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Need advice on analyzing SNP data
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5.8 years ago
Australia

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 92.76

T wo are intronic and 2 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.

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

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I guess you could have just bumped your older thread.
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4.8 years ago
David W 4.7k
New Zealand

Typically, the first thing you do with data is plot it.

Make a scatter plot the the number of minor alleles (i.e. AA=0, AB=1, BB=2) for each each SNP against the raw protein expression data, you should be get a feel for wether any of the SNPS are consistently changing expression.

Once you have feel for the data, you can do regressions to see if there are statistically significant effects for the various SNP genotypes

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3 days ago
RamRS 21k
Houston, TX

IMHO you should be thinking along the lines of what question you're trying to answer. 5 SNPs is way too small in terms of data volume to drive a meaningful analysis, at least in silico.

In your case, you might wanna look at if you can establish correlation between SNPs and protein expression levels. Then, you might wanna dig into the genome browser for possible correlations between SNPs and expression/regulation loci (TF binding sites, DNAse hypersensitivity loci, etc). Maybe extract a few bases upstream and downstream of each SNP and check for possible conserved motifs.

I reiterate, there are quite a few (read: tons of) analyses you can do. The principal question is, what are you seeking answers for?

Also, mods ( https://www.biostars.org/u/7403/ ), this is a repeat of https://www.biostars.org/p/115310/ . Since this current post has a more comprehensive question, we might look at possibly closing that one.

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