For all differential expression comparisons, only the significant results that agreed between edgeR and DESeq2 methods were used in downstream analysis. Once individual fold changes and P values for dysregulated genes in all 4 SCZ hGPC lines were established relative to control lines, the differential expression of pooled SCZ to pooled CTR lines was performed. For each SCZ cell line, separate DE comparisons were performed against each control line and the intersection of the DE genes was taken as a representative list for that SCZ line against the control population. Fold changes and FDR-adjusted P values reported were calculated by edgeR. Functional annotation of the conserved set of SCZ-dysregulated genes was done using ToppCluster (Kaimal et al., 2010) and Ingenuity Pathway Analysis (IPA) (http://www.qiagen.com/ingenuity). Network visualization and analysis of the results of functional annotation were performed in Gephi (Jacomy et al., 2014) visualization software.
