We aggregated the outcome of the overlap of modules with differentially expressed genes and genetic associations with SCZ, as follows. 1. Overlaps with differentially expressed genes: The genes in each module were used to define a gene set, and each such gene set was tested for overlap with the gene set of differentially expressed genes for schizophrenia (from our CMC data). Briefly, we assess the overlap with genes in each module using Fisher’s exact test, and Bonferroni correction is applied across all modules. Overlaps with genetic associations: The genes in each module were used to define a gene set, and each such gene set was tested for overlap with genetic associations for schizophrenia as described above in the section on differential expression. Briefly, for each module, we consider the genetic overlap for each of the four classes of genetic variation tested (GWAS, CNV, de novo mutations, rare variants), where overlaps within each class of variation are combined by choosing the minimal P value after Bonferroni correction. In Supplementary table 3, we report nominal P values without correction for multiple testing of all modules, since we use this only as a secondary filter for choosing modules of interest.
