Effectively Identifying eQTLs from Multiple Tissues by Combining Mixed Model and Meta-analytic Approaches
The number of eQTLs detected by the tissue-by-tissue approach (TBT), Meta-Tissue FE, and Meta-Tissue RE in A) four and B) ten tissues of mouse, and the overlap of eQTLs detected by the three methods in C) four and D) ten tissues.
The datasets consist of the gene expression levels from 50 individuals (four tissues) and 22 individuals (ten tissues). We apply a p-value threshold of for Meta-Tissue and a threshold of /the number of tissues for tissue-by-tissue. The Venn diagrams (C and D) show the number of eQTLs detected by either TBT, FE, or RE, by TBT and either of FE and RE, by FE and RE, and by all three methods.