FIGURE 3.

Downregulated genes in NT outgrowth are largely rescued in SNT outgrowth. (A) Venn diagrams showing the intersection between the downregulated genes in NT outgrowth compared with NF outgrowth and the upregulated gene SNT outgrowth compared with NT outgrowth. Representation factor (RF) was calculated using real observation/expected observation. The statistical analysis is hypergeometric test with all expressed genes at outgrowth as background. The intersection genes are defined as the rescued genes. (B) The pseudotime of NT (top) or SNT (bottom) TSC derivation inferred from the transcriptomes of the 75 TFs in Clusters 1–3 (Supplementary Figure 3D). (C) Boxplots showing the expression of the 75 TFs in Clusters 1–3. Paired t-test is performed for statistical comparisons, and “holm” is used for adjusting p-values. (D) Expression changes of the component TFs in the PPI network (Figure 2D) in NT outgrowth are recued in SNT outgrowth. Each box is divided into two parts. Left part represents the expression difference between NT and NF outgrowth. Right part represents the expression difference between SNT and NF outgrowth. Color scale bar indicates the fold change of gene expression between NT/SNT and NF in the form of Log2. Red indicates increased expression. Blue indicates decreased expression. (E) Scatterplot showing the significance of the motif enrichment in the proximal TSS regions of the two gene sets in (A). (F) Bubble plot showing gene expressions of the TFs whose motifs are identified in (E). The size of the bubble indicates the mean gene expression at NF, NT, and SNT outgrowths. The color indicates the difference from the mean. (G) ZFP281 ChIP-seq signal distribution around transcript start sites (TSSs) in the rescued genes [the intersection part in (A)]. TSC ZFP281 ChIP-seq data is from GSE111824 (Ishiuchi et al., 2019). The dark blue line indicates ZFP281 ChIP-seq data, while the gray line indicates the input signal.