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Table 3 Pathways identified for T2D

From: Hierarchical structural component model for pathway analysis of common variants

Pathway

HisCoM-PCAa

HisCoM-PCAb

MAGMA

GSA-SNP2

P value (q-value)

folate biosynthesis

0.004 (0.1518)

0.002 (0.0633)

0.0537 (0.891)

0.0019 (0.2936)

hedgehog signaling pathway

0.006 (0.1627)

0.016 (0.2531)

0.3073 (0.917)

0.028 (0.5284)

olfactory transduction*

0.006 (0.1627)

0.002 (0.0633)

0.0482 (0.891)

0.0036 (0.2936)

biosynthesis of unsaturated fatty acids

0.01 (0.2373)

0.012 (0.2071)

0.089 (0.891)

0.0373 (0.5284)

Alzheimer’s disease

0.014 (0.2657)

0.036 (0.4555)

0.1808 (0.891)

0.0446 (0.5284)

calcium signaling pathway

0.014 (0.2657)

0.026 (0.3796)

0.0791 0.891)

0.0329 (0.5284)

asthma

0.016 (0.2761)

0.008 (0.1687)

0.0517 0.891)

0.0737 (0.6529)

acute myeloid leukemia

0.032 (0.4302)

0.042 (0.4621)

0.0781 (0.891)

0.5442 (1)

melanogenesis

0.034 (0.4302)

0.012 (0.2071)

0.0786 (0.891)

0.0223 (0.5284)

long term potentiation

0.04 (0.4466)

0.028 (0.3796)

0.1284 (0.891)

0.1616 (0.8349)

phosphatidylinositol signaling system

0.1119 (0.5185)

0.006 (0.1424)

0.7656 (0.9778)

0.1107 (0.7355)

dilated cardiomyopathy

0.03 (0.4302)

0.0819 (0.5188)

0.3994 (0.917)

0.0408 (0.5284)

renin angiotensin system

0.038 (0.4466)

0.0539 (0.4621)

0.3794 (0.917)

0.0917 (0.6923)

  1. HisCoM-PCAa is HisCoM-PCA with the first PC of each gene. HisCoM-PCAb 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