Difference between revisions of "Researching SNPs (PKU)"

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(→‎HGMD)
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! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0;"| Comment
 
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0; font-style:italic;"| HGMD
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; font-style:italic;"| HGMD
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| public after 3 years (quarterly updated)
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| public after 3 years (quarterly updated)
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 50129 (only mis-/nonsense)
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 50,129 (only mis-/nonsense)
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| 397 (only mis-/nonsense)
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 397 (only mis-/nonsense)
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| all types of mutations
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| all types of mutations
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 0 0;"| current literature
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| 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 0 0;"| manual and computerised search in current literature
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| manual and computerised search in current literature
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 0 0;"| too much advertising
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0;"| too much advertising
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; font-style:italic;"| dbSNP
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| Oct 2011
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 292,031,791
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| 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, a few others
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| 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
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0;"|
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; font-style:italic;"| SNPdbe
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| Mar 2012
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1,691,464
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 328
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| nonsyn. SNPs
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| Swissprot, dbSNP, PMD, OMIM, 1000 genomes
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| cf. sources
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0;"| Predictions of functional effect, experimental evidence if available in source
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; font-style:italic;"| OMIM
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| June 2012
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 21,257 (Summary entries)
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1 (64 selected SNPs)
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| catalog of human genes and genetic disorders and traits
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| 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
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 0px 1px 0;"| source
 
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Revision as of 17:03, 5 June 2012

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, a few 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 source

</figtable>

HGMD

http://www.hgmd.cf.ac.uk/ac/gene.php?gene=PAH

dpSNP

http://www.ncbi.nlm.nih.gov/snp/?term=PAH

OMIM

http://omim.org/entry/612349

SNPdbe

http://www.rostlab.org/services/snpdbe/dosearch.php?id=name&val=PAH&organism2=human&organism1=

SNPedia

http://www.snpedia.com/index.php/PAH

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