Table 1.
Pathways associated with melanoma risk in MELARISK and MDACC studies
| Pathway (Gene Ontology (GO) class) | MELARISK |
MDACC |
||||||
|---|---|---|---|---|---|---|---|---|
| No. of genes1 | p 2 | FDR2 | No. of genes driving a pathway (%)3 | No. of genes1 | p 2 | FDR2 | No. of genes driving a pathway (%)3 | |
| Response to light stimulus (GO:0009416) | 75 | <10−5 | 0.001 | 31 (41.3) | 75 | <10−5 | 0.002 | 34 (45.3) |
| Regulation of mitotic cell cycle (GO:0007346) | 52 | <10−5 | 0.001 | 13 (25.0) | 52 | 5.6×10−3 | 0.05 | 13 (25.0) |
| Induction of programmed cell death (GO:0012502) | 193 | 5.0×10−5 | 0.004 | 71 (36.8) | 193 | 3.0×10−4 | 0.02 | 76 (39.4) |
| Cytokine activity (GO:0005125) | 183 | 3.6×10−3 | 0.05 | 79 (43.2) | 188 | 9.1×10−3 | 0.05 | 63 (33.5) |
| Oxidative phosphorylation (GO:0006119) | 54 | 1.6×10−3 | 0.04 | 20 (37.0) | 54 | 6.5×10−4 | 0.02 | 18 (33.3) |
1
Number of genes in a pathway having at least one GWAS SNP mapped to a gene
2
Empirical p-value and False Discovery Rate (FDR) of a pathway estimated by 100,000 permutations of SNP statistics
3
Number of genes driving the enrichment score of a pathway and proportion (%) over total number of genes in that pathway