Context-Specific Notch Targets Figure 2. Identification of cell-context specific Notch1 target genes by genome wide gene expression arrays. (A) 3-dimensional principle component analysis (3D PCA). Notch1 signaling was induced with OHT for 4 h in EB5 NERT or EB5 control cells (Con.) as outlined in Figure 1A. Mesodermal cells (Mesoderm) were additionally treated with or without CHX. The various culture conditions clearly cluster to different areas in the plot, whereas differences induced by Notch1 are rather subtle. An animated presentation of the 3D PCA is available in the supplemental material. (B) Expression heatmap of the Notch1 induced genes. 465 transcripts were identified as differentially expressed due to Notch1 induction in at least one of the conditions (ESCe, ESCm, Mesoderm (Mes.), or Mesoderm+CHX) according to the criteria outlined in Material and Methods. Expression values of the samples were Log2 transformed and normalized within each gene. (C) Venn diagram of Notch1 induced genes in mesodermal cells in the presence or absence of CHX. Of the 262 genes regulated without CHX treatment, 170 are up-regulated and 92 are down- regulated, whereas with CHX treatment 160 of the 179 differentially expressed genes were positively and 19 were negatively regulated. Importantly, PLoS ONE | www.plosone.org 3 July 2010 | Volume 5 | Issue 7 | e11481