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. Original research article available at: https://www.biorxiv.org/content/10.1101/2025.01.18.633728v1

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.

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/)

Additionally, we also include a processed folder, which includes all generated files required to reproduce the figures in the mentioned article, without needing to run all the provided code.