Table 2

DER values for T2DM and false positive genes from GWAS

Locus or SNP

Gene

Associated in populations

DER

Correct?a


2q37.3

CAPN10

Finish. [55], Korean [56], Mexican. [55], Tunisian [57]

0.57

True positive


3p25

PPARG

Caucasian. [58], Finish. [59], German. [60], Indian Sikhs. [61], Japanese. [62], Mexican. [63]

0.53

False negative


3q27.2

IGF2BP2

Asian. [64], Caucasian. [33], Chinese [65], Danish. [66], French. [67], German. [60], Hispanic. [68], Indian Sikhs. [61], Japanese. [69], Norwegian. [70]

0.54

False negative


6p22.3

CDKAL1

Asian. [64], Ashkenazi Jewish. [71], Caucasian. [33], Chinese [65], German. [60], Hispanic. [68], Japanese. [69], Norwegian. [70]

0.55

True positive


8q24.11

SLC30A8

Asian. [64], African. [68], Caucasian. [33], Chinese [65], Hispanic. [68], Japanese. [69], Norwegian. [70]

0.42

False negative


9p21

CDKN2A

Asian. [64], Caucasian. [34], Chinese [65], Danish. [66], French [72], Japanese. [69]

0.59

True positive


9p21

CDKN2B

Asian. [64], Caucasian. [33], Chinese [65], Danish. [66], French [72], Japanese. [69], Norwegian. [70]

0.49

False negative


10q23

HHEX

Asian. [64], Caucasian. [33], Chinese [65], Danish. [66], German. [60], Japanese. [69], Norwegian. [70]

0.58

True positive


10q23

IDE

Caucasian. [73], Chinese [65], Danish. [66], Japanese. [74], Korean. [75]

0.61

True positive


10q24

KIF11

Caucasian, Chinese [65], Danish. [66], Japanese. [74]

0.54

False negative


10q25.3

TCF7L2

African. [76], Ashkenazi Jewish. [71], Asian. [64], Caucasian. [33], Chinese. [77], German. [60], Hispanic. [78], Indian Sikhs. [61], Japanese. [79], Spanish, UK white. [80]

0.64

True positive


11p15.1

KCNJ11

Arab. [81], Caucasian. [33], Czech [82], Japanese. [69]

0.39

False negative


11p15.5

KCNQ1

Singaporean. [35], European. [35], Japanese. [35]

0.6

True positive


16q12.2

FTO

Asian. [64], Caucasian. [34], Indian Sikhs. [61], German. [60], Japanese. [83], Norwegian. [70]

0.55

True positive


20q12

HNF4A

Amish. [84], Ashkenazim [85], Danish. [86], Finish. [87], Swedish. [87], Mexican. [88], Norwegian. [89], UK Caucasian. [90]

0.63

True positive


rs11078674

NLGN2

No

0.53

True negative


rs2866016

TSPAN5

No

0.53

True negative


rs12629276

RFTN1

No

0.54

True negative


rs8101509

ZNF649

No

0.4

True negative


rs945384

FAM69B

No

0.53

True negative


rs2050831

VPS13A

No

0.63

False positive


rs6670163

RYR2

No

0.55

False positive


rs859101

SLC44A3

No

0.5

True negative


rs11084127

ZNF615

No

0.46

True negative


rs7950175

KIRREL3

No

0.48

True negative


rs13064991

SLC6A20

No

0.45

True negative


rs6541240

TTC13

No

0.51

True negative


rs2278419

ZNF350

No

0.45

True negative


aThe predicted result using DER ≥ 0.55. DER, differential expression ratio; GWAS, genome-wide association study; T2DM, type 2 diabetes mellitus.

Chen et al. Genome Biology 2008 9:R170   doi:10.1186/gb-2008-9-12-r170

Open Data