Figure 3. Network-level convergence resolves cell-type-specific and developmental-specific node genes.
“Convergent networks” are co-expressed genes that share similar expression patterns across NDD gene perturbations, here resolved for the nine NDD knockouts resolved across all four cell types: ARID1B, ASH1L, CHD2, MED13L, NRXN1, PHF21A, SETD5, SIN3A, SMARCC2. (A) Schematic explaining cell-type specific convergence at the network level using Bayesian bi-clustering and unsupervised network reconstruction. (B) Strength of network convergence across all random combinations of 9 NDD KO perturbations by cell-type. (i) The mean strength of network convergence is significantly different by cell-type, with the highest convergence present in immature iGLUTs. The same KO combinations tested in one cell type may not resolve convergence in another cell type. Each point represents a resolved network, and its calculated convergence strength. Dots that represent the same combinations of KO perturbations, but tested in each cell type, are connected by a line. (C) Convergent network strength was most correlated between mature iGLUTs and iGABAs (Pearson’s Correlation Coefficient (PCC) = 0.6, PHolm <2.2e-16). Convergent network strength in iNPCs was not correlated with network strength in neurons. (D) Venn diagrams of the total number of unique node genes within convergent networks for each cell-type. The lack of overlapping node genes between cell types (D), as well as the weak correlations of convergence strength between immature and mature cell-types (C), suggest greater cell-type specificity in the magnitude of network-level convergence compared to gene-level convergence. (E) Enrichment ratios from over-representation analysis (ORA) of cell-type specific (color of bars) convergent node genes for rare variant targets. (#unadjusted p-value=<0.05, *FDR<=0.05, **FDR<0.01, ***FDR<0.001). (F, G) Representative cell-type specific network plots for convergence across 15 genes (ARID1B, ASH1L, ASXL3, BCL11A, KDM5B, CHD2, MBD5, MED13L, NRXN1, PHF12, PHF21A, SETD5, SIN3A, SKI, SMARRC2) from (F) iNPCs and (G) mature iGLUTs. Network genes were filtered for protein-coding genes, clustered, and annotated based on the primary node gene for each cluster. Gene set enrichment analysis of the networks identified unique functions by cell type. Convergent networks in iNPCs were enriched for pathways associated with neurogenesis (e.g., cell cycle, cell division, EPO signaling), while in mature iGLUTs for pathways associated with synaptic function (transmembrane transport and receptor signaling, secretory vesicles, SNARE complex).