Skip to main content

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.