SCOPE: Stabilized COre gene and Pathway Election

This repository contains code (SCOPE_Functions.R) and TCGA data required to run SCOPE reflecting the results produced in the "Stabilized COre gene and Pathway Election uncovers pan-cancer shared pathways and a cancer specific driver" manuscript. It also includes code and base GTEx data required to run simulations also present in the manuscript as well as sample data and a script to help users get started with the pipeline.

The abstract of the manuscript follows: 

Approaches systematically characterizing interactions via transcriptomic data usually follow two systems: (1) co-expression network analyses focusing on correlations between genes; (2) linear regressions (usually regularized) to select multiple genes jointly. Both suffer from the problem of stability: a slight change of parameterization or dataset could lead to dramatic alternations of outcomes. Here, we propose Stabilized Core gene and Pathway Election, or SCOPE, a tool integrating bootstrapped LASSO and co-expression analysis, leading to robust outcomes insensitive to variations in data. By applying SCOPE to six cancer expression datasets (BRCA, COAD, KIRC, LUAD, PRAD and THCA) in The Cancer Genome Atlas, we identified core genes capturing interaction effects in crucial pan-cancer pathways related to genome instability and DNA damage response. Moreover, we highlighted the pivotal role of CD63 as an oncogenic driver and a potential therapeutic target in kidney cancer. SCOPE enables stabilized investigations towards complex interactions using transcriptome data.