Difference between revisions of "SNPdbe conservation score (PKU)"
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| + | <figure id="fig:pssm_wt">[[Image:Conservation_PSSM_score_wt.jpg|200px|thumb|right|<caption>Distribution of PSSM scores of SNP positions in the wildtype of the PAH gene</caption>]]</figure> |
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| − | To find a quick-and-dirty way do decide whether a SNP in SNPdbe is disease causing without looking at the predictions, we looked at the conservation scores, specificially the pssm score. We find low percentage scores and low PSSM scores of the wildtype and higher scores of the wildtype even if there is no known effect associated or predicted, so these scores are probably not a good indicator. Nonetheless we try to find a sensible cut-off of conservation values, below which we say a SNP has 'no effect'. The distribution of PSSM scores in wildtype and mutant can be found in <xr id="fig:pssm_wt"> and <xr id="fig:pssm_mt">. Almost all mutants have a PSSM score below 12, whereas the PSSM score of the wildtype is roughly equally distributed from 0 to 50 and declines linearly from 50 to 100. From these observations and for simplicity, we decided to call SNPs in SNPdbe with a PSSM of 12 or less 'not disease-causing'. |
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| + | <figure id="fig:pssm_mt">[[Image:Conservation_PSSM_score_mt.jpg|200px|thumb|right|<caption>Distribution of PSSM scores of SNP positions in mutants of the PAH gene</caption>]]</figure> |
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| + | To find a quick-and-dirty way do decide whether a SNP in SNPdbe is disease causing without looking at the predictions, we looked at the conservation scores, specificially the pssm score. We find low percentage scores and low PSSM scores of the wildtype and higher scores of the wildtype even if there is no known effect associated or predicted, so these scores are probably not a good indicator. Nonetheless we try to find a sensible cut-off of conservation values, below which we say a SNP has 'no effect'. The distribution of PSSM scores in wildtype and mutant can be found in figure <xr id="fig:pssm_wt"/> and <xr id="fig:pssm_mt"/>. Almost all mutants have a PSSM score below 12, whereas the PSSM score of the wildtype is roughly equally distributed from 0 to 50 and declines linearly from 50 to 100. From these observations and for simplicity, we decided to call SNPs in SNPdbe with a PSSM of 12 or less 'not disease-causing'. |
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Revision as of 15:25, 7 June 2012
<figure id="fig:pssm_wt">
</figure> <figure id="fig:pssm_mt">
</figure>
To find a quick-and-dirty way do decide whether a SNP in SNPdbe is disease causing without looking at the predictions, we looked at the conservation scores, specificially the pssm score. We find low percentage scores and low PSSM scores of the wildtype and higher scores of the wildtype even if there is no known effect associated or predicted, so these scores are probably not a good indicator. Nonetheless we try to find a sensible cut-off of conservation values, below which we say a SNP has 'no effect'. The distribution of PSSM scores in wildtype and mutant can be found in figure <xr id="fig:pssm_wt"/> and <xr id="fig:pssm_mt"/>. Almost all mutants have a PSSM score below 12, whereas the PSSM score of the wildtype is roughly equally distributed from 0 to 50 and declines linearly from 50 to 100. From these observations and for simplicity, we decided to call SNPs in SNPdbe with a PSSM of 12 or less 'not disease-causing'.
