Difference between revisions of "Canavan Disease: Task 08 - Supplement"
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Link back to Task 08: [[Canavan_Disease:_Task_08_-_Sequence-based_Mutation_Analysis|Sequence-based Mutation Analysis]] |
Link back to Task 08: [[Canavan_Disease:_Task_08_-_Sequence-based_Mutation_Analysis|Sequence-based Mutation Analysis]] |
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| − | ==== SIFT ==== |
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| + | == SIFT == |
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| + | Complete result as shown by SIFT. SIFT was one of the most promising tools for a sequence based mutation analysis. |
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<figtable id="sift"> |
<figtable id="sift"> |
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{| border="1" cellpadding="5" cellspacing="0" align="center" |
{| border="1" cellpadding="5" cellspacing="0" align="center" |
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| − | ! colspan="5" style="background:#87cefa;" | Results |
+ | ! colspan="5" style="background:#87cefa;" | SIFT - Results |
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! style="background:#BFBFBF;" align="center" | Mutation |
! style="background:#BFBFBF;" align="center" | Mutation |
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| − | <center><small>'''<caption>''' |
+ | <center><small>'''<caption>''' Complete result as shown by SIFT </caption></small></center> |
</figtable> |
</figtable> |
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| + | == PolyPhen == |
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| − | |||
| + | Complete result as shown by PolyPhen. PolyPhen was the most promising tools for a sequence based mutation analysis. |
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| − | ==== PolyPhen ==== |
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| − | |||
<figtable id="poly"> |
<figtable id="poly"> |
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{| border="1" cellpadding="5" cellspacing="0" align="center" |
{| border="1" cellpadding="5" cellspacing="0" align="center" |
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| − | ! colspan="5" style="background:#87cefa;" | Results |
+ | ! colspan="5" style="background:#87cefa;" | PolyPhen - Results |
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! style="background:#BFBFBF;" align="center" | Mutation |
! style="background:#BFBFBF;" align="center" | Mutation |
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| − | <center><small>'''<caption>''' |
+ | <center><small>'''<caption>''' Complete result as shown by PolyPhen </caption></small></center> |
</figtable> |
</figtable> |
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| − | + | == MutationTaster == |
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| + | Complete result as shown by MutationTaster. MutationTaster was the least promising tools for a sequence based mutation analysis. |
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<figtable id="muttast"> |
<figtable id="muttast"> |
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{| border="1" cellpadding="5" cellspacing="0" align="center" |
{| border="1" cellpadding="5" cellspacing="0" align="center" |
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| − | ! colspan="5" style="background:#87cefa;" | Results |
+ | ! colspan="5" style="background:#87cefa;" | MutationTaster - Results |
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! style="background:#BFBFBF;" align="center" | Mutation |
! style="background:#BFBFBF;" align="center" | Mutation |
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| − | <center><small>'''<caption>''' |
+ | <center><small>'''<caption>''' Complete result as shown by MutationTaster </caption></small></center> |
</figtable> |
</figtable> |
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| + | == SNAP == |
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| − | |||
| + | Complete result as shown by SNAP. SNAP was also one of the most promising tools for a sequence based mutation analysis. |
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| − | |||
| − | ==== SNAP ==== |
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<figtable id="snap"> |
<figtable id="snap"> |
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{| border="1" cellpadding="5" cellspacing="0" align="center" |
{| border="1" cellpadding="5" cellspacing="0" align="center" |
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| − | ! colspan="5" style="background:#87cefa;" | Results |
+ | ! colspan="5" style="background:#87cefa;" | SNAP - Results |
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! style="background:#BFBFBF;" align="center" | Mutation |
! style="background:#BFBFBF;" align="center" | Mutation |
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| − | <center><small>'''<caption>''' |
+ | <center><small>'''<caption>''' Complete result as shown by SNAP </caption></small></center> |
</figtable> |
</figtable> |
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Latest revision as of 20:06, 30 August 2013
Link back to Task 08: Sequence-based Mutation Analysis
Contents
SIFT
Complete result as shown by SIFT. SIFT was one of the most promising tools for a sequence based mutation analysis. <figtable id="sift">
| SIFT - Results | ||||
|---|---|---|---|---|
| Mutation | Prediction | Prediction score | Median Sequence Conservation | Sequences represented at this Position |
| Arg233Trp | affect function | 0.00 | 2.99 | 18 |
| Asn121Asp | affect function | 0.03 | 2.99 | 18 |
| His21Pro | affect function | 0.00 | 3.02 | 17 |
| Ile157Thr | tolerated | 0.49 | 3.02 | 17 |
| Leu272Pro | affect function | 0.00 | 3.01 | 17 |
| Lys213Glu | tolerated | 0.92 | 2.99 | 18 |
| Pro149Ala | tolerated | 0.60 | 3.02 | 17 |
| Pro257Arg | tolerated | 0.13 | 3.01 | 17 |
| Thr166Ile | affect function | 0.05 | 3.02 | 17 |
| Tyr288Cys | affect function | 0.00 | 3.01 | 17 |
</figtable>
PolyPhen
Complete result as shown by PolyPhen. PolyPhen was the most promising tools for a sequence based mutation analysis.
