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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.