Abstract
Our database tool, called Real-Time Engine for Expression Quantitative Trait Loci Analyses (RTeQTL), can efficiently provide eQTL association results that are not available in existing eQTL databases browsers. These functions include (i) single SNP (single-nucleotide polymorphism) and (ii) two-SNP conditional eQTL effects on gene expression regardless of the magnitude of P-values. The database is based on lymphoblastoid cell lines from >900 samples with global gene expression and genome-wide genotyped and imputed SNP data. The detailed result for any pairs of gene and SNPs can be efficiently computed and browsed online, as well as downloaded in batch mode. This is the only tool that can assess the independent effect of a disease- or trait-associated SNP on gene expression conditioning on other SNPs of interest, such as the top eQTL of the same gene. It is also useful to identify eQTLs for candidate genes, which are often missed in existing eQTL browsers, which only store results with genome-wide significant P-value. Additional analyses stratifying by gender can also be easily achieved by this tool.Database URL: http://eqtl.rc.fas.harvard.edu/
Highlights
The ability to interrogate and study the genetics of functional phenotypes that are intermediate between a DNA variant and a disease phenotype of interest can point to the true biological mechanism, critical to disease etiology
We provide a manual on our website and readers will find detailed description on how to use our database http://eqtl.rc.fas.harvard.edu/mrce/static/ RTeQTL_manual_20130623.pdf
Full details for regression results are available, including effect size, standard error, test statistics, P-value as well as gene annotation of the expression probe and SNPs and the column to indicate the samples used for analysis
Summary
The ability to interrogate and study the genetics of functional phenotypes that are intermediate between a DNA variant and a disease phenotype of interest can point to the true biological mechanism, critical to disease etiology. Our database tool, called Real-Time Engine for Expression Quantitative Trait Loci Analyses (RTeQTL), can efficiently provide eQTL association results that are not available in existing eQTL databases browsers. These functions include (i) single SNP (singlenucleotide polymorphism) and (ii) two-SNP conditional eQTL effects on gene expression regardless of the magnitude of P-values.
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