Table 3

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

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


* p = Probability of the gene overlap in two independent populations. Multiple testing adjusted threshold of p = .05/49 = 10-3

** Pathways with p < 10-3

Yang et al. BMC Medical Genomics 2011 4:63   doi:10.1186/1755-8794-4-63

Open Data