Difference between revisions of "Researching SNPs (PKU)"
From Bioinformatikpedia
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2590 |
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2590 |
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| − | | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| SNPs, short in/dels, polymorphisms, |
+ | | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| SNPs, short in/dels, polymorphisms, [http://www.ncbi.nlm.nih.gov/SNP/snp_legend.cgi?legend=snpClass others] |
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| submitted by registered sources (labs, institutes,.. ) |
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| submitted by registered sources (labs, institutes,.. ) |
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| clustering of identical submissions by NCBI |
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| clustering of identical submissions by NCBI |
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| current literature |
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| current literature |
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| manually curated |
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| manually curated |
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| + | | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| SNPedia |
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| + | | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| continuous, Wiki-style |
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| + | | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 29,058 |
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| + | | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 53 |
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| + | | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| SNPs |
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| + | | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| publicly edited |
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| + | | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| publicly edited |
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| + | | style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 0 0;"| get genotyped and [http://www.snpedia.com/index.php/Promethease predicted] |
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Revision as of 17:18, 5 June 2012
Contents
Short Task Description
In this weeks task, we will research SNPs in the PAH gene that cause or do not cause a different phenotype of the phenylalanine hydroxylase. The chosen databases are: The public release of the Human Gene Mutation Database (HGMD), dbSNP, SNPdbe, OMIM and SNPedia. You may find a detailed task description here.
Databases
Overview
<figtable id="tab:modelling_scores"> Key Values of the different SNP databases
| Database | Last Update | Number of Entries | Number of Entries concerning PAH | Type of information | Sources | Curation/Verification | Comment |
|---|---|---|---|---|---|---|---|
| HGMD | public after 3 years (quarterly updated) | 50,129 (only mis-/nonsense) | 397 (only mis-/nonsense) | all types of mutations | current literature | manual and computerised search in current literature | too much advertising |
| dbSNP | Oct 2011 | 292,031,791 | 2590 | SNPs, short in/dels, polymorphisms, others | submitted by registered sources (labs, institutes,.. ) | clustering of identical submissions by NCBI | |
| SNPdbe | Mar 2012 | 1,691,464 | 328 | nonsyn. SNPs | Swissprot, dbSNP, PMD, OMIM, 1000 genomes | cf. sources | Predictions of functional effect, experimental evidence if available in source |
| OMIM | June 2012 | 21,257 (Summary entries) | 1 (64 selected SNPs) | catalog of human genes and genetic disorders and traits | current literature | manually curated | |
| SNPedia | continuous, Wiki-style | 29,058 | 53 | SNPs | publicly edited | publicly edited | get genotyped and predicted |
</figtable>
HGMD
http://www.hgmd.cf.ac.uk/ac/gene.php?gene=PAH
dpSNP
http://www.ncbi.nlm.nih.gov/snp/?term=PAH
OMIM
SNPdbe
http://www.rostlab.org/services/snpdbe/dosearch.php?id=name&val=PAH&organism2=human&organism1=
