Skip to main content
. Author manuscript; available in PMC: 2015 Feb 1.
Published in final edited form as: Hum Genet. 2014 Feb;133(2):125–138. doi: 10.1007/s00439-013-1377-1

Figure 3.

Figure 3

Two types of hypothesis testing in GWAS gene set enrichment analysis. Starting with the original GWAS data, the competitive null hypothesis (Q1) tests whether the genes in a gene set have the same association pattern compared with the remaining genes in the genome. The self-contained null hypothesis (Q2) tests whether the genes in a gene set are associated with the studied disease or not. To test Q1, a randomization of SNP markers or genes is typically adopted, and to test Q2, a permutation of case/control labels is utilized.