Table 2.

qPCR results validate the microarray results in 13 out of 16 comparisons

		SD vs. PCK qPCR			SD vs. PCK microarray
Probe target	Gene Name	SD	PCK	Significance	Fold Change	significance
1368224_AT	Serpina3	1 ± 0.24	74.47 ± 18.61	P < 0.05	27.44	P < 0.05
1371970_AT	Fam111A	1 ± 0.22	40.62 ± 4.89	P < 0.05	32.08	P < 0.05
1391262_AT	LOC690251	1 ± 0.13	11.86 ± 3.48	P < 0.05	−7.70	P < 0.05
1369663_AT	Ephx2	1 ± 0.17	2.58 ± 0.66	P < 0.05	−6.05	P < 0.05
1391864_AT	Enpp6	1 ± 0.17	0.24 ± 0.06	P < 0.05	−6.65	P < 0.05
1397688_AT	Pcdh9	1 ± 0.47	0.28 ± 0.03	P < 0.05	−2.06	P < 0.05
1379420_AT	RGD1565002	1 ± 0.14	1.14 ± 0.15	NS	1.01	NS
1383783_AT	Pcdh9	1 ± 0.32	0.43 ± 0.09	P < 0.05	−5.96	P < 0.05
		FHH vs. FHH.Pkhd1 qPCR			FHH vs. FHH.Pkhd1 microarray
		FHH	FHH.Pkhd1	Significance	Fold Change	significance
1368224_AT	Serpina3	1 ± 0.14	0.98 ± 0.27	NS	−1.14	NS
1371970_AT	Fam111A	1 ± 0.15	1.84 ± 0.15	P < 0.05	1.12	P < 0.05
1391262_AT	LOC690251	1 ± 0.22	0.48 ± 0.11	NS	−1.14	NS
1369663_AT	Ephx2	1 ± 0.10	1.49 ± 0.22	NS	1.03	NS
1391864_AT	Enpp6	1 ± 0.09	0.95 ± 0.12	NS	1.01	NS
1397688_AT	Pcdh9	1 ± 0.24	0.33 ± 0.07	P < 0.05	−2.32	P < 0.05
1379420_AT	RGD1565002	1 ± 0.08	1.80 ± 0.40	P < 0.05	1.04	NS
1383783_AT	Pcdh9	1 ± 0.17	0.52 ± 0.13	P < 0.05	−3.39	P < 0.05

PCR primers were designed over 9 different Affymetrix probes (probe target) that correspond to 8 different genes (Gene Name). delta Ct values (probe of interest Ct - GAPDH Ct) between SD, PCK, FHH, and FHH.Pkhd1 were compared by 1-way ANOVA to determine significance status (either significant [P < 0.05] or not significant [NS]). Data are presented as PCK fold change vs. SD and FHH.Pkhd1 fold change vs. FHH. Microarray fold changes and significance for each respective Affymetrix probe is listed to the right of the qPCR result. Microarray fold changes in boldface indicate that the result (fold change direction and significance status) was reproduced by qPCR.