|
QRT-PCR validation and phenotype prediction |
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| qRT-PCR results: MFS/UC ratio (Wilcoxon p-value) |
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|
|
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| Gene symbol |
Array ratio |
Array subjects |
New subjects |
All subjects |
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|
|
|||||||
| 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. | |||||||
Yao et al. BMC Genomics 2007 8:319 doi:10.1186/1471-2164-8-319 |
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