Enrichment results of serum urate
Xiang Zhu
2017-04-12
Last updated: 2018-10-05
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Input data
Results below were generated from the GWAS summary statistics published in the paper “Genome-Wide Association Analyses Identify 18 New Loci Associated with Serum Urate Concentrations” (Nature Genetics, 2013). The summary data file is available at http://metabolomics.helmholtz-muenchen.de/gugc.
Analysis results
Enrichment analyses are summarized by the following three quantities.
- BF: Bayes factor comparing the enrichment model against the baseline model;
- Outside \(\pi\): proportion of trait-associated SNPs that are “outside” the gene set;
- Inside \(\pi\): proportion of trait-associated SNPs that are “inside” the gene set.
The first quantity reflects the significance of enrichment, whereas the last two capture the magnitude of enrichment. For each gene set, we report these three quantities in the last three columns of tables below, on log 10 scale.
Biological pathways
Tissue highly expressed genes
Tissue selectively expressed genes
Cluster distinctively expressed genes
The relationship between tissues and clusters is shown in Figure 1 of Dey et al. (2017); see below.
Session information
Session info ------------------------------------------------------------- setting value
version R version 3.5.1 (2018-07-02)
system x86_64, darwin15.6.0
ui X11
language (EN)
collate en_US.UTF-8
tz America/Los_Angeles
date 2018-10-05 Packages ----------------------------------------------------------------- package * version date source
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withr 2.1.2 2018-03-15 CRAN (R 3.5.0)
workflowr 1.1.1 2018-07-06 CRAN (R 3.5.0)
xtable 1.8-3 2018-08-29 CRAN (R 3.5.0)
yaml 2.2.0 2018-07-25 CRAN (R 3.5.0)This reproducible R Markdown analysis was created with workflowr 1.1.1