The landscape of metabolic pathway dependencies in cancer cell lines
Fig 1
Integration of gene expression and CRISPR gene dependencies to identify metabolic pathway dependencies.
A) Schematic outlining the approach for Genetic Pathway Dependency Enrichment Analysis (Genetic PDEA). Cancer cell lines from the CCLE were first stratified by culture type (adherent, suspension) and culture medium (RPMI, DMEM), and then their metabolic pathway activity was inferred using single-sample GSEA (ssGSEA). The resulting pathway activities were integrated with gene dependency to assess association with metabolic pathway activity. B-C) Simulated data (see Methods) was used to assess the sensitivity of the Genetic PDEA approach. The heatmaps represent the percentage of significant results at each gradient added. Values added to the expression gradient resulted in slightly stronger correlation coefficients and Genetic PDEA results compared to values added to dependency gradient.