Hierarchical structural component model for pathway analysis of common variants

BMC Medical Genomics

Table 4 Pathways identified for BP

Pathway	HisCoM-PCA^a	HisCoM-PCA^b	MAGMA	GSA-SNP2
Pathway	P value (q-value)
inositol phosphate metabolism	0.002 (0.0633)	0.004 (0.1265)	0.1966 (1)	9.008e-06 (0.0017)
phosphatidylinositol signaling system	0.002(0.0633)	0.004 (0.1265)	0.2256 (1)	1e-04 (0.013)
ubiquitin mediated proteolysis	0.002 (0.0633)	0.002 (0.0949)	0.1076 (1)	0.5963 (0.9839)
calcium signaling pathway	0.008 (0.2169)	0.006 (0.1627)	0.0994 (1)	0.0228 (0.4708)
neurotrophin signaling pathway	0.01 (0.2373)	0.01 (0.2373)	0.6801 (1)	0.3157 (0.971)
epithelial cell signaling in helicobacter pylori infection	0.012 (0.2531)	0.05 (0.4126)	0.0826 (1)	0.1245 (0.7719)
complement and coagulation cascades	0.014 (0.2657)	0.03 (0.3417)	0.1428 (1)	0.3405 (0.9839)
maturity onset diabetes of the young	0.018 (0.3106)	0.036 (0.3417)	0.067 (1)	0.0239 (0.4708)
snare interactions in vesicular transport	0.022 (0.348)	0.012 (0.2531)	0.2071 (1)	0.0653 (0.5878)
hypertrophic cardiomyopathy (HCM) ^*	0.1259 (0.5573)	0.03 (0.3417)	0.0074(1)	3e-04 (0.0157)

HisCoM-PCA^a is HisCoM-PCA with the first PC of each gene. HisCoM-PCA^b is HisCoM-PCA with the PCs whose cumulative proportion of variance is more than 30%. MAGMA is competitive version of MAGMA. The q-value is the FDR corrected p-value. Pathway with “*” was identified by 3 methods

ISSN: 1755-8794