While the multiple-tissue analysis included annotations for many different brain regions, the gene sets for the different brain regions were often highly overlapping so that for many traits, many brain regions were identified as enriched. For example, nearly every brain region in either the GTEx or Franke lab data was found to be enriched at FDR<5% in schizophrenia (Figure 2). To differentiate among brain regions, we restricted ourselves to gene expression data only from samples from the brain in the GTEx data. We computed t-statistics within the brain-only data set; e.g. we computed t-statistics for cortex vs. other brain regions instead of cortex vs. other tissues in GTEx, and we used these new t-statistics to construct and test gene sets as in the multiple-tissue analysis. In this analysis, we set each tissue to be its own category for computation of t-statistics, and we used age and sex as covariates. Individual-level data was not available for the Franke lab data set, and thus we could not compute within-brain t-statistics for this data set.
