Fig. 3

Genes co-expression analysis and enrichment. a A total of 19 co-expression modules were identified in hiPSC-NPCs and 22 modules were identified in hiPSC-neurons, and each module was tested for enrichment of genetic risk loci for ASD, ID, and DD using findings from other large-scale studies. Modules were also examined for enrichment of target genes of FMRP, an RNA binding protein that is associated with ASD risk, as well as differentially expressed genes identified in the current study (see Fig. 2). Enrichment was assessed using a Fisher’s exact test to assess the statistical significance and p values were adjusted for multiple testing using the Bonferroni procedure. We required an adjusted p value < 0.05 (*) to claim that a gene set is enriched within a user-defined list of genes. b Module eigengene (ME) values were associated with PMS for hiPSC-NPCs (triangles) and hiPSC-neurons (circles). Next, genes in hiPSC-NPCs were then forced to construct modules using the gene-module assignments identified in hiPSC-neurons, and vice versa, and these ME values were also associated with PMS. c Functional enrichment was performed on four PMS-associated modules and the top eight enrichment terms (removing redundant annotations) are displayed