Agglomerative hierarchical clustering with a weighted pair-group average was performed using a Pearson correlation coefficient as the similarity metric on the matrix of NanoString PsychGene probes that showed statistically significant differential expression in either the NPCs or neurons comparing the BD and unaffected parental control samples with XLSTAT (v2014.3.02). Disease Association Protein-Protein Link Evaluator (DAPPLE) v2.0 was run using the web based tool available at www.broadinstitute.org/mpg/dapple/dappleTMP.php. The resulting direct and indirect network was constructed. Of the input seed list of 53 differentially expressed genes, 43 were mappable by DAPPLE while a subset of genes that were also differentially expressed (C4ORF45, CACNG8, FNIP2, HLA-B, IRX3, NKX2.2, NKX6.1, POTED, SOX5, VEPH1) were not. The p-value for the global network parameters and individual p-values for seed proteins representing the probability that by chance the seed protein would be as connected to other seed proteins (directly or indirectly) as is observed were calculated with 5,000 within-degree, node-label permutations. For Gene Ontology (GO) analysis of RNA-seq profiles, DAVIDv6.7 bioinformatics software was used to determine GO categories with significant representation (p<0.05, Benjamini-Hochberg corrected).
