For some analyses, we modified our approach to constructing sets of specifically expressed genes to better take advantage of the data available. Franke lab data set. The values in the publicly available matrix are not a quantification of expression intensity, but rather a quantification of differential expression relative to other tissues in this data set17,18. Thus, it was not appropriate to compute t-statistics in this data set. We used the original values in place of our t-statistics, then proceeded as described in Figure 1.Cahoy data set. The data set of Cahoy et al. had available sets of specifically expressed genes for the three cell types that each had between 1,700 and 2,100 genes. We took these to be the gene sets for the three cell types, then proceeded as in the standard approach, adding a 100kb window and applying stratified LD score regression.PsychENCODE data set. The PsychENCODE data set had available t-statistics for GABAergic neurons vs. Glutamatergic neurons. We used these t-statistics, rather than computing our own.
