Table 3.
Top ranking pathways of genome-wide pathway analysis using regulatory SNPs
| P-value distribution of SNPs | ||||||
|---|---|---|---|---|---|---|
| Pathway name (KEGG ID) Class |
SRT P | P < 0.01 | 0.01 ≤ P < 0.05 | 0.05 ≤ P < 0.1 | N | P of most significant SNP in pathway |
| Glioma (hsa05214) Cancers |
0.0394 | 1 | 5 | 4 | 26 | 0.0028 |
| Long-term potentiation (hsa04720) Nervous System |
0.0394 | 0 | 3 | 2 | 16 | 0.0314 |
| Non-small cell lung cancer (hsa05223) Cancers |
0.0394 | 1 | 5 | 3 | 24 | 0.0028 |
| Pancreatic cancer (hsa05212) Cancers |
0.0413 | 2 | 5 | 3 | 33 | 0.0028 |
| Prostate cancer (hsa05215) Cancers |
0.0488 | 3 | 3 | 6 | 32 | 0.0003 |
| Focal adhesion (hsa04510) Cell Communication |
0.0525 | 1 | 7 | 9 | 71 | 0.0028 |
| Chemokine signaling pathway (hsa04062) Immune System |
0.0582 | 1 | 8 | 7 | 72 | 0.0080 |
| Pathways in cancer (hsa05200) Cancers |
0.0582 | 2 | 12 | 15 | 151 | 0.0028 |
| Melanogenesis (hsa04916) Endocrine System |
0.0657 | 2 | 2 | 2 | 26 | 0.0003 |
| B cell receptor signaling pathway (hsa04662) Immune System |
0.0713 | 0 | 5 | 3 | 29 | 0.0314 |
| GnRH signaling pathway (hsa04912) Endocrine System |
0.0732 | 0 | 6 | 6 | 46 | 0.0115 |
| Fc epsilon RI signaling pathway (hsa04664) Immune System |
0.0769 | 0 | 6 | 6 | 33 | 0.0314 |
| VEGF signaling pathway (hsa04370) Signal Transduction |
0.0769 | 0 | 3 | 0 | 17 | 0.0115 |
| ErbB signaling pathway (hsa04012) Signal Transduction |
0.0788 | 0 | 5 | 5 | 25 | 0.0314 |
| Acute myeloid leukemia (hsa05221) Cancers |
0.0957 | 1 | 3 | 3 | 25 | 0.0028 |
| Gap junction (hsa04540) Cell Communication |
0.0976 | 0 | 5 | 3 | 42 | 0.0314 |
KEGG ID, Kyoto Encyclopedia of Genes and Genomes pathway identifier; P, P-value of association test in the genome-wide study; SNP, single nucleotide polymorphism; SRT P, P-value of permutation test for pathway tested