Fabry:Mapping point mutations/Journal

Fabry Disease » Mapping point mutations » Journal

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OMIM

In this database we searched for the gene GLA and downloaded the Table View table of the Allelic Variants (Allelic_variants.txt), which can be found in the Table of Contents. This table was parsed with the perl scripts readOMIM.pl and Omim2table.pl, which created all the output we needed for creation of the tables and statistics.

perl readOMIM.pl
perl Omim2table.pl > omim.wiki

SNPedia

Since there is no special site for the gene GLA, we performed a query with the search term "Gene=GLA". These dbSNP identifiers were downloaded and mapped onto a list of all informations on all identifiers (201) found, when searching for ""snp"[SNP_CLASS] AND GLA[GENE] AND "human"[ORGN]" in the dbSNP (Flat File display). This was done with the perl script parse_dbSNP.pl, which needed the input files snp_result.txt and rsnumber.txt. A wiki table was created with SNPedia2table.pl.

perl parse_dbSNP.pl
perl SNPedia2table.pl > SNPedia.wiki

SNPdbe

The textfile containing all informations gathered in SNPdbe (snps.txt) was downloaded after searching for the gene identifier "NP_000160" in the organism "human" (see). The textfile was parsed with the perl scripts readSNPdbe.pl and SNPdbe2table.pl and vizualised with the R script Hotspots_SNPdbe.R. For now, a SNP was considered disease causing if there was a disease listed, if it was a "N/A" it was assigned "non-disease".

perl readSNPdbe.pl
perl SNPdbe2table.pl > SNPdbe.wiki
R CMD BATCH Hotspots_SNPdbe.R

Mapping

First of all, we created the plots showing the distribution of SNPs along the sequence of the gene GLA with the R Script snp_distr.R. For this we prepared the data with map.pl

perl map.pl
R CMD BATCH snp_distr.R

Afterwards we tried to vizualise disease and non-disease causing point mutations in one plot with Hotspots_all.R. We needed R tables of all databases for this, so some preparation had to be done with readHGMDforR.pl and readdbSNPforR.pl

perl readHGMDforR.pl
perl readdbSNPforR.pl
R CMD BATCH Hotspots_all.R