Figure 7.

Downregulation of SALL3 and loss of 18q result in the deregulation of genes in pathways associated with pluripotency and differentiation

(A and B) Unsupervised clustering heatmap (A) and PCA (B) of the coding genes with a count per million >1 in at least 2 samples.

(C–E) Volcano plots of differential gene expression analysis for VUB13^del18q vs. hESC^WT and hESC^WT−NT. The labeled genes are the top 20 commonly deregulated genes across the 3 comparisons (C), hESC^WT_SALL3KD vs. hESC^WT and hESC^WT−NT (D), and VUB13^{del18q_SALL3OE} vs. VUB13^del18q (E), with a cutoff value of |log₂fold change|> 1 and FDR < 0.05.

(F) Venn diagrams show the genes downregulated in VUB13^{del18q_SALL3OE} and upregulated in VUB13^del18q and hESC^WT_SALL3KD.

(G) Venn diagrams showing the genes upregulated in VUB13^{del18q_SALL3OE} and downregulated in VUB13^del18q and hESC^WT_SALL3KD.

(H) Venn diagrams of the pathways in the H library common among VUB13^del18q, hESC^WT_SALL3KD, VUB13^{del18q_SALL3OE}, and hESC^WT.

(I) Venn diagrams of the pathways in the C2 library common among VUB13^del18q, hESC^WT_SALL3KD, VUB13^{del18q_SALL3OE}, and hESC^WT.

(J) Pathways commonly deregulated among the different samples are associated with pluripotency and differentiation.