Table 1. significant pathways from the pathway analysis of differently expressed AD genes in expression dataset.
| Classification | Pathway ID | Pathway Name | C | O | E | R | rawP | adjP |
|---|---|---|---|---|---|---|---|---|
| Immunity | hsa05322 | Systemic lupus erythematosus | 136 | 13 | 3.72 | 3.5 | 9.70E-05 | 4.00E-04 |
| Immunity | hsa05323 | Rheumatoid arthritis | 91 | 7 | 2.49 | 2.81 | 1.25E-02 | 1.70E-02 |
| Immunity | hsa04666 | Fc gamma R-mediated phagocytosis | 94 | 9 | 2.57 | 3.5 | 1.10E-03 | 2.90E-03 |
| Immunity | hsa04062 | Chemokine signaling pathway | 189 | 13 | 5.17 | 2.52 | 2.20E-03 | 4.80E-03 |
| Immunity | hsa04640 | Hematopoietic cell lineage | 88 | 8 | 2.41 | 3.33 | 2.80E-03 | 5.50E-03 |
| Immunity | hsa04650 | Natural killer cell mediated cytotoxicity | 136 | 10 | 3.72 | 2.69 | 4.30E-03 | 7.30E-03 |
| Immunity | hsa04670 | Leukocyte transendothelial migration | 116 | 9 | 3.17 | 2.84 | 4.70E-03 | 7.80E-03 |
| Immunity | hsa04660 | T cell receptor signaling pathway | 108 | 8 | 2.95 | 2.71 | 9.70E-03 | 1.41E-02 |
| Immunity | hsa04622 | RIG-I-like receptor signaling pathway | 71 | 6 | 1.94 | 3.09 | 1.31E-02 | 1.75E-02 |
| Immunity | hsa04662 | B cell receptor signaling pathway | 75 | 6 | 2.05 | 2.93 | 1.68E-02 | 2.22E-02 |
| Immunity | hsa04612 | Antigen processing and presentation | 76 | 6 | 2.08 | 2.89 | 1.78E-02 | 2.29E-02 |
| Metabolism | hsa00190 | Oxidative phosphorylation | 132 | 17 | 3.61 | 4.71 | 1.33E-07 | 2.19E-06 |
| Metabolism | hsa00360 | Phenylalanine metabolism | 17 | 7 | 0.46 | 15.06 | 1.72E-07 | 2.43E-06 |
| Metabolism | hsa00020 | Citrate cycle (TCA cycle) | 30 | 7 | 0.82 | 8.54 | 1.32E-05 | 9.48E-05 |
| Metabolism | hsa00250 | Alanine, aspartate and glutamate metabolism | 32 | 7 | 0.87 | 8 | 2.07E-05 | 1.00E-04 |
| Metabolism | hsa00830 | Retinol metabolism | 64 | 9 | 1.75 | 5.14 | 5.91E-05 | 3.00E-04 |
| Metabolism | hsa00500 | Starch and sucrose metabolism | 54 | 8 | 1.48 | 5.42 | 1.00E-04 | 4.00E-04 |
| Metabolism | hsa00350 | Tyrosine metabolism | 41 | 7 | 1.12 | 6.25 | 1.00E-04 | 4.00E-04 |
| Metabolism | hsa00270 | Cysteine and methionine metabolism | 36 | 6 | 0.98 | 6.1 | 4.00E-04 | 1.30E-03 |
| Metabolism | hsa00983 | Drug metabolism - other enzymes | 52 | 7 | 1.42 | 4.92 | 5.00E-04 | 1.50E-03 |
| Metabolism | hsa00053 | Ascorbate and aldarate metabolism | 26 | 5 | 0.71 | 7.03 | 6.00E-04 | 1.70E-03 |
| Metabolism | hsa00980 | Metabolism of xenobiotics by cytochrome P450 | 71 | 8 | 1.94 | 4.12 | 7.00E-04 | 2.00E-03 |
| Metabolism | hsa00982 | Drug metabolism - cytochrome P450 | 73 | 8 | 2 | 4.01 | 9.00E-04 | 2.50E-03 |
| Metabolism | hsa00040 | Pentose and glucuronate interconversions | 32 | 5 | 0.87 | 5.72 | 1.70E-03 | 3.90E-03 |
| Metabolism | hsa00140 | Steroid hormone biosynthesis | 56 | 6 | 1.53 | 3.92 | 4.20E-03 | 7.30E-03 |
| Metabolism | hsa00620 | Pyruvate metabolism | 40 | 5 | 1.09 | 4.57 | 4.50E-03 | 7.60E-03 |
| Metabolism | hsa00380 | Tryptophan metabolism | 42 | 5 | 1.15 | 4.35 | 5.60E-03 | 8.90E-03 |
| Metabolism | hsa00860 | Porphyrin and chlorophyll metabolism | 43 | 5 | 1.18 | 4.25 | 6.20E-03 | 9.60E-03 |
| Metabolism | hsa00514 | Other types of O-glycan biosynthesis | 46 | 5 | 1.26 | 3.98 | 8.20E-03 | 1.23E-02 |
| Metabolism | hsa00561 | Glycerolipid metabolism | 50 | 5 | 1.37 | 3.66 | 1.16E-02 | 1.59E-02 |
| Metabolism | hsa00562 | Inositol phosphate metabolism | 57 | 5 | 1.56 | 3.21 | 1.96E-02 | 2.49E-02 |
| Metabolism | hsa00010 | Glycolysis / Gluconeogenesis | 65 | 5 | 1.78 | 2.81 | 3.25E-02 | 3.83E-02 |
| Metabolism | hsa00534 | Glycosaminoglycan biosynthesis - heparan sulfate / heparin | 26 | 5 | 0.71 | 7.03 | 6.00E-04 | 1.70E-03 |
C, the number of reference genes in the category; O, the number of genes in the gene set and also in the category; E, expected number in the category; R, the ratio of enrichment, rawP, the p value from hypergeometric test; adjP, the p value adjusted by the multiple test adjustment.