Table 3

Overrepresentation test for pQTL candidate genes in lists of differentially expressed genes in QTL/microarray experimentsa

Phenotype

pQTL genes

Microarray Experiment

Selected Genes

Genome

Microarray

References





Platform

Probes

GW

QTL

OR

P

OR

P


Rat

Congenic

Hypertension

198

RGU34

26379

45

3

8.15

0.007

9.57

0.005

[44]

Hypertension

267

RGU34

26379

27

0

0.00

1.0

0.00

1.0

[30]

Hypertension

78

RGU34

26379

20

1

15.31

0.067

17.95

0.058

[42,99]

Kidney stones

551

RAE230

31042

50

16

19.27

3.1e-14

26.76

2.2e-16

[37]

Parental

Aerobic running capacity

467

RGU34

26379

199

9

2.26

0.024

2.66

0.009

[34,95,96]


Mouse

Congenic

Anxiety

187

MOE430

45037

9

3

17.60

0.062

30.12

0.037

[105]

IBD

5541

U74Av2

12488

94

16

0.77

0.377

0.26

2.6e-08

[35,110]

Macronutrient intake

1230

ABI

32991

3101

185

1.35

3.9e-04

1.75

1.4e-10

[103]

Obesity

503

Spotted

14938

13

1

4.30

0.221

2.39

0.359

[111]

Osteoporosis

27

Spotted

8734

283

1

3.56

0.253

1.15

0.59

[28,113]

Type I diabetes

1294

Affy.Eos Custom

39000

170

17

2.17

0.006

3.27

5.6e-05

[116]

Parental

Alcohol addiction

3251

MGU74Av2

12488

169

6

0.26

1.4e-04

0.10

6.3e-15

[39,102]

Alcohol addiction

4423

U74Av2

12488

996

151

0.88

0.18

0.30

1.5e-49

[48]

Arthritis

649

MOE430A

22000

1396

18

0.50

0.002

0.41

3.9e-05

[107]

Gallstones

416

Spotted

8734

57

0

0.00

1.0

0.00

0.114

[108,109]

HSCP

867

Filter

5184

200

11

1.72

0.105

0.28

1.6e-06

[49]

5079

Mu11k

13069

77

14

0.93

0.886

0.35

1.4e-04

[47]

Pulmonary capacity

1261

Spotted/Operon

31775

933

1

0.02

4.9e-19

0.03

2.0e-15

[114]

Extremes

EIAD

460

NIA15k

15000

30

0

5.59

4.8e-12

3.10

9.3e-07

[52]

Obesity

1610

Spotted

11000

50

5

1.71

0.23

0.65

0.427

[112]


Phenotype abbreviations: EIAD: Endotoxin-induced airway disease, HSCP: Hematopoietic stem cells proliferation, IBD: Inflammatory bowel disease.

aNumber of pQTL candidate genes was extracted from references or calculated from UCSC Genome Browser within the limits of the pQTL confidence intervals or congenic donor regions. Selected Genes columns indicate number of differentially expressed genes genome-wide (GW) or in candidate regions (pQTL). OR columns denote the ratio of odds, i.e. fraction of candidate genes in the selected and in the references sets. P-values (P) for over- (OR > 1) or under-representation (OR < 1) of QTL candidate genes in list of selected genes were calculated using the genome and microarray probes as reference (see methods). Significant p-values (P < 0.05) are shown in bold.

Verdugo et al. BMC Biology 2010 8:96   doi:10.1186/1741-7007-8-96

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