Figure 1.
Scatter plot of differential gene expression values upon E/R KD in two cell lines.
Each dot represents the mean regulation value (log2-fold change of E/R-repressed versus control cells) of three and two replicas, for REH and AT-2 cell lines, respectively. x-axis: REH cell line, y-axis: AT-2 cell line. Negative values indicate a decrease and positive values an increase in gene expression upon fusion gene KD. Green and red dots depict concordantly and significantly modulated genes in a joint analysis of both cell lines.
Table 1.
Top 50 regulated genes from microarray analysis upon E/R KD.
Figure 2.
Functional annotation clustering of differentially expressed genes upon E/R KD.
Visualization of the similarity of functional annotations that were determined by DAVID for down- (left) and up-regulated (right) genes upon E/R KD. The 100 most significant terms (ranked by P-value) are shown for both sets of annotation terms. Significance levels of functional terms are indicated by a color code shown at the bottom of the figure. Due to large differences in the range of P-values for the functional groups resulting from up- and down-regulated genes upon KD, a different color-scheme was used in each panel.
Figure 3.
Meta-groups of functional annotations for up-regulated genes upon E/R KD.
Meta-groups were curated based on gene-clustering of annotation terms. A: Top 100 annotation terms from KD-UP genes, their P-values and their affiliation to meta-groups. Similarity of the meta-groups was based on the number of shared genes. For distance calculations between the meta-groups genes from all contributing terms were taken together. B: Change in expression of individual genes in meta-groups that contain significant annotation terms. The color code at the bottom of the figure indicates the extent of log2-fold changes in gene expression.
Table 2.
Top 50 E/R regulated genes from microarray analysis of KD experiments and primary ALL.
Figure 4.
Validation of selected differentially expressed genes from the KD experiments by RT-qPCR.
Quantification of transcripts of differentially expressed genes. A: Concordantly de-regulated by E/R in the KD and primary leukemias. B: Only regulated in the KD experiments. Boxes cover the median and the interquartile range (25–75th percentiles) and whiskers the minimum and maximum values. *, P≤0.05; **, P≤0.01; ***, P≤0.001 (paired t-test).