Fig. 3

The gene essentiality scores (β scores) reported from MAGeCK-MLE on two conditions. a, b the β scores of two leukemia cell lines in the leukemia dataset (a), and two biological replicates of mouse ESC cells in the ESC dataset (b). In (a), some well-known driver genes and cell type-specific genes are also labeled. These genes may play distinct roles in two different leukemia subtypes (HL60: acute myeloid leukemia; KBM7: chronic myeloid leukemia), including CDK6 and TRIB1 for HL60, and RUNX1 in KBM7. CDK6 is required in AML growth [17] and TRIB1 over-expression is observed in AML patients compared with CML patients [18]. On the other hand, the frequent RUNX1 loss-of-function mutations are observed in CML to AML transformations [19]. c An illustration of differentially selected genes identified by two-condition comparison algorithms (like RRA, blue rectangles). MAGeCK-MLE can further distinguish cell type-specific genes (red dots) from other genes. Cell type-specific genes are genes having no essentiality in one condition but strong essentiality in the other, and are usually more biologically interesting