Pathway-based approach using hierarchical components of rare variants to analyze multiple phenotypes

BMC Bioinformatics

Table 2 Significant pathways of PHARAOH-multi and MARV, and their q-values of multivariate and univariate analyses

DB	Pathway	# of variants	Multivariate q-value			Univariate q-value (PHARAOH)
DB	Pathway	# of variants	P_M	aSPU	MARV	tg	sbp	dbp	fastglu	hdl	waistc
KEGG
Peroxisome		421	0.0396	0	0.9826	0.6886	0.7	0.9138	0.9899	0.9942	1
Glutathione metabolism		187	0.044	0.0076	0.9826	0.999	0.0939	0.9138	0.993	0.9942	1
Biocarta
CDMAC pathway		63	0.0858	0.5739	0.9638	0.9817	0.1094	0.5743	0.953	0.9967	0.9962
Cell2cell pathway		112	0.0208	0	0.9638	0.7293	0.3063	0.5722	0.8234	0.9967	0.9962
GABA pathway		46	0.0497	0.0085	0.8134	0.9783	0.1094	0.5722	0.8234	0.9967	0.9962
MPR pathway		179	0.0208	0	0.9638	0.9783	0.1094	0.2188	0.8234	0.9845	0.9962
Caspase pathway		649	0.8358	0.1741	0.0634	0.997	0.8863	0.6418	0.7584	0.999	0.9928
D4GDI pathway		422	0.7626	0.3727	0.0634	0.997	0.9867	0.6418	0.4377	0.999	0.995
Reactome
Glutathione conjugation		99	0.0979	0.0567	0.9979	0.9813	0.3859	0.9254	0.999	0.9793	0.979
Phase II conjugation		270	0.0571	0	0.9979	0.9813	0.3859	0.9254	0.999	0.9793	0.99

Bold numbers are the q-values below the significance threshold 0.1. P_M, aSPU and MARV indicate q-values from the joint testing method of multiple phenotypes, and univariate q-values indicate the q-values of PHARAOH analysis for each phenotype

ISSN: 1471-2105