Analysis of associations between cancer driver mutations and PPI neighbours

Data files necessary to reproduce the analysis of associations between cancer driver mutation status and its protein physical interactors. Code for the analysis is available at: https://github.com/GamaPintoLab/driver_neighbours. Clone the code repository and extract the data folder to the directory's root. The raw data files were retrieved from the TCGA Pan Cancer cohort through the UCSC Xena online tool (https://pancanatlas.xenahubs.net): gene expression RNAseq—Batch effects normalized mRNA data: EB++AdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena phenotype—Curated clinical data: Survival_SupplementalTable_S1_20171025_xena_sp phenotype—sample type and primary disease: TCGA_phenotype_denseDataOnlyDownload.tsv somatic mutation (SNP and INDEL): mc3.v0.2.8.PUBLIC.xena somatic mutation (SNP and INDEL)—Gene level non-silent mutation: mc3.v0.2.8.PUBLIC.nonsilentGene.xena Protein-protein interaction data: HuRI (Version HI-III-22): http://www.interactome-atlas.org/ APID (August 2024): http://apid.dep.usal.es:8080/APID/init.action STRING (Version 12.0): https://string-db.org/ BioGRID (Release 4.4.225): https://thebiogrid.org/ Cancer driver genes from the Network of Cancer Genes and Heathy Drivers (NCG7.0): http://network-cancer-genes.org/ Consensus RNA data from The Human Protein Atlas (version 24.0): https://www.proteinatlas.org/humanproteome/tissue/data#consensus_tissues_rna The “opentargets” folder contains files from the Open Targets Platform (Version 24.09): (https://platform.opentargets.org/)