Pathway-based analysis using reduced gene subsets in genome-wide association studies

BMC Bioinformatics

Table 4 The pathways detected by at least one method in GAIN data set

	*FPC-BIC*	*FPC-AIC*	*GSEA*	*AML*
*Pathway*	*P-value (FDR, FWER)*	*P-value (FDR, FWER)*	*P-value (FDR, FWER)*	*P-value (FDR, FWER)*
1. Cytokine Network	<0.001 (0.006, 0.006)	<0.001 (0.001, 0.001)	0.020 (0.182, 0.945)	0.888 (0.911, 1.000)
2. Jak-STAT signaling pathway	<0.001 (0.004, 0.008)	<0.001 (0.001, 0.002)	0.001 (0.017, 0.080)	0.104 (0.518, 1.000)
3. Dendritic cells in regulating TH1 and TH2 Development	<0.001 (0.005, 0.015)	<0.001 (0.004, 0.019)	0.108 (0.448, 1.000)	0.634 (0.906, 1.000)
4. Cytokines and Inflammatory Response	<0.001 (0.005, 0.020)	0.001 (0.006, 0.057)	0.127 (0.455, 1.000)	0.710 (0.917, 1.000)
5. Cytokine-cytokine receptor interaction	<0.001 (0.005, 0.023)	<0.001 (0.004, 0.027)	0.004 (0.090, 0.534)	0.005 (0.494, 0.624)
6. Role of BRCA1, BRCA2 and ATR in Cancer Susceptibility	<0.001 (0.005, 0.037)	<0.001 (0.001, 0.001)	0.243 (0.560, 1.000)	0.014 (0.390, 0.871)
7. TNFR2 Signaling Pathway	0.001 (0.009, 0.099)	<0.001 0.004, 0.021	0.249 (0.559, 1.000)	0.303 (0.641, 1.000)
8. Calcium signaling pathway	0.022 (0.166, 1.000)	0.001 (0.040, 0.591)	<0.001 (0.009, 0.009)	0.002 (0.362, 0.655)
9. Axon guidance	0.017 (0.165, 0.997)	0.040 (0.139, 1.000)	0.001 (0.005, 0.010)	0.238 (0.600, 1.000)
10. ECM-receptor interaction	0.792 (0.858, 1.000)	0.392 (0.461, 1.000)	<0.001 (0.004, 0.012)	0.197 (0.600, 1.000)
11. Cell adhesion molecules (CAMs)	0.332 (0.520, 1.000)	0.011 (0.081, 0.957)	0.001 (0.007, 0.027)	0.023 (0.363, 0.994)

All the p-values, false discovery rates (FDRs) and family-wise error rates (FWERs) were obtained via 1000 permutations. Gene p-value in pathway enrichment method was the p-value of the most significant SNP within gene. The AML method was based on the test statistic of Cochan-Armitage trend test.

ISSN: 1471-2105