathways previously shown to be associated with HCC are marked.