Table 2.

Correlations of genes of included in microarray trend analysis versus genes excluded from microarray trend analysis.

	Genes included in array trend analysis			Genes excluded from array trend analysis
Data Set	Correlation	p-value	n	Correlation	p-value	n
All Primers	0.882	<0.0001	45	0.306	0.049	42
Up-regulated on array	0.898	<0.0001	33	0.048	0.8278	23
down-regulated on array	-0.140	0.6641	12	-0.243	0.3155	19
Fold Change ≥ ± 1.4 by array	0.893	<0.0001	28	ND	ND	0
Fold Change < ± 1.4 by array	0.586	0.0134	17	0.306	0.049	42
Fold Change ≥ ± 1.4 by qPCR	0.893	<0.0001	25	0.562	0.0366	14
Fold Change < ± 1.4 by qPCR	0.537	0.0147	20	-0.009	0.9629	28
Ct > median	0.870	<0.00011	22	0.465	0.0339	21
Ct < median	0.895	<0.0001	23	0.004	0.9866	21
Log(Intensity) > median	0.843	<0.0001	22	-0.072	0.7557	21
Log(Intensity) < median	0.934	<0.0001	23	0.443	0.0444	21
p-value ≤ 0.0001	0.910	<0.0001	26	0.872	0.0539	5
p-value > 0.0001	0.708	0.0007	19	0.180	0.2875	37
Up or down-regulated conserved	80.00%*		36	76.19%		32
For verification of the mouse brain DA time course 14 genes included in the array trend set (≥1.7 fold change in at least one time point and a composite p-value ≤0.0001) determined to be of biological interest, given their known responses to DA or the degree of change exhibited by microarray, were selected for validation by qPCR. In addition, 13 genes of lesser confidence that were excluded from array trend analysis were verified by qPCR. Both data sets were normalized to tubulin, alpha 4. The effects of direction of regulation, degree of fold change, Ct value, spot intensity, and array p-value on correlation were examined. All correlations were calculated using Spearman’s Rho. *This value is the percentage of genes for which the direction of change was determined to be the same by both array and qPCR analyses. ND: no data (insufficient sample size, n≤2).