Difference between revisions of "Task 8 (MSUD)"
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=== Polyphen2 === |
=== Polyphen2 === |
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− | The prediction resuls of Polyphen2 are shown in the following table. 7 out of 10 mutations are predicted to be probably damaging (at least for the trained set HumDiv). |
+ | The prediction resuls of Polyphen2 are shown in the following table. 7 out of 10 mutations are predicted to be probably damaging (at least for the trained set HumDiv). For the mutation T151M, this does not agree with the results of SIFT. But for this mutations the Polyphen scores are also the lowest of all mutations that are predicted to be damaging. So Polyphen sees an uncertainty for this mutation too, if it is damaging. |
Revision as of 16:06, 27 June 2013
Results
SIFT
The following table shows the prediction of mutation effects by SIFT. 6 out of 10 mutations are predicted to affect protein function.
mutation | prediction | score | median sequence conservation | sequences represented at position |
---|---|---|---|---|
P38H | tolerated | 0.16 | 3.16 | 17 |
M82L | tolerated | 0.56 | 3.03 | 43 |
T151M | tolerated | 0.05 | 3.03 | 46 |
A222T | affect protein function | 0.04 | 3.03 | 46 |
C264W | affect protein function | 0.00 | 3.03 | 46 |
R265W | affect protein function | 0.00 | 3.03 | 46 |
R314Q | affect protein function | 0.01 | 3.03 | 46 |
R346H | affect protein function | 0.00 | 3.03 | 46 |
I361V | tolerated | 0.12 | 3.03 | 46 |
Y413H | affect protein function | 0.00 | 3.03 | 46 |
Polyphen2
The prediction resuls of Polyphen2 are shown in the following table. 7 out of 10 mutations are predicted to be probably damaging (at least for the trained set HumDiv). For the mutation T151M, this does not agree with the results of SIFT. But for this mutations the Polyphen scores are also the lowest of all mutations that are predicted to be damaging. So Polyphen sees an uncertainty for this mutation too, if it is damaging.
HumDiv | HumVar | |||||||
---|---|---|---|---|---|---|---|---|
mutation | prediction | score | sensitivity | specificity | prediction | score | sensitivity | specificity |
P38H | benign | 0.118 | 0.93 | 0.96 | benign | 0.042 | 0.93 | 0.62 |
M82L | benign | 0.002 | 0.99 | 0.30 | benign | 0.006 | 0.97 | 0.45 |
T151M | probably damaging | 0.963 | 0.78 | 0.95 | possibly damaging | 0.622 | 0.80 | 0.85 |
A222T | probably damaging | 1.000 | 0.00 | 1.00 | probably damaging | 0.943 | 0.65 | 0.91 |
C264W | probably damaging | 0.989 | 0.72 | 0.97 | possibly damaging | 0.887 | 0.71 | 0.89 |
R265W | probably damaging | 1.000 | 0.00 | 1.00 | probably damaging | 1.000 | 0.00 | 1.00 |
R314Q | probably damaging | 1.000 | 0.00 | 1.00 | probably damaging | 0.998 | 0.18 | 0.98 |
R346H | probably damaging | 1.000 | 0.00 | 1.00 | probably damaging | 0.993 | 0.47 | 0.96 |
I361V | benign | 0.386 | 0.90 | 0.89 | possibly damaging | 0.610 | 0.80 | 0.83 |
Y413H | probably damaging | 1.000 | 0.00 | 1.0 | probably damaging | 0.999 | 0.09 | 0.99 |