Zmiz1 and Notch1 coregulate a subset of target genes. (A) Schematic of the strategy used to harvest DN3 cells deprived of Notch1 or Zmiz1 signals. Notch1 target genes were defined as q < 0.1 for the comparison of fragments per kilobase of transcript per million mapped (FPKM) read counts at 24 hours after injection between 10 mg/kg anti-Notch1 antibody (Genentech) and isotype control IgG (“Notch1 data set”). Zmiz1 target genes were defined as q < 0.1 for the comparison of read counts at 43 to 44 hours after injection of 0.2 mg/g tamoxifen between Zmiz1^ΔTamCre mice and TamCre mice (“ΔTamCre data set”). Zmiz1 target genes were also defined as q < 0.1 for the comparison of read counts at 8 weeks after pI-pC injection (40 μg × 5 doses) between Zmiz1^ΔMx1Cre mice and Mx1Cre mice (“ΔMx1Cre data set”). (B) Gene set enrichment analysis (GSEA) analysis plots of genes enriched in the class H MSigDB data set HALLMARK_MYC_TARGETS_V2 (Myc-induced genes) for the Notch1 data set or the ΔMx1Cre data set. The genes are ranked from highest fold change on the left (Notch1_DN or Zmiz1_DN) to lowest fold change on the right (Notch1_UP or Zmiz1_UP). (C) Venn diagram of differentially expressed genes resulting from Notch1 inhibition or Zmiz1 deletion in panel A. Known Notch1 direct target genes in the intersection with known importance for the DN-DP transition are shown. (D) Fold change of known direct Notch1 target genes in the Notch1 data set (red columns) and the ΔTamCre data set (blue columns). The y-axis (fold change) is inverted so that target genes that are induced by Notch1 or Zmiz1 go up from the horizontal axis and target genes that are repressed go down from the horizontal axis. *P < .05; **P < .01; ****P < .0001. TamCre = Rosa26CreER^T2.