We conducted pathway enrichment analysis of genes with at least one marker with q-values lower than 0.16 from the joint testing of schizophrenia and COT/FTND/TFC traits. If a marker was within a gene region, it was assigned to the gene; otherwise, it was mapped to its most proximate gene using the 50-kb flanking regions (both 5′ and 3′ sides). Genes identified using SNPs associated with COT, FTND, or TFC were merged for the pathway enrichment analysis, for which we used the hypergeometric test implemented in the tool WebGestalt (2013 update)74 and the canonical pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. We required each pathway to have at least three genes from our gene list and no more than 300 genes from the reference genome. The P-values from hypergeometric tests were further adjusted by the Benjamini-Hochberg method23. Only pathways with adjusted P-values < 0.05 were considered statistically significantly enriched.
