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Table 7 Significant pathways (P < 0.01) by a combined analysis using the Plink set-based test and GSEA.

From: Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer

Pathway (KEGG ID)

GSEA

Plink

P combined

FDR

Fc gamma R-mediated phagocytosis (hsa04666)

< 0.001

0.003

6.18 × 10-8

9.15 × 10-6

Regulation of actin cytoskeleton (hsa04810)

0.009

0.003

3.34 × 10-4

2.47 × 10-2

Jak-STAT signaling pathway (hsa04630)

0.084

0.001

8.79 × 10-4

3.56 × 10-2

Dilated cardiomyopathy (hsa05414)

0.003

0.024

9.63 × 10-4

3.56 × 10-2

Small cell lung cancer (hsa05222)

0.266

0.001

2.45 × 10-3

7.27 × 10-2

Hypertrophic cardiomyopathy (HCM) (hsa05410)

0.009

0.051

4.20 × 10-3

9.62 × 10-2

Cell cycle (hsa04110)

0.251

0.003

6.16 × 10-3

9.62 × 10-2

Arrhythmogenic right ventricular cardiomyopathy (ARVC) (hsa05412)

0.012

0.068

6.46 × 10-3

9.62 × 10-2

Chronic myeloid leukemia (hsa05220)

0.843

0.001

6.80 × 10-3

9.62 × 10-2

Bladder cancer (hsa05219)

0.422

0.002

6.80 × 10-3

9.62 × 10-2

Wnt signaling pathway (hsa04310)

0.297

0.003

7.14 × 10-3

9.62 × 10-2

TGF-beta signaling pathway (hsa04350)

0.508

0.002

8.01 × 10-3

9.66 × 10-2

Axon guidance (hsa04360)

0.016

0.074

9.18 × 10-3

9.66 × 10-2