Table 3.
Pathway namea | LCT |
GSEAb |
Fisher’s exact test |
|||
---|---|---|---|---|---|---|
Italian P-value (FDR) |
Canadian P-value (FDR) |
Italian P-value |
Canadian P-value |
Italian P-value (Ratioc) |
Canadian P-value (Ratioc) |
|
Phosphatidylinositol signaling system | 0.0156 | 0.0335 | 0.003 | NS | 1.4E-04 | 0.0003 |
(0.436) | (0.693) | (0.416) | (0338) | |||
Hedgehog signaling pathway | 0.0438 | 0.0407 | 0.005 | NS | 0.103 | 1.000 |
(0.636) | (0.693) | (0.281) | (0.158) |
Abbreviations: FDR, false discovery rate; GSEA, gene set enrichment analysis; LCT, linear combination test; NS, not significant.
These pathways were defined in the Kyoto Encyclopedia of Genes and Genomes (KEGG).
This analysis was performed using the i-GSEA4GWAS modification of GSEA.
Ratio of number of genes containing at least one SNP with P < 0.05 to the total number of genes in the pathway.