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

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

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.

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