Last updated: 2018-07-01

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Input data

Results below were generated from the GWAS summary statistics published in the paper “Seventy-Five Genetic Loci Influencing the Human Red Blood Cell” (Nature, 2012). The summary data file is available from the European Genome–Phenome Archive (EGA, http://www.ebi.ac.uk/ega) under accession number EGAS00000000132.

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

R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DT_0.4         plyr_1.8.4     dplyr_0.7.5    R.matlab_3.6.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17      compiler_3.5.0    pillar_1.2.3     
 [4] later_0.7.3       git2r_0.21.0      workflowr_1.0.1  
 [7] bindr_0.1.1       R.methodsS3_1.7.1 R.utils_2.6.0    
[10] tools_3.5.0       digest_0.6.15     jsonlite_1.5     
[13] evaluate_0.10.1   tibble_1.4.2      pkgconfig_2.0.1  
[16] rlang_0.2.1       shiny_1.1.0       crosstalk_1.0.0  
[19] yaml_2.1.19       bindrcpp_0.2.2    stringr_1.3.1    
[22] knitr_1.20        htmlwidgets_1.2   rprojroot_1.3-2  
[25] tidyselect_0.2.4  glue_1.2.0        R6_2.2.2         
[28] rmarkdown_1.10    purrr_0.2.5       magrittr_1.5     
[31] whisker_0.3-2     backports_1.1.2   promises_1.0.1   
[34] htmltools_0.3.6   assertthat_0.2.0  mime_0.5         
[37] xtable_1.8-2      httpuv_1.4.4.1    stringi_1.2.3    
[40] R.oo_1.22.0

This reproducible R Markdown analysis was created with workflowr 1.0.1