Table 1.
KEGG pathway enrichment analysis of RNASeq data of 470 TCGA SKCM patients with adjusted p-values below 1.00E-03. Pathway enrichment on pyrimidine metabolism is highlighted in italic.
| Pathway name | KEGG ID | Number of deregulated genes in TCGA SKCM RNASeq | Expected number | Ratio of enrichment | p-value from hypergeometric test | adjusted p-value by multiple test adjustment | Number of reference genes in pathway | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| down | up | down | up | down | up | down | up | down | up | |||
| Metabolic pathways | ID:01100 | 359 | 216 | 107.77 | 119.87 | 3.33 | 1.80 | 3.16E-99 | 5.34E-18 | 6.79E-97 | 9.19E-17 | 1130 |
| Pathways in cancer | ID:05200 | 76 | 108 | 31.09 | 34.58 | 2.44 | 3.12 | 1.64E-13 | 3.70E-28 | 5.88E-12 | 1.94E-26 | 326 |
| Pyrimidine metabolism | ID:00240 | 34 | 23 | 9.44 | 10.50 | 3.60 | 2.19 | 1.30E-11 | 2.00E-04 | 3.49E-10 | 4.00E-04 | 99 |
| Purine metabolism | ID:00230 | 42 | 44 | 15.45 | 17.19 | 2.72 | 2.56 | 1.37E-09 | 3.14E-09 | 3.27E-08 | 1.35E-08 | 162 |
| Melanogenesis | ID:04916 | 31 | 27 | 9.63 | 10.71 | 3.22 | 2.52 | 2.41E-09 | 4.49E-06 | 5.18E-08 | 1.18E-05 | 101 |
| Endocytosis | ID:04144 | 47 | 60 | 19.17 | 21.32 | 2.45 | 2.81 | 5.73E-09 | 5.40E-14 | 1.03E-07 | 4.73E-13 | 201 |
| Phagosome | ID:04145 | 38 | 50 | 14.59 | 16.23 | 2.60 | 3.08 | 2.86E-08 | 1.40E-13 | 4.10E-07 | 1.09E-12 | 153 |
| Peroxisome | ID:04146 | 24 | 21 | 7.53 | 8.38 | 3.19 | 2.51 | 1.84E-07 | 5.44E-05 | 2.20E-06 | 1.00E-04 | 79 |
| Spliceosome | ID:03040 | 32 | 34 | 12.11 | 13.47 | 2.64 | 2.52 | 2.41E-07 | 2.68E-07 | 2.73E-06 | 8.28E-07 | 127 |
| Focal adhesion | ID:04510 | 43 | 68 | 19.07 | 21.22 | 2.25 | 3.21 | 3.12E-07 | 5.81E-19 | 3.35E-06 | 1.11E-17 | 200 |
| Wnt signaling pathway | ID:04310 | 35 | 46 | 14.31 | 15.91 | 2.45 | 2.89 | 5.01E-07 | 1.59E-11 | 4.49E-06 | 1.04E-10 | 150 |
| MAPK signaling pathway | ID:04010 | 52 | 86 | 25.56 | 28.43 | 2.03 | 3.02 | 6.02E-07 | 1.11E-21 | 5.18E-06 | 2.91E-20 | 268 |
| Neurotrophin signaling | ID:04722 | 31 | 36 | 12.11 | 13.47 | 2.56 | 2.67 | 7.79E-07 | 2.45E-08 | 6.44E-06 | 8.72E-08 | 127 |
| Actin cytoskeleton regulation | ID:04810 | 43 | 68 | 20.31 | 22.60 | 2.12 | 3.01 | 1.86E-06 | 2.51E-17 | 1.45E-05 | 3.51E-16 | 213 |
| Protein processing in ER | ID:04141 | 36 | 58 | 15.74 | 17.50 | 2.29 | 3.31 | 1.91E-06 | 3.70E-17 | 1.45E-05 | 4.86E-16 | 165 |
