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Table 3 Overrepresentation test for pQTL candidate genes in lists of differentially expressed genes in QTL/microarray experimentsa

From: Serious limitations of the QTL/Microarray approach for QTL gene discovery

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]
  1. Phenotype abbreviations:EIAD: Endotoxin-induced airway disease, HSCP: Hematopoietic stem cells proliferation, IBD: Inflammatory bowel disease.
  2. 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.