We analyzed the five gene expression data sets listed in Table 1, mapping mouse genes to orthologous human genes when necessary. To assess the enrichment of a focal tissue for a given trait, we follow the procedure described in Figure 1. We begin with a matrix of normalized gene expression values across genes, with samples from multiple tissues including the focal tissue. For each gene, we compute a t-statistic for specific expression in the focal tissue (Online Methods). We rank all genes by their t-statistic, and define the 10% of genes with the highest t-statistic to be the gene set corresponding to the focal tissue; we call this the set of specifically expressed genes, but we note that this includes not only genes that are strictly specifically expressed (i.e. only expressed in the focal tissue), but also genes that are weakly specifically expressed (i.e. higher average expression in the focal tissue). For a few of the data sets analyzed, we modified our approach to constructing the set of specifically expressed genes to better take advantage of the data available (Online
