Supporting information for BE1 experiment.

ccle.xlsx: Cancer Cell Line Encyclopedia (CCLE) derived information for 6 of the 7 cell lines used in BE1 experiment. The following files were retrieved from CCLE (ccle folder): Cell_lines_annotations_20181226.txt, CCLE_Fusions_20181130.txt, CCLE_metabolomics_20190502.csv, OmicsExpressionProteinCodingGenesTPMLogp1.csv, OmicsSomaticMutations.csv. Using the command.R script, in ccle folder, we extract only the information referring to the following cell lines: PC9, A549, NCI-H596,NCI-H1395, DV90, HCC78.
Excel sheets:
celllines: cell lines annotation
fusions: detected fusion genes
metabolomic: dataset of 225 metabolite levels, profiled using liquid chromatography–mass spectrometry (LC-MS)
log2TPM: gene expression, TPM values of the protein coding genes. Values are inferred from RNA-seq data using the RSEM tool and are reported after log2 transformation, using a pseudo-count of 1; log2(TPM+1)).
somatic: all the somatic point mutations and indels called using Mutect2.
drivers_genes_relations.xlsx: IPA/TRRUST2 derived Information referring to tumor driver genes (EGFR, MET, KRAS, BRAF, ERBB2, ALK, ROS1) expressed in the seven cell lines used in this experiment. The analysis was performed on IPA on June 2nd 2023 (this dataset folder ipa) and on TRRUST2 database (https://www.grnpedia.org/trrust/). For each driver gene (EGFR, MET, KRAS, BRAF, ERBB2, ALK, ROS1) were detected the directly connected genes (upstream and downstream) using grow function in IPA. The genes information and the connections were retrieved.
Excel sheets:
all type of connection detected
drivers-connections all types of connection depicted in IPA for EGFR, MET, KRAS, BRAF, ERBB2, ALK, ROS1
activity only functional connections, e.g. expression, activation. (IPA and TRRUST2)
activity 1st layer (v 2.0 only functional connections, e.g. expression, activation. (IPA and TRRUST2))
activity 2nd layer (v 2.0 only functional connections of the downstream genes from the 1st layer (e.g. 1st layer: ALK -> MAPK3; 2nd layer MAPK3 -> CDK4))
membership expansion of the subset of IPA ids including multiple genes
modification protein modification, e.g. phosphorylation
prot-prot protein protein interaction
prot-DNA protein-DNA interaction
XXX connected genes description of the genes involved in the connections