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Table 2 Replication Study of Candidate Genes

From: Genetical genomic determinants of alcohol consumption in rats and humans

 

Affymetrix Results

CodeLink Results

 

Gene Symbol

HXB23

HXB26

Ratio

p-value

HXB23

HXB26

Ratio

p-value

Match Direction

Afap1l1

6.44

6.69

0.84

0.0344

1.22

1.58

0.78

0.0199

Yes

Cckbr

7.92

8.31

0.76

0.0063

2.25

2.84

0.66

0.0110

Yes

P2rx4

8.45

7.52

1.90

0.0122

2.53

1.50

2.04

<.0001

Yes

Tnk2

8.80

8.68

1.09

0.3473

4.17

3.59

1.50

0.0214

Yes

Tubb6

6.92

7.00

0.94

0.5960

0.30

0.69

0.76

0.0400

Yes

Ptpre

7.70

7.63

1.05

0.2589

1.93

0.77

2.23

<.0001

Yes

Mogat2

5.26

5.10

1.12

0.3124

0.63

-0.63

2.39

0.0005

Yes

Nek3

6.05

5.90

1.10

0.1681

-0.36

-0.54

1.13

0.0388

Yes

Tmem2

7.25

7.32

0.95

0.3860

2.47

2.82

0.78

0.0086

Yes

Mc4r

6.01

5.82

0.87

0.0360

-0.39

-0.26

0.91

0.2058

Yes

F2rl1

6.16

6.26

0.94

0.3674

-2.10

-1.72

0.77

0.3943

Yes

Abat

10.52

10.35

1.13

0.0669

4.71

4.66

1.04

0.4464

Yes

Mboat2

8.73

8.46

1.21

0.0797

0.95

1.31

0.78

0.0051

No

Coq7

8.22

8.02

1.15

0.2095

2.60

3.76

0.45

<.0001

No

Dynlrb1

11.27

11.23

1.03

0.7064

5.96

6.00

0.97

0.4726

No

Tpst1

7.70

7.56

1.10

0.1642

3.12

3.77

0.64

0.0004

No

Fgfr2

9.44

9.41

1.02

0.7038

-1.10

4.25

0.02

<.0001

No

Pop5

7.53

7.55

0.98

0.9056

2.58

2.45

1.09

0.1509

No

Rab35

8.91

8.87

1.03

0.7719

4.18

4.28

0.93

0.0107

No

Spire1

9.78

9.74

1.03

0.3554

1.50

3.26

0.30

<.0001

No

  1. Expression levels of the identified candidate genes were determined in brains (n = 5 per strain) of rats from two of the RI strains, HXB RI 26 (high alcohol consumption) and HXB RI 23 (low alcohol consumption) using CodeLink Rat Whole Genome Bioarrays and Affymetrix GeneChip Rat Gene 1.0ST arrays. These strains were chosen because the expression levels of all candidate genes (on CodeLink arrays) that were significantly correlated with alcohol consumption when all the RI strains were analyzed, showed an appropriate direction of differential expression in these two strains compared to the correlation analysis, even if the difference in expression between these 2 particular strains was not statistically significant. Details on analysis, normalization and statistical comparisons are provided in the text. Values represent mean of the log base 2 transformed expression data. "Ratio" is the HXB23/HXB26 ratio of the unlogged intensity values. P values are from the two-sample t-test, and "match direction" refers to the comparison between the two array experiments.
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BMC Biology

ISSN: 1741-7007

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