A Marfan syndrome gene expression phenotype in cultured skin fibroblasts

BMC Genomics

Table 4 QRT-PCR validation and phenotype prediction

		qRT-PCR results: MFS/UC ratio (Wilcoxon p-value)
Gene symbol	Array ratio	Array subjects		New subjects		All subjects
VDR	1.42^-1	4.59 ^-1	(9.5e-5)	1.25	(8.1e-1)	2.53 ^-1	(7.3e-3)
FBN1	1.89^-1	1.47 ^-1	(5.2e-2)	2.71	(3.3e-9)	N/A
INHBA	1.61^-1	2.20	(1.1e-1)	1.06 ^-1	(6.7e-1)	1.05	(5.0e-1)
ELN	3.34^-1	12.53 ^-1	(2.4e-3)	9.68 ^-1	(2.3e-4)	15.04 ^-1	(1.6e-8)
COL1A2	1.80^-1	1.24 ^-1	(1.1e-1)	2.41 ^-1	(2.3e-8)	2.27 ^-1	(1.4e-4)
PCOLCE	1.26^-1	1.27 ^-1	(5.8e-2)	2.02	(4.6e-6)	N/A
PLOD2	1.22	3.01	(3.8e-4)	1.69	(8.2e-3)	1.85	(2.7e-4)
PDCD10	1.15	1.98	(1.9e-6)	1.65	(4.8e-3)	1.41	(5.0e-5)
PTGES	1.72	3.42 ^-1	(5.8e-4)	1.88	(9.3e-3)	1.68^-1	(6.8e-2)
LMO7	1.13	2.01	(1.0e-3)	4.67	(3.0e-6)	2.77	(1.7e-6)
Overall Significance		Array subjects		New subjects		All subjects
		5	(6.4e-5)	6	(2.8e-6)	6	(2.8e-6)

Column 2: average MFS/UC ratio from array experiments. Remaining columns: ratios of geometric mean transcript abundances of MFS affected vs unaffected control for three subject groups, and Wilcoxon p values for the null hypothesis of no between group differences. The three groups are: (1) "Array Subjects": 30 of the original 36 array subjects (16 known FBN1 mutations and 14 unaffected controls); (2) "New Subjects": 32 new subjects including 16 MFS based on clinical criteria and 16 unaffected controls; and (3) "All Subjects": 42 MFS affected compared to 32 unaffected (all of the above groups plus 10 additional characterized FBN1 mutations and 2 additional controls). (See Table 1 for subject details.) Bold: array validation or significant p value (p < 0.05). Italic: significant p-value but difference opposite to the expected direction. N/A: see text. The bottom section of the table provides a summative assessment: the (binomial) p-value of the observed number of significant qRT-PCR validations (p < 0.05) under the null hypothesis of no between-group differences.

ISSN: 1471-2164