Extending differential gene expression testing to handle genome aneuploidy in cancer
Fig 4
Cross-cancer comparison of gene-dosage classes and their functional associations.
(A) Venn diagrams illustrate the overlap of DeConveil defined gene categories (DSGs, DIGs, and DCGs) across LUAD, LUSC, and BRCA. Selected oncogenes (ONC) and tumor suppressor genes (TSGs) found in each category are highlighted. Additionally, lncRNAs were identified within the DCGs category. Genes classified differently across cancer types are assigned to all relevant categories. (B) Gene Ontology (GO) over-representation analysis for biological processes associated with DSGs, DIGs, and DCGs across three cancer types. Dot size indicates the number of genes per term, and color denotes enrichment significance (–log10 adjusted p-value). (C) Distribution of ONC and TSGs within each gene category across private DEGs of three cancer types.