Question: Single-Tissue eQTLs: P-value threshold in GTEX ??
0
gravatar for GabrielMontenegro
2.8 years ago by
United Kingdom
GabrielMontenegro540 wrote:

Hi all,

eQTL is not my area of research, however I am interested to see if a particular SNP has a significant expression in the GTEX database.

I have queried this SNP rs4888622 (found on a paper on gene expression on the human brain). This is the result: (link: https://www.gtexportal.org/home/snp/rs4888622)

Gencode Id  Gene Symbol Variant Id  P-Value Effect Size Effect Size
ENSG00000140873.11  ADAMTS18    16_77396849_T_C_b37 8.0897e-20  -1.09348    -1.1
ENSG00000140873.11  ADAMTS18    16_77396849_T_C_b37 7.24774e-17 -1.0366 -1.0
ENSG00000140873.11  ADAMTS18    16_77396849_T_C_b37 1.43283e-16 -1.12875    -1.1
ENSG00000140873.11  ADAMTS18    16_77396849_T_C_b37 1.02893e-13 -0.900694   -0.90
ENSG00000140873.11  ADAMTS18    16_77396849_T_C_b37 3.07218e-12 -1.00953    -1.0
ENSG00000140873.11  ADAMTS18    16_77396849_T_C_b37 9.55899e-11 -0.973495   -0.97
ENSG00000140873.11  ADAMTS18    16_77396849_T_C_b37 3.60757e-8  -0.780061   -0.78
ENSG00000140873.11  ADAMTS18    16_77396849_T_C_b37 2.51812e-7  -0.786018   -0.79

Now, the P-value is highly significant (top is 8.0897e-20) in many of this tissue, but what P-value threshold should I use? Should I use for a Bonferroni correction based on the number of SNPs and tissues there? How do I get these numbers?

Thank you in advance.

rna-seq snp • 1.7k views
ADD COMMENTlink modified 10 months ago by Kevin Blighe54k • written 2.8 years ago by GabrielMontenegro540

I also have this question, so what the p value should be used when consider the eQTL?

ADD REPLYlink modified 10 months ago • written 10 months ago by dongguiying20170
0
gravatar for Kevin Blighe
10 months ago by
Kevin Blighe54k
Kevin Blighe54k wrote:

You will have to calculate the nominal p-value at which the FDR (false discovery rate) is 5%, and then use that as the cut-off. You can choose other thresholds too, of course. Prior to the association testing, your input SNPs should also be filtered based on HWE (Hardy-Weinberg Equilibrium), e..g, filter out those with HWE p < 5 × 10^−6.

My answer is to merely point you to other material to help link up some of these other posts and work in the field:

Kevin

ADD COMMENTlink modified 10 months ago • written 10 months ago by Kevin Blighe54k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1216 users visited in the last hour