| Tight junction | ID:04530 | 30 | 32 | 12.59 | 14.00 | 2.38 | 2.29 | 5.59E-06 | 6.03E-06 | 3.43E-05 | 1.54E-05 | 132 |
| Ubiquitin mediated proteolysis | ID:04120 | 30 | 43 | 12.87 | 14.32 | 2.33 | 3.00 | 9.00E-06 | 1.80E-11 | 5.09E-05 | 1.15E-10 | 135 |
| Calcium signaling pathway | ID:04020 | 36 | 52 | 16.88 | 18.78 | 2.13 | 2.77 | 1.03E-05 | 4.91E-12 | 5.68E-05 | 3.33E-11 | 177 |
| GnRH signaling pathway | ID:04912 | 24 | 27 | 9.63 | 10.71 | 2.49 | 2.52 | 2.13E-05 | 4.49E-06 | 1.00E-04 | 1.18E-05 | 101 |
| Small cell lung cancer | ID:05222 | 21 | 26 | 8.11 | 9.02 | 2.59 | 2.88 | 3.67E-05 | 4.06E-07 | 2.00E-04 | 1.24E-06 | 85 |
| Oocyte meiosis | ID:04114 | 25 | 29 | 10.68 | 11.88 | 2.34 | 2.44 | 4.48E-05 | 4.05E-06 | 2.00E-04 | 1.10E-05 | 112 |
| ECM-receptor interaction | ID:04512 | 21 | 24 | 8.11 | 9.02 | 2.59 | 2.66 | 3.67E-05 | 5.36E-06 | 2.00E-04 | 1.39E-05 | 85 |
| N-Glycan biosynthesis | ID:00510 | 15 | 16 | 4.67 | 5.20 | 3.21 | 3.08 | 3.24E-05 | 2.71E-05 | 2.00E-04 | 6.39E-05 | 49 |
| Renal cell carcinoma | ID:05211 | 18 | 33 | 6.68 | 7.43 | 2.70 | 4.44 | 7.37E-05 | 1.18E-14 | 3.00E-04 | 1.13E-13 | 70 |
| Acute myeloid leukemia | ID:05221 | 16 | 23 | 5.44 | 6.05 | 2.94 | 3.80 | 5.84E-05 | 5.29E-09 | 3.00E-04 | 2.10E-08 | 57 |
| VEGF signaling pathway | ID:04370 | 19 | 25 | 7.25 | 8.06 | 2.62 | 3.10 | 7.13E-05 | 1.41E-07 | 3.00E-04 | 4.42E-07 | 76 |
| Fc gamma phagocytosis | ID:04666 | 21 | 38 | 8.96 | 9.97 | 2.34 | 3.81 | 2.00E-04 | 5.66E-14 | 7.00E-04 | 4.75E-13 | 94 |
| RNA transport | ID:03013 | 29 | 49 | 14.40 | 16.02 | 2.01 | 3.06 | 2.00E-04 | 3.31E-13 | 7.00E-04 | 2.48E-12 | 151 |
| Adipocytokine signaling | ID:04920 | 17 | 22 | 6.49 | 7.21 | 2.62 | 3.05 | 2.00E-04 | 1.07E-06 | 7.00E-04 | 3.16E-06 | 68 |
| Phosphatidylinositol signaling | ID:04070 | 18 | 31 | 7.44 | 8.27 | 2.42 | 3.75 | 3.00E-04 | 1.94E-11 | 9.00E-04 | 1.20E-10 | 78 |
| Gap junction | ID:04540 | 20 | 30 | 8.58 | 9.55 | 2.33 | 3.14 | 3.00E-04 | 5.82E-09 | 9.00E-04 | 2.26E-08 | 90 |
| Melanoma | ID:05218 | 17 | 20 | 6.77 | 7.53 | 2.51 | 2.66 | 3.00E-04 | 3.29E-05 | 9.00E-04 | 7.51E-05 | 71 |
| Natural killer cell cytotoxicity | ID:04650 | - | 61 | - | 14.43 | - | 4.23 | - | 2.13E-24 | - | 7.46E-23 | 136 |
| Cell adhesion molecules | ID:04514 | - | 54 | - | 14.11 | - | 3.83 | - | 2.46E-19 | - | 5.17E-18 | 133 |
| Jak-STAT signaling pathway | ID:04630 | - | 59 | - | 16.44 | - | 3.59 | - | 2.37E-19 | - | 5.17E-18 | 155 |
