Table 6

Further validation of genes having bimodal expression (FDR < 0.05) in Pima Indians with bimodal expression of those genes in other populations.

Gene symbol

Chr.

Pima

Bimodality

p-valuea

GSE1485

Bimodality

p-valueb

GSE13070

Bimodality

p-valuec

GSE5086

Bimodality

p-valued

GSE1485

ID

GSE13070

ID

GSE5086

ID


Genes with no Association of Expression and Gender


GSTM1

1

3.54E-44

0.042

0.532

0.405

204550_x_at

215333_x_at

215333_x_at


ERAP2

5

8.76E-18

2.19E-26

0.038

0.00768

219759_at

227462_at

227462_at


HLA-DRB1

6

8.33E-15

1.74E-13

0.859

0.515

204670_x_at

208306_x_at

208306_x_at


ACTN3

11

3.41E-10

-

3.34E-06

9.09E-08

206891_at

206891_at


MAOA

X

3.97E-10

-

9.55E-06

5.48E-04

204388_s_at

204389_at


HLA-DRB5

6

1.20E-09

-

-

-


NR4A2

2

3.21E-08

-

1.37E-04

0.468

216248_s_at

204622_x_at


HLA-C

6

2.02E-07

1.84E-07

0.471

0.607

216526_x_at

216526_x_at

216526_x_at


SLC44A5

1

1.76E-06

-

0.324

0.043

235763_at

235763_at


NR4A3

9

6.63E-06

-

0.690

0.347

207978_s_at

207978_s_at


HSPC157

1

1.13E-05

-

0.987

0.204

219865_at

219865_at


THNSL2

2

1.42E-05

-

0.022

0.315

219044_at

239949_at


ABCC6

16

3.73E-05

-

0.721

0.045

208480_s_at

208480_s_at


C19orf62

19

5.60E-05

-

0.230

0.094

221711_s_at

221711_s_at


Genes with Association of Expression and Gender


DDX3Y

Y

7.86E-54

4.27E-86

1.31E-16

2.30E-18

205000_at

205000_at

205000_at


EIF1AY

Y

3.91E-49

1.36E-75

1.02E-28

2.87E-23

204409_s_at

204409_s_at

204409_s_at


RPS4Y1

Y

7.50E-45

1.20E-138

1.22E-34

7.20E-42

201909_at

201909_at

201909_at


UTY

Y

1.15E-42

8.33E-05

0.00269

1.39E-14

211149_at

211149_at

211149_at


USP9Y

Y

1.46E-32

1.68E-22

2.81E-09

5.08E-16

206624_at

228492_at

228492_at


ZFY

Y

6.01E-22

-

3.86E-04

1.89E-12

230760_at

230760_at


CYorf15B

Y

9.51E-21

-

0.0324

0.00508

214131_at

223646_s_at


ACTB

7

1.94E-14

-

0.111

3.75E-04

AFFX-HSAC07/X0

AFFX-HSAC07/X0


TTTY10

Y

1.48E-11

-

0.194

0.798

224293_at

224293_at


CD24

Y

9.99E-08

0.998

1.18E-04

0.0101

208650_s_at

216379_x_at

266_s_at


ARG2

14

1.23E-06

-

1.45E-04

0.910

203946_s_at

203945_at


TPRG1

3

2.10E-06

-

0.0353

0.961

229764_at

229764_at


a Present study in skeletal muscle tissue of non-diabetic Pima Indians. P-value from Fisher's meta-analysis of trimmed Group A (n = 65) and trimmed Group B (n = 43) for bimodality of RNA expression; shown are all genes having an FDR < 0.05. See additional files 3 and 4.

b Bimodality of RNA expression assessed in lymphoblastoid cells from CEPH Utah residents (n = 193). Not all genes were represented on the chip or had excessive intra-individual variation (-). ID shown is affy_id. P-values < 0.001 from a likelihood ratio test with 6 d.f. shown in bold. GSE1485 expression data provided to GEO as part of unrelated study [28].

c Bimodality of RNA expression assessed in abdominal muscle from patients undergoing gastrointestinal surgery (n = 59). Not all genes were represented on the chip (-). ID shown is affy_id. P-values < 0.001 from a likelihood ratio test with 6 d.f. shown in bold. GSE13070 expression data provided to GEO as part of unrelated study [14].

d Bimodality of RNA expression assessed in skeletal muscle from subjects with a broad range of insulin sensitivity/resistance (n = 62). Not all genes were represented on the chip (-), ID shown is affy_id. P-values < 0.001 from a likelihood ratio test with 6 d.f. shown in bold. GSE5086 expression data provided to GEO as part of unrelated study [15].

Mason et al. BMC Genomics 2011 12:98   doi:10.1186/1471-2164-12-98

Open Data