Additional file 6 of Mapping in silico genetic networks of the KMT2D tumour suppressor gene to uncover novel functional associations and cancer cell vulnerabilities

Additional file 6: Table S5. Results GI predictions using GRETTA. A. List of DepMap cancer cell lines by KMT2DWT/KMT2DLOF genotypes and cancer type. DepMap_ID: DepMap cancer cell lines IDs. stripped_cell_line_name: cell line names provided by DepMap without special characters or spaces. disease: cancer type assigned by DepMap. disease_subtype: cancer subtype assigned by Depmap. TCGA_type: matched TCGA cancer type abbreviation (see Methods for details). Total_mutations: total number of mutations detected (LOF and non-LOF). LOF_mutations: number of LOF SNVs and insertion deletions detected (see Methods). CN_status: copy number status. Group: KMT2D group assigned (Control refers to the KMT2DWT group). B. All KMT2D GI prediction results by cancer context. Cancer type context: cancer context KMT2D GI screens were performed in. GeneNameID: hugo gene name with Entrez gene ID. GeneNames: gene name without Entrez gene ID. Control_median: median lethality probability of KMT2DWT cell line group. Mutant_median: median of KMT2DLOF group lethality probabilities. Control_sd: standard deviation of KMT2DWT lethality probabilities. Mutant_sd: standard deviation of KMT2DLOF lethality probabilities. Pval: uncorrected Mann Whitney U-test p-values comparing KMT2DWT and KMT2DWT lethality probabilities. log2FC_by_median: log2-transformed fold change of KMT2DLOF over KMT2DWT lethality probabilities. Interaction_score: GI interaction score for visualisation (see Methods). Adj_pval: Mann Whitney U-test p-values adjusted for multiple testing using permutation test with 10,000 random samplings. GI_direction: whether a GI is alleviating (AL) or synthetic lethal (SL). C. Prioritisation classification assigned to significant GIs (GI prediction tiers I, II, and III). First 17 column names are the same as A. Drug group: drug tractability group assigned to GI. Priority_class: priority class assigned to GI.