Table 2 |
||||
| Network enrichment analysis of lung cancer-related gene sets to patient-specific altered gene sets | ||||
| Functional gene set | FNEA (k = 100) | MNEA | GEA (k = 100) | GSEA |
| Ding et al., 2008 | ||||
| All (623 genes) | 66 | 114 | 1 | 102 |
| Drivers (26) | 74 | 95 | 21 | 16 |
| Mutated ≤1 (153) | 39 | 102 | 2 | 75 |
| COSMIC | ||||
| Detected >1 (110) | 34 | 33 | 22 | 30 |
| Detected once (median)∗ (110) | 18 | 52 | 9 | 28.5 |
| KEGG05223 non-small cell lung cancer (56) | 48 | 99 | 2 | 40 |
| Largest contrast GEA > FNEA | ||||
| KEGG00362 Benzoate degradation via hydroxylation (3) | 4 | 27 | 123 | 31 |
| KEGG00513 High-mannose type N-glycan biosynthesis (4) | 2 | 5 | 123 | 24 |
| KEGG00780 Biotin metabolism (4) | 1 | 13 | 123 | 11 |
| KEGG00300 Lysine biosynthesis (5) | 0 | 6 | 123 | 34 |
| KEGG00785 Lipoic acid metabolism (4) | 0 | 2 | 123 | 18 |
| Largest contrast FNEA > GEA | ||||
| GO0001666 Response to hypoxia (163) | 119 | 114 | 11 | 105 |
| KEGG05200 Pathways in cancer (254) | 112 | 118 | 6 | 99 |
| GO0001525 Angiogenesis (129) | 115 | 113 | 10 | 118 |
| KEGG04010 MAPK signaling pathway (286) | 107 | 114 | 4 | 82 |
| KEGG04020 Calcium signaling pathway (183) | 99 | 108 | 5 | 60 |
KEGG05223 is non-small cell lung cancer pathway. ‘COSMIC’ genes include the lung-cancer somatic mutations in the COSMIC database, but exclude those in [26]. ∗ indicates the median from 50 randomly sampled sets.
Alexeyenko et al. BMC Bioinformatics 2012 13:226 doi:10.1186/1471-2105-13-226
