Table 1

DER values for T1DM and false positive genes in the top 7 WTCCC T1DM loci

Loci

Genea

Associated?b

DER

Correct?c


4q27

TENR

No

0.54

True negative


4q27

IL2

No

0.48

True negative


4q27

IL21

No

0.46

True negative


6p21

HLA-DQB1

Yes

0.68

True positive


6p21

HLA-DRB1

Yes

0.61

True positive


6p21

HLA-B

Yes

0.59

True positive


6p21

HLA-A

Yes

0.59

True positive


6p21

HLA-DPB1

Yes

0.54

False negative


6p21

TAP2

Yes

0.58

True positive


6p21

CFB

Yes

0.59

True positive


6p21

MICA

No

0.5

True negative


6p21

MICB

No

0.53

True negative


6p21

MASIL

No

0.35

True negative


6p21

UBD

No

0.48

True negative


6p21

ITPR3

No

0.62

False positive


12p13

CLEC2D

No

0.51

True negative


12q13

ERBB3

Yes

0.63

True positive


12q24

C12orf30

Yes

0.52

False negative


12q24

SH2B3

Yes

0.58

True positive


16p13

KIAA0350

Yes

0.5

False negative


18p11

PTPN2

Yes

0.64

True positive


aThe positive candidate genes from WTCCC GWAS with reported validation results. bValidated to be associated or unassociated with T2DM in the high-quality genotyping. cThe predicted result using DER ≥ 0.55. DER, differential expression ratio; GWAS, genome-wide association study; T1DM, type 1 diabetes mellitus; WTCCC, Wellcome Trust Case Control Consortium.

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

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