<figtable id="poly">
| PolyPhen - Results | ||||
|---|---|---|---|---|
| Mutation | Prediction | Prediction score | sensitivity | specificity |
| Arg233Trp | probably damaging | 1.000 | 0.00 | 1.00 |
| Asn121Asp | probably damaging | 0.978 | 0.76 | 0.96 |
| His21Pro | probably damaging | 1.000 | 0.00 | 1.00 |
| Ile157Thr | benign | 0.023 | 0.95 | 0.81 |
| Leu272Pro | probably damaging | 0.991 | 0.71 | 0.97 |
| Lys213Glu | benign | 0.003 | 0.98 | 0.44 |
| Pro149Ala | possibly damaging | 0.901 | 0.82 | 0.94 |
| Pro257Arg | possibly damaging | 0.13 | 0.00 | 0.00 |
| Thr166Ile | probably damaging | 0.993 | 0.70 | 0.97 |
| Tyr288Cys | probably damaging | 1.000 | 0.00 | 1.00 |
</figtable>
MutationTaster
Complete result as shown by MutationTaster. MutationTaster was the least promising tools for a sequence based mutation analysis.
<figtable id="muttast">
| MutationTaster - Results | ||||
|---|---|---|---|---|
| Mutation | Prediction | Prediction Probability | ||
| Arg233Trp | disease causing | 0.99 | ||
| Asn121Asp | disease causing | 0.99 | ||
| His21Pro | disease causing | 0.99 | ||
| Ile157Thr | disease causing | 0.98 | ||
| Leu272Pro | disease causing | 0.99 | ||
| Lys213Glu | disease causing | 0.61 | ||
| Pro149Ala | disease causing | 0.99 | ||
| Pro257Arg | disease causing | 0.99 | ||
| Thr166Ile | disease causing | 0.99 | ||
| Tyr288Cys | disease causing | 0.99 | ||
</figtable>
SNAP
Complete result as shown by SNAP. SNAP was also one of the most promising tools for a sequence based mutation analysis.
<figtable id="snap">
| SNAP - Results | ||||
|---|---|---|---|---|
| Mutation | Prediction | SNAP score (simplified) | SNAP score | Prediction Probability |
| Arg233Trp | Non-neutral | 6 | 65 | 80% |
| Asn121Asp | Non-neutral | 7 | 73 | 85% |
| His21Pro | Non-neutral | 5 | 50 | 75% |
| Ile157Thr | Neutral | 8 | -84 | 93% |
| Leu272Pro | Non-neutral | 3 | 39 | 66% |
| Lys213Glu | Neutral | 9 | -90 | 97% |
| Pro149Ala | Neutral | 6 | -65 | 82% |
| Pro257Arg | Neutral | 8 | -82 | 93% |
| Thr166Ile | Non-neutral | 7 | 71 | 85% |
| Tyr288Cys | Non-neutral | 9 | 90 | 95% |
</figtable>
