Journal Article

RTeQTL: Real-Time Online Engine for Expression Quantitative Trait Loci Analyses

Baoshan Ma, Jinyan Huang and Liming Liang

in Database

Volume 2014, issue ISSN: 0000-0000
Published online July 2014 | e-ISSN: 1758-0463 | DOI: https://dx.doi.org/10.1093/database/bau066

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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/

Journal Article.  2648 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Ecology and Conservation ; Evolutionary Biology

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