RRHO outputs two gene sets consisting of most up and downregulated genes, with most upregulated genes referring to a list of genes that are associated with both conditions, and most downregulated genes referring to a list of genes that are not associated with both conditions. Therefore, we employed most upregulated genes as a gene list that is shared between two disorders, hence representing pleiotropic genes. We then generated pleiotropic genes shared in at least four disorders by intersecting RRHO most upregulated genes between the following disorder pairs (ADHD vs. ASD/BD/SCZ/MDD; ASD vs. BD/SCZ/MDD; BD vs. SCZ/MDD; and SCZ vs. MDD). Since psychiatric disorder-associated genes showed neurodevelopmental and neuronal enrichment, we used fetal brain and neuronal H-MAGMA results. We merged the gene sets by a union function in R and obtained uniquely identified genes. The code is provided in the github repository: https://github.com/thewonlab/H-MAGMA. In the end, we obtained 1,841 genes that are shared in more than four disorders, and defined them as pleiotropic genes. These genes were compared with the genes mapped to pleiotropic versus non-pleiotropic GWS loci from the meta-analysis
