When computing the t-statistic of each gene for a focal tissue, we excluded all samples from similar tissues category (described for each data set below). For example, when computing the t-statistic of specific expression for each gene in cortex using GTEx data, we compared expression in cortex samples to expression in all other samples, excluding other brain regions. We chose to exclude other brain regions because we wanted to include genes that are more highly expressed in brain tissues than in non-brain tissues, even if they are not specific to cortex within the brain. This procedure results in a higher correlation among the t-statistics for the different brain regions; in a separate analysis, we compute within-brain t-statistics to disentangle this signal.
