Table 3 The numbers of genes identified by each method for the two SCZ data sets. The subscript denotes BT, SKAT, and SKATO using eQTL—derived weights; CMC, METSIM, NTR, and YFS indicate the resources to obtain the eQTL—derived weights. 0 indicates the methods without using any weights.

From: Gene-based association tests using GWAS summary statistics and incorporating eQTL

 

SCZ1

SCZ2

SCZoverlap

GWASSCZ1

GWASSCZ2

BT0

97

166

7

1

38

SKAT0

47

305

20

15

153

SKATO0

136

394

27

15

153

BTCMC

44

137

2

1

56

SKATCMC

12

225

6

1

134

SKATOCMC

30

263

2

1

130

BTMETSIM

44

136

5

1

48

SKATMETSIM

23

223

9

4

132

SKATOMETSIM

31

205

3

0

100

BTNTR

48

119

7

6

48

SKATNTR

27

230

9

8

141

SKATONTR

40

280

8

6

143

BTYFS

89

166

14

1

53

SKATYFS

20

223

6

7

137

SKATOYFS

47

321

7

0

140

S-PrediXcanCMC

42

43

7

0

38

S-PrediXcanMETSIM

41

44

8

1

30

S-PrediXcanNTR

48

70

14

6

59

S-PrediXcanYFS

83

128

29

2

72

S-TWASCMC

33

45

6

0

43

S-TWASMETSIM

36

29

5

1

20

S-TWASNTR

37

54

13

6

46

S-TWASYFS

64

105

29

2

58

OT

133

522

17

6

166

Overall

271

559

45

16

167

  1. SCZ1 indicates the number of genes identified by each method for SCZ1 data; SCZ2 indicates the number of genes identified by each method for SCZ2 data; SCZoverall indicates the number of overlapping genes identified by both SCZ1 and SCZ2 data sets; GWASSCZ1 and GWASSCZ2 indicate the numbers of genome-wide significant genes that are reported in the GWAS catalog and are also identified by each method for SCZ1 and SCZ2, respectively.
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