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.

Alexeyenko et al. BMC Bioinformatics 2012 13:226   doi:10.1186/1471-2105-13-226

Open Data