Question: Differential gene expression using GWAS/SNPs data
gravatar for Star
23 months ago by
Star20 wrote:

Hi all,

I have the list of genes (~6000) along with heritability values, heritability standard error and heritability p-value. I have calculated the z-score, p-values for z-score and FDR for each gene using R. After applying the threshold of z-score > 7 and FDR < 0.05, I have 841 genes. My ultimate goal is to see the association of the shortlisted genes w.r.t gene expression to a certain phenotype of interest. One approach might be doing the association test (logistic regression) followed by the permutations and calculating the empirical p-value for each gene? Will this be the right direction? What else direction can I follow?

As I am pretty new to this field, so my question may sound a bit naive, but I don't know how to proceed. Any guidance would be much appreciated!!!


snp R gene • 477 views
ADD COMMENTlink written 23 months ago by Star20

Can you clarify the exact dataset(s) that you have? - genotype and expression data?

ADD REPLYlink written 23 months ago by Kevin Blighe68k
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