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Table 3 Pathways that contain significant SNPs (p < 10-3) inferred from both AGS and TCGA samples

From: Combinations of newly confirmed Glioma-Associated loci link regions on chromosomes 1 and 9 to increased disease risk

PATHWAY* AGS_SNP GENE TCGA_SNP GENE
Purine metabolism (p = 3.50E-04)**     
Small cell lung cancer (p = 4.35E-04) **     
Non-small cell lung cancer (p = 2.6E-04) ** rs7617530 FHIT rs13059601 FHIT
Neuroactive ligand-receptor interaction (p = 8.00E-04) ** rs1011455 GABRG3   
  rs4887546 GABRG3   
  rs1011456 GABRG3 rs12904325 GABRG3
Vascular smooth muscle contraction (p = 3.48E-04) **     
Gap junction (p = 1.30E-04) ** rs4400745 PRKG1   
Long-term depression (p = 6.95E-04) **     
Olfactory transduction (p = 3.47E-04) ** rs4466778 PRKG1 rs1922139 PRKG1
Axon guidance (p = 3.91E-04) **    rs11082983 DCC
Pathways in cancer (p = 2.13E-03)    rs11872471 DCC
Colorectal cancer (p = 8.69E-05) ** rs1145245 DCC rs12604940 DCC
Focal adhesion (p = 1.95E-03)     
ECM-receptor interaction (p = 8.69E-04) **     
Cell adhesion molecules (CAMs) (p = 1.74E-04) ** rs3779505 ITGB8   
Regulation of actin cytoskeleton (p = 1.56E-03) rs2301727 ITGB8   
Hypertrophic cardiomyopathy (HCM) (p = 1.22E-03) rs3807936 ITGB8   
Arrhythmogenic right ventricular cardiomyopathy (ARVC) (p = 9.12E-04) **     
Dilated cardiomyopathy (p = 1.04E-03) rs2158250 ITGB8 rs3779505 ITGB8
  1. * p = Probability of the gene overlap in two independent populations. Multiple testing adjusted threshold of p = .05/49 = 10-3
  2. ** Pathways with p < 10-3