Fig. 2: Compensated and toxic genes.
From: A compendium of Amplification-Related Gain Of Sensitivity genes in human cancer
a Using a Bayesian Negative Binomial regression model, we split the expression of each gene in CCLE and TCGA into components that are scaling (orange) and deviating (red) from DNA content. For TCGA data, we explicitly take into account non-cancer cells (blue). We apply this model across (pan-cancer) and for individual cancer types (tissue-specific). b In the pan-cancer model, deregulation is well correlated between CCLE and TCGA, and we identify commonly compensated (red) and hyperactivated genes (blue). These are genes that show a compensation score in both data sets of less than − 0.3 or more than 0.3, respectively (dotted lines). c Number of pan-cancer (left) and tissue-specific (right) compensated genes, specific to either CCLE or TCGA datasets or common to both. Numbers mentioned in the text are highlighted. d We utilize ORF overexpression screens to quantify barcode abundance for outgrowth after the selection marker, which (e) identifies genes that are promoting (green) or attenuating (red) cell growth when overexpressed. Genes passing the significance threshold of the linear regression model are shown with a black outline. f Numbers of pan-cancer vs. tissue-specific toxic (attenuating) genes and their overlap. Figure 2d was created in BioRender. Beroukhim, R. (2024) https://BioRender.com/z69q647.
