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Table 2 Common gene sets associated with different diabetes traits

From: The uniform-score gene set analysis for identifying common pathways associated with different diabetes traits

GWAS\PID

1461

2247

2268

2240

2076

2239

1551

 

Stage I: p e (sig%)

pha000417

2.89E-21

5.77E-11

3.34E-14

1.90E-12

9.98E-16

1.78E-07

2.29E-08

(12.1)

(9.8)

(10.8)

(10.0)

(18.8)

(11.1)

(17.7)

pha000423

2.57E-18

2.25E-12

1.06E-19

2.19E-08

9.39E-08

1.45E-07

5.07E-09

(11.5)

(10.1)

(11.9)

(9.0)

(13.7)

(11.1)

(18.4)

pha000427

2.82E-21

1.91E-13

1.64E-10

3.00E-09

1.52E-11

6.56E-08

2.89E-13

(11.9)

(10.2)

(9.7)

(9.1)

(16.0)

(11.1)

(22.2)

pha000429

1.60E-23

5.14E-11

1.81E-09

8.90E-08

2.69E-11

1.07E-10

2.08E-10

(12.4)

(9.7)

(9.6)

(8.8)

(16.0)

(12.5)

(19.7)

pha000433

5.38E-20

4.47E-15

3.19E-11

3.41E-08

1.35E-12

5.28E-08

4.27E-10

(12.0)

(10.8)

(10.2)

(9.1)

(17.1)

(11.4)

(19.6)

pha000437

1.06E-13

8.91E-13

7.21E-11

5.99E-08

2.46E-07

1.91E-09

1.15E-09

(10.5)

(10.2)

(10.0)

(8.9)

(13.3)

(12.0)

(19.0)

pha000447

1.08E-23

4.96E-12

9.30E-16

1.30E-08

4.90E-09

9.70E-09

6.31E-12

(12.2)

(9.8)

(10.9)

(8.9)

(14.3)

(11.4)

(20.9)

pha000451

1.01E-15

1.15E-14

2.67E-08

1.19E-08

6.53E-10

4.79E-11

3.01E-08

(11.1)

(10.7)

(9.4)

(9.2)

(15.4)

(12.8)

(17.7)

pha000453

3.44E-28

5.34E-15

1.10E-12

6.90E-09

1.18E-09

5.22E-15

4.56E-13

(13.2)

(10.7)

(10.4)

(9.2)

(15.0)

(14.2)

(22.3)

pha000457

3.20E-25

7.46E-15

2.61E-14

2.58E-09

3.71E-07

3.49E-11

1.93E-11

(12.9)

(10.7)

(10.9)

(9.4)

(13.3)

(12.9)

(20.9)

pha000461

3.68E-16

7.82E-12

1.36E-10

1.04E-8

4.46E-9

2.80E-11

7.52E-11

(11.1)

(10.0)

(10.0)

(9.2)

(14.7)

(12.8)

(20.3)

 

Stage I: Chi2 (Rank)

 

1008.84 (13)

626.50 (14)

596.97 (15)

415.33(21)

474.90 (17)

462.18 (18)

499.03 (16)

 

Stage II: p e (sig%) (p adj )

pha002839

8.3E-35

5.78E-21

3.73E-18

4.60E-22

1.61E-11

1.73E-16

1.28E-8

(13.8)

(11.5)

(11.3)

(11.0)

(15.4)

(14.1)

(17.2)

(<1E-4)

(<1E-4)

(<1E-4)

(<1E-4)

(<1E-4)

(<1E-4)

(4E-4)

pha002862

6.70E-20

1.41E-13

1.34E-15

2.14E-12

5.85E-13

8.35E-8

3.33E-11

(11.4)

(10.0)

(11.3)

(9.4)

(16.0)

(10.7)

(19.2)

(<1E-4)

(<1E-4)

(<1E-4)

(<1E-4)

(<1E-4)

(0.003)

(<1E-4)

pha002864

2.23E-32

2.11E-21

1.43E-18

8.33E-20

2.67E-10

3.95E-11

1.10E-14

(13.3)

(11.4)

(11.3)

(10.6)

(14.6)

(12.2)

(22.2)

(<1E-4)

(<1E-4)

(<1E-4)

(<1E-4)

(1E-4)

(<1E-4)

(<1E-4)

pha003005

6.84E-29

2.64E-15

2.72E-13

2.47E-15

1.72E-9

4.51E-11

6.41E-7

(13.0)

(10.5)

(10.4)

(10.0)

(14.3)

(12.3)

(15.5)

(<1E-4)

(<1E-4)

(<1E-4)

(<1E-4)

(1E-4)

(<1E-4)

(<1E-4)

pha002901

6.45E-42

9.05E-23

4.39E-17

2.47E-20

8.43E-12

6.59E-15

2.28E-11

(14.7)

(11.8)

(11.2)

(10.8)

(15.7)

(13.6)

(19.7)

(<1E-4)

(<1E-4)

(<1E-4)

(<1E-4)

(<1E-4)

(<1E-4)

(<1E-4)

  1. p e : Pathway empirical p-value; sig%: percentage of genes in the gene set that are at the top 5% of gene association over genome; p adj : Pathway adjusted p-value; Chi2 = ∑ i  − 2 x log((p e ) i ) is the summary of a gene set’s association over all stage I GWAS; Rank: the rank of chi2 in decreasing order.