SL-scan identifies synthetic lethal interactions in cancer using metabolic networks

Datasets

The gene expression data, mutation data, CRISPR, and drug perturbation data sets used in this study were obtained from the Depmap project https://depmap.org/portal/download/all/. The gene expression data set consists of the log2 transformed transcript per million (TPM) values of 19,221 protein-coding genes from 1406 cell lines across 33 cancer types. We obtained the mutation data from the MAF file CCLE_mutations_21Q4.csv, which contains information on all somatic point mutations called in the DepMap cell lines ²⁷. We used Achilles_gene_effect.csv (22Q2) for the CRISPR data set,…