Jackson laboratory, version 11/22/2016). We then calculated a metric of gene expression specificity by dividing the expression of each gene in each cell type/tissue by the total expression of that gene in all cell types/tissue, leading to values ranging from 0 to 1 for each gene (0: meaning that the gene is not expressed in that cell type/tissue, 1 that 100% of the expression of that gene is performed in that cell type/tissue). We selected the 10% most specific genes per cell type (or tissue) with an expression level of at least 1TPM, or 1 UMI per million, for downstream analyses and used MAGMA v1.0826 to test whether they were enriched for genetic associations. We performed a one-sided test as we were only interested in enrichments for genetic associations (in contrast with depletions). We also applied partitioned LD score regression (LDSC) as described27 to the top 10% genes for each cell type for heritability enrichment. We selected the one-sided coefficient z-score p-value as a measure of the association of the cell type/tissue with schizophrenia.
