Beyond Synthetic