| Toll-like receptor signaling | ID:04620 | - | 41 | - | 10.82 | - | 3.79 | - | 7.37E-15 | - | 7.37E-14 | 102 |
| TGF-beta signaling pathway | ID:04350 | - | 31 | - | 8.91 | - | 3.48 | - | 1.81E-10 | - | 9.27E-10 | 84 |
| NOD-like receptor signaling | ID:04621 | - | 24 | - | 6.15 | - | 3.90 | - | 1.34E-09 | - | 5.99E-09 | 58 |
| Allograft rejection | ID:05330 | - | 18 | - | 3.93 | - | 4.59 | - | 6.72E-09 | - | 2.52E-08 | 37 |
| Antigen processing presentation | ID:04612 | - | 26 | - | 8.06 | - | 3.22 | - | 3.22E-08 | - | 1.13E-07 | 76 |
| Basal transcription factors | ID:03022 | - | 15 | - | 3.93 | - | 3.82 | - | 2.26E-06 | - | 6.33E-06 | 37 |
| Oxidative phosphorylation | ID:00190 | 76 | - | 12.59 | - | 6.04 | - | 5.25E-43 | - | 5.64E-41 | - | 132 |
| Proteasome | ID:03050 | 19 | - | 4.20 | - | 4.53 | - | 5.22E-09 | - | 1.02E-07 | - | 44 |
| RNA polymerase | ID:03020 | 14 | - | 2.77 | - | 5.06 | - | 9.76E-08 | - | 1.31E-06 | - | 29 |
| Glycosphingolipid biosynthesis | ID:00601 | 13 | - | 2.48 | - | 5.24 | - | 1.67E-07 | - | 2.11E-06 | - | 26 |
| Metabolism of xenobiotics P450 | ID:00980 | 22 | - | 6.77 | - | 3.25 | - | 4.02E-07 | - | 4.12E-06 | - | 71 |
| Tyrosine metabolism | ID:00350 | 16 | - | 3.91 | - | 4.09 | - | 4.56E-07 | - | 4.40E-06 | - | 41 |
| Glutathione metabolism | ID:00480 | 17 | - | 4.77 | - | 3.57 | - | 1.95E-06 | - | 1.45E-05 | - | 50 |
| Arginine and proline metabolism | ID:00330 | 17 | - | 5.15 | - | 3.30 | - | 6.44E-06 | - | 3.85E-05 | - | 54 |
| Glycosylphosphatidylinositol | ID:00563 | 11 | - | 2.38 | - | 4.61 | - | 7.33E-06 | - | 4.26E-05 | - | 25 |
| Drug metabolism P450 | ID:00982 | 20 | - | 6.96 | - | 2.87 | - | 1.09E-05 | - | 5.86E-05 | - | 73 |
| Fructose mannose metabolism | ID:00051 | 12 | - | 3.43 | - | 3.50 | - | 7.82E-05 | - | 3.00E-04 | - | 36 |
| Sulfur relay system | ID:04122 | 6 | - | 0.95 | - | 6.29 | - | 1.00E-04 | - | 4.00E-04 | - | 10 |
| Arachidonic acid metabolism | ID:00590 | 16 | - | 5.63 | - | 2.84 | - | 9.20E-05 | - | 4.00E-04 | - | 59 |
| Sphingolipid metabolism | ID:00600 | 12 | - | 3.81 | - | 3.15 | - | 2.00E-04 | - | 7.00E-04 | - | 40 |
| Glycosaminoglycan degradation | ID:00531 | 8 | - | 1.81 | - | 4.41 | - | 2.00E-04 | - | 7.00E-04 | - | 19 |
| Hedgehog signaling pathway | ID:04340 | 15 | - | 5.34 | - | 2.81 | - | 2.00E-04 | - | 7.00E-04 | - | 56 |
| Drug metabolism | ID:00983 | 14 | - | 4.96 | - | 2.82 | - | 3.00E-04 | - | 9.00E-04 | - | 52 |