Extended Data Figure 10. Sharing information across tissues for cis-eQTLs.

a, The proportion of expressed genes for which cis-eGenes are discovered in single tissues (5% FDR; origin) and the multi-tissue meta-analysis (m > 0.9; arrow), stratified by the sample size of individual tissues. In the meta-analysis, cis-eQTL discoveries are made using Meta-Tissue to identify tissues where the posterior probability a given cis-eQTL effect exists (that is, the tissue’s m value for the variant) is >0.9. b, The proportion of expressed genes that had a cis-eQTL in the subsampled data (n = 70) is shown on the y-axis, and the actual sample size of the tissue is shown on the x-axis. The proportion is shown for the tissue-by-tissue approach (5% FDR; origin) and using Meta-Tissue (m >0.9; arrow). c, For each of the subsampled tissue data sets (n = 70), we identified the additional K discoveries that were made using Meta-Tissue but were not significant at the 5% FDR threshold in the tissue-by-tissue analysis; we then identified the K most significant cis-eQTLs in the tissue-by-tissue analysis with a q value greater than 5% representing the additional discoveries we would make by simply relaxing the FDR. We then compared these two sets of K cis-eQTLs to the list of significant cis-eQTLs found in the full tissue-by-tissue analysis by calculating the proportion of the K cis-eQTLs that were significant in the full analysis (y-axis). The tissues are ordered along the x-axis by increasing sample size in the actual data set. d, The proportion of annotated and expressed genes that were found to be eGenes using the tissue-by-tissue approach and the hierarchical selection procedure implemented by TreeQTL. e, The number of cis-eGene discoveries per tissue (y-axis) against sample size (x-axis). The number of discoveries for the tissue-by-tissue approach are represented by the origin of each segment, while the number of discoveries from the hierarchical selection procedure are shown as arrows. As with Meta-Tissue, the hierarchical procedure improves cis-eGene discovery for tissues with low sample sizes, albeit fewer tissues overall have the benefits of this effect. Furthermore, an outcome of this procedure is that for tissues with high sample sizes, reported numbers of cis-eGenes are more conservative than those observed in the tissue-by-tissue analyses or Meta-Tissue. f, Improvement of cis-eGene discovery by incorporating genomic annotations. For the 26 tissues for which we can relate cell-type specific chromHMM annotations, we identify cis-eGenes accounting for the variant-level genomic annotations and corresponding enrichment estimates using the Bayesian FDR control procedure described previously⁸⁰. For each tissue, the number of cis-eGenes identified by the Bayesian procedure (arrow) is plotted against the tissue-by-tissue results (origin).