Table 3 Correlation of geneset enrichment scores between EWAS and GWAS

From: A comparison of the genes and genesets identified by GWAS and EWAS of fifteen complex traits

trait

n EWAS genes

n GWAS genes

Geneset overlap

obs cor

exp cor

p diff

Body mass index

232

3,228

1,243

0.187

0.20

0.2287

Current versus never smoking

1933

312

1,053

0.200

0.22

0.0343

Former versus never smoking

282

323

661

0.298

0.30

0.9936

Alcohol consumption per day

361

190

562

0.259

0.27

0.5753

C-reactive protein

189

302

600

0.265

0.26

0.7983

Educational attainment

25

1,594

215

0.105

0.13

0.1729

Fasting glucose

15

50

50

0.153

0.16

0.7723

Fasting insulin

36

5

19

0.093

0.12

0.4400

Systolic blood pressure

99

3,210

631

0.145

0.14

0.7679

Diastolic blood pressure

56

3586

594

0.160

0.11

0.0013

Birthweight

894

162

683

0.224

0.24

0.2476

Cognitive abilities: digit test

26

875

198

0.164

0.14

0.2064

FEV1

51

1,664

403

0.158

0.14

0.1948

eGFR

256

2611

1,264

0.233

0.20

0.0332

Urate

251

666

877

0.306

0.27

0.0414

  1. For each geneset, odds of study genes being in the geneset divided by the odds of the study genes not being in the geneset were assessed and correlation between these odds ratios are given here.
  2. exp cor = the mean correlation between odds ratios after repeating the analysis 1000 times, randomly sampling EWAS genes equal to the number identified in the empirical analysis.
  3. geneset overlap indicates the number of gene ontology terms that map to both genes identified by the EWAS and GWAS.
  4. p diff = P value from a two-sided Z-test assessing the difference between the observed and expected correlations.
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