Supplementary Figure 10: Gene network analysis of maturing iPSC-iNs.

a, Schematic of FACS-based purification of iPSCs (SSEA4⁺/TRA1–81⁺) and iPSC-iNs (eGFP⁺/PSA-NCAM⁺) over the time course of in vitro differentiation. b, Module-trait associations. Detailed analysis showing Pearson’s correlation coefficients and student p-values for associations between covariates (x-axis) and module eigengenes; n = 52 iPSC-iN time series samples; ASD iPSC-iNs: n = 8 independent cell lines at 4 time points, control iPSC-iNs: n = 5 independent cell lines at 4 time points. c, Scatterplots showing ranked expression (left) and connectivity (right) between the two temporal datasets (NSC-derived neurons (NSC-Ns) and iPSC-iNs). The highly significant Pearson correlations between the NSC-N and the iPSC-iN network (P < 1 × 10⁻²⁰⁰, two-sided Student t-test) suggests that the datasets are comparable; n = 22,111 genes. d, Gene set enrichment analysis comparing the 18 co-expression modules of the iPSC-iN network with the TM1, TM2 and TM3 gene sets from the network of NSC-derived neurons. Boxes are filled if the enrichment P < 0.05 and odd ratios are presented (Fisher’s exact test); TM1: n = 1,530 genes, TM2: n = 294 genes, TM3: n = 401 genes. e, Scatterplot between Gene Significance (GS time; days of iN conversion) and intramodular connectivity (kME) of TM1 genes within the TM1-equivalent module MEblue in the iPSC-iN network. Each point corresponds to a gene in the blue module. GS time and kME exhibit a very significant Pearson correlation, implying that the hub genes of the blue module also tend to be highly correlated with time in the iPSC-iN network (P < 1 × 10⁻²⁰⁰, two-sided Student t-test); n = 1,530 genes. f, Module eigengene (ME) dynamics of the iPSC-iN module blue averaged across developmental time. Upper panel: Heatmap showing average MEs of iPSC-iN module blue across time. Blue: low expression, Red: high expression. Lower panels: Plots of iPSC-iN module blue showing trajectories of module eigengenes for control (black) and ASD (red) across time, with dots representing values for each individual. g, GS values of the top 60 hub genes across developmental time and between conditions. Box plots show median (center line) and IQR, with whiskers representing the minimum and maximum; n = 60 TM1 genes.