To statistically assess the overlap between the genetic and the mRNA expression associations with schizophrenia, we integrated the overlap individually found for each of the four classes of SCZ genetic variation using Fisher’s method for combining P values. For each class of genetic variation and corresponding disease association data, we tested the associations for enrichment in a gene set consisting of the 693 genes found to be significantly (FDR ≤ 5%) differentially expressed between SCZ cases and controls (up- or down-regulated). To control for the fact that some genetically-associated genes may not be brain-expressed, we conditioned all enrichment tests on the background set of 16,423 genes with above-threshold expression that we had included in differential expression analysis (and were thus candidates for being labeled as differential in the first place). Note that all genetic variants and regions were annotated using RefSeq transcripts as downloaded from the UCSC Genome Browser in April 2013; see references 5 and 7 for more details.
