Skip to main content
. Author manuscript; available in PMC: 2013 Oct 1.
Published in final edited form as: Genes Immun. 2013 Feb 7;14(3):179–186. doi: 10.1038/gene.2013.1

Table 3.

Complementary tests for pathways identified at the P < 0.05 level in both datasets using LCT

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.

a

These pathways were defined in the Kyoto Encyclopedia of Genes and Genomes (KEGG).

b

This analysis was performed using the i-GSEA4GWAS modification of GSEA.

c

Ratio of number of genes containing at least one SNP with P < 0.05 to the total number of genes in the pathway.