Fig. 1

Methodological overview. Left A cancer cell transcriptional regulatory network (CCTN) was inferred from gene expression and corresponding gene copy number data of 768 cancer cell lines of the Cancer Cell Line Encyclopedia (CCLE) and validated using data of thousands of tumor patients from The Cancer Genome Atlas (TCGA) and thousands of gene-specific perturbation experiments from the Library of Integrated Network-based Cellular Signatures (LINCS). Right Signature genes whose expression correlated with patient survival were determined for individual TCGA cohorts and validated on independent test data. Center CCTN was applied to gene copy number profiles of individual tumor patients of TCGA cohorts to predict the impacts of individual gene CNAs on cohort-specific survival signature genes and to separate short- from long-lived patients. The impact prediction was validated using LINCS data, known cancer genes, and data from two independent clinical cohorts and new TCGA patients. CCLE Cancer Cell Line Encyclopedia, CNA copy number alteration, CCTN cancer cell transcriptional regulatory network, LINCS Library of Integrated Network-Based Cellular Signatures, TCGA The Cancer Genome Atlas