Analysis of associations between cancer driver mutations and PPI neighbours
Authors/Creators
- 1. BioISI – BioSystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa
- 2. Universidade de Lisboa Faculdade de Ciencias
Description
Data files necessary to run 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
The raw data files were retrieved from the TCGA Pan Cancer cohort through the UCSC Xena online tool (https://pancanatlas.xenahubs.net):
1- gene expression data
https://tcga-pancan-atlas-hub.s3.us-east-1.amazonaws.com/download/EB%2B%2BAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena.gz
2- mutation data
https://tcga-pancan-atlas-hub.s3.us-east-1.amazonaws.com/download/mc3.v0.2.8.PUBLIC.nonsilentGene.xena.gz
3- clinical data
https://tcga-pancan-atlas-hub.s3.us-east-1.amazonaws.com/download/Survival_SupplementalTable_S1_20171025_xena_sp
4- disease and sample type data
https://tcga-pancan-atlas-hub.s3.us-east-1.amazonaws.com/download/TCGA_phenotype_denseDataOnlyDownload.tsv.gz
Cancer driver genes included in the study were collected from http://network-cancer-genes.org/