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Table 1 Gene and SNP sets generated by the database: interrogation schemes for each of the metabolites

From: Automated workflow-based exploitation of pathway databases provides new insights into genetic associations of metabolite profiles

Metabolite

BioCyc Pathway

BioCyc Reaction

KEGG Pathway

KEGG Reaction

Size of unique gene set1

Size of unique SNP set2

Number of tests3

Arginine

20

104

57

179

257

10788

10788

Glutamine

51

132

100

282

388

15591

15591

Glycine

90

192

173

432

523

20767

20767

Histidine

8

9

45

155

181

7126

7126

Leucine

8

0

44

83

117

5037

5037

Methionine

27

104

35

243

284

11532

11532

Ornithine

16

150

103

159

247

10089

10089

Phenylalanine

6

113

25

163

196

8419

8419

Proline

10

12

57

83

119

5075

5075

Serine

37

135

152

219

360

14996

14996

Threonine

1

11

39

49

75

2633

2633

Tryptophan

15

19

78

221

261

10419

10419

Tyrosine

14

106

61

158

219

9365

9365

Valine

15

93

80

137

211

9365

9365

Carnitine

32

206

81

94

263

11239

460799

Phosphatidylcholine

188

361

312

343

640

31676

2914192

Sphingomyelin

160

331

189

241

460

21290

319350

Sum

698

2078

1631

3241

4801

205407

3835543

Unique set

399

806

703

768

1246

55952

55952

  1. The number of genes for each metabolite and the corresponding database:interrogation scheme is shown. 1 The size of the union of the gene set obtained from all the four database:interrogation schemes. 2 The size of the corresponding SNP set. 3 The number of tests is the same as the size of the SNP set for the amino acids whereas for aggregated entities like the lipids and carnitine the SNP set is multiplied by the number of compounds present in that class.