Enrichment results of type 2 diabetes

Last updated: 2018-10-05

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File	Version	Author	Date	Message
html	1c85967	Xiang Zhu	2018-10-05	Build site.
html	17348de	Xiang Zhu	2018-06-28	Build site.
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Input data

Results below were generated from the GWAS summary statistics published in the paper “Large-Scale Association Analysis Provides Insights into the Genetic Architecture and Pathophysiology of Type 2 Diabetes” (Nature Genetics, 2012). The summary data file is available at http://diagram-consortium.org/downloads.html.

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

devtools::session_info()

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        
 assertthat    0.2.0   2017-04-11 CRAN (R 3.5.0)
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 base        * 3.5.1   2018-07-05 local         
 bindr         0.1.1   2018-03-13 CRAN (R 3.5.0)
 bindrcpp      0.2.2   2018-03-29 CRAN (R 3.5.0)
 compiler      3.5.1   2018-07-05 local         
 crayon        1.3.4   2017-09-16 CRAN (R 3.5.0)
 crosstalk     1.0.0   2016-12-21 CRAN (R 3.5.0)
 datasets    * 3.5.1   2018-07-05 local         
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 stats       * 3.5.1   2018-07-05 local         
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 tools         3.5.1   2018-07-05 local         
 utils       * 3.5.1   2018-07-05 local         
 whisker       0.3-2   2013-04-28 CRAN (R 3.5.0)
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 xtable        1.8-3   2018-08-29 CRAN (R 3.5.0)
 yaml          2.2.0   2018-07-25 CRAN (R 3.5.0)

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