Figure 4.

Single-cell differential gene expression analysis identifies early- and late-stage convergent modules of ASD genes. (A) Hierarchical clustering of ASD knockdown profiles using genes differentially expressed in three or more ASD-candidate perturbations reveals a convergence of the transcriptional pathways dysregulated at early and late stages. At the early stage (left column), ADNP, CHD2, ASH1L, DYRK1A, and ARID1B form a transcriptionally convergent module of “delayed differentiation” (purple). At the late stage (right column), ADNP, CHD2, and ASH1L continue to converge. (B) Venn diagram shows significant overlap of differentially expressed genes across five ASD genes at the early stage. All pairwise overlaps have P-values <10⁻²² by hypergeometric testing. (C) Gene Ontology enrichment analysis of early-stage recurrently dysregulated genes highlights relevant biological processes disrupted and predicts disrupted G2/M transition and cellular maturation for “delayed differentiation” genes. Genes driving this enrichment are provided in Supplemental Table S4. (D) Enrichment analysis of late-stage recurrently dysregulated genes highlights relevant biological processes disrupted. (E) Expression of neuron projection genes (Gene Ontology 0010975) in the late-stage samples predicts disrupted neurite extension for PTEN but an enhanced phenotype for ADNP, CHD2, and ASH1L.