Table 2

Replication Study of Candidate Genes

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


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.

Tabakoff et al. BMC Biology 2009 7:70   doi:10.1186/1741-7007-7-70

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