Difference between revisions of "Researching SNPs (PKU)"
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== Mapping ==
== Mapping ==
<figure id="fig:SNPMapping"> [[File:PkuSNPmappingbig.png|thumb|center|5000px|<caption>Mapping of SNP entries found in the different databases. The bar on the left symbolizes the sequence of the PAH-gene. Every horizontal line refers to at least one entry from any of the databases. The numbers on the left of the bar refer to their amino acid position. Colorcoding in the middle section which contains the different mutations:<br> red means: disease causing according to HGMD<br> orange: missense, but no entry in HGMD<br>green: silent mutation<br>
Colorcoding in the last column of the picture is for better overview and is according to the meaning of the effect from SNPdbe:<br>red: probably disease causing <br>green: probably not disease causing</caption>]]</figure
Colorcoding in the last column of the picture is for better overview and is according to the meaning of the effect from SNPdbe:<br>red: probably disease causing <br>green: probably not disease causing</caption>]]</figure>
Revision as of 17:37, 9 June 2012
Mutants walk the earth.
There are mutants on your block. There's a mutant right next door. There's one in your shoes.
We are, face it, all mutants. Humanity amounts to a string of mutations millennia-old, tweaks that gave us an edge over the next brute down the line. Upright posture; opposable thumb; prefrontal lobes.
The all-time specifically human thing is language. Familiar yet mysterious, language is the angelic part of us angel/beasts. It is spiritual, evanescent, fugitive - even gorgeous words like those have an unearthly shimmer. - from philly.com
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. A very dense journal, which offers only a small overview over the things we did can be found here.
<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|
29 synonymous SNPs
use to annotate common variants/interesting SNPs (e.g. .0002)
Following the task description, we looked at the conservation score, to determine quickly, whether a mutation found here is disease causing or not. Our reasoning can be found at this subpage.
redundant to dbSNP, no additional information => ignore