help needed for SNP Analysis these are silent snps and don't change any amino acid

Question

[iconforbest]

Hi I have lots of snp data like gg=82, ga=34, aa=05 and on the same subjects I have protein expression data as well.

I have data of five snps and don't know how to present it, and analyse it? or logically tell the whether this snp has something to do with protein expression.

just for an example:

genotype    size     mean protein expressed
gg          145      97.959
ag          38       92.142
aa          4        92.767

please can some one tell what kind of analysis I should do and also what can be done with this kind of data. thanks

[iconforbest]

sorry just very new to it

Answer 1

[Ram]

IMHO, let's say you're looking to establish a correlation between genotype of a silent DNA mutation and the level of protein expression. There are so many different explanations to that. But the first question I'd ask is: are these mutations in the same gene that produces the protein? If not, where are these located and are there any interactions between the mutations' loci and this gene?

If they're located on the same gene, then are these exonic? intronic? Which exon or intron are they in?

These might seem like basic questions, but I always like to ensure I'm working with the correct assumptions. Once these are answered, we can start asking the right questions.

Also, disclaimer: I'm a bit new to this as well.

[russhh]

also, is this locus linked to a more fundamental regulatory locus

[iconforbest]

First of all thanks for the response.

I have four SNPs and two are intronic and in the promotor region and only one in the exon of the same gene. I have also found for intronic and promotor snps there is no amino acid change but exonic snp has L/L not sure what that mean. All snps are in or around the gene encoding for that protein.

Can you please explain how can I find out the interactions between the mutations and loci and this gene?

I will be really really obliged if you could help me through it.

thanks