Fig. 2: Summary of cell type compositions and the number of eGenes.

a Cell type proportion estimates of six cell types astrocytes (Astro), excitatory neuron (Exc), inhibitory neuron (Inh), microglia (Micro), oligodendrocytes (Oligo), and oligodendrocyte precursor cells (OPC) from the brain samples of schizophrenia patients and controls from the CommonMind Consortium (CMC) as well as samples from GTEx Brain. Box plots are derived from n = 283 CMC-Control, n = 250 CMC-SCZ, and n = 175 GTEx Brain samples. b Cell type proportion estimates of seven cell types from whole blood samples of GTEx. Cell type proportions were first estimated for 22 cell types (Supplementary Fig. 8) and then collapsed to seven cell types to avoid individual cell types with very low proportions and variances. Box plots are derived from n = 670 GTEx whole blood samples. In both (a) and (b), for each boxplot, the box ranges from Q1 (the first quartile) to Q3 (the third quartile). The median is indicated by a line across the box. The whiskers extend from Q1 and Q3 to the most extreme data points within the 1.5 IQR of the box and IQR = Q3 − Q1. c A summary of the number of detected eGenes per stratum by method and case/control status for CMC. d A summary of detected eGenes by method for GTEx whole blood. For (c) and (d), the X-axis is the (number of cell type-specific eGenes + 1) in log (base 10) scale. The Y-axis denotes the percentage of cell type-specific eGenes that overlap with eGenes from bulk eQTL mapping.