Fig. 4: Analyses of de novo and gene shut-down by the DAGE module.

The Filemaker Database program was used to identify reliably all genes that were either de novo induced or were completely shut-down due to the presence of fusion proteins. The resulting VENN diagrams show the distribution of the identified target genes by number, and which target gene is induced or repressed by which fusion protein. Along with the number of genes (colored in green or red), the “number of reads” for these gene sets is displayed; in case of upregulation, the reads of the de novo genes is displayed; in case of downregulation, the displayed number reads are deriving from the mock cell line. Certain areas in the VENN diagrams were colored in light blue, light orange and light red. These parts of the VENN diagrams correspond with the right colored areas, where we have displayed gene names. The genes which we displayed were overlapping between de novo upregulated genes and the highly significant gene sets identified to be at least 4-fold upregulated (980 genes for CO1 cells, 608 genes for exMLL-AF6, and 655 for CO2 cells). The 21 highly upregulated genes found in CO1 cells (light blue) did not reveal a convincing pathway, however, the genes displayed in the light orange (37 genes) and red boxes (49 genes) overlapped nearly completely. The two underlined gene names in the light orange box derived from exMAF6, all genes not underlined in the light orange and red box (n = 35) derived from the intersection, and the 14 underlined gene names in the light red box derived from CO2 cells. Of interest, these few genes revealed a pathway-specific for myeloid cells.