Fig. 3: Volcano and Circos plot analysis of the two data sets of t(6;11) fusion genes.

A Gene entries for protein-coding genes of all six cell lines were used to visualize the significant changes by volcano plots. Gene symbols together with p values, log2 changes and - log10 (p value) data were used of each cell line to perform the analyses (VolcaNoseR website, huygens.science.uva.nl). The number of gene entries used for the plots is displayed in the top left corner. We used very stringent parameters to visualize in red and in blue the most significant changes in gene expression (log2 = ±2, −log₁₀(p value) > 5). Also, here a significant up- and downregulation are only seen on CO1 cells, while the patterns in exMLL-AF6 and CO2 cells are nearly identical and display mostly upregulated genes. B The identified signatures deriving from MACE- and ATAC-Seq experiments were used to create Circos plots in order to help to interpret and understand the findings for each of the six cell lines. Green and red numbers display the number of up-and down-regulated genes with a log2 value of ±1. Similarly, the numbers of increased and decreased chromatin accessibility of the ATAC-Seq experiments are shown for all chromatin fragments that displayed a p value of smaller than 0.05. The comparison between ATAC-Seq and MACE-data allows to intuitively understand the actions of single MLL fusion proteins, as well as of their co-expression. Again, CO1 and CO2 cells displayed the highest numbers of deregulated genes or differential chromatin accessibility. Above the Circos plots, important protein domains are displayed that are present by the fusion proteins in each of the six cell lines (MEN1, CXXC, PHD/BD, and SET).