Table 1.

Pathway-based analysis from GWA data methods comparison

Method Used	Pathway Databases available for use	Requires original dataset	LD correction	Gene Size Correction	Study designs allowed	Reference
PARIS	any	No	genomic randomization	yes	any	Yaspan, 2010
SRT	any	Yes	case-control status randomization	yes	case-control§	O’Doulishaine, 2009
EVA	any	Dependent on correction (LD)	done prior to EVA analysis	Done prior to EVA analysis	any	Askland, 2009
ProxyGeneLD	any	No	Bonferroni-type based # SNPs typed in areas of LD and LE	yes	any	Hong, 2009
ALIGATOR	GO	No	none (assumes LD = across pathways)	yes	any	Holmans, 2009
Modified GSEA	GO, KEGG	Yes	case-control status randomization	yes	case-control§	Wang, 2007

^§modifiable for use with family-based datasets by using non-transmitted alleles to create pseudo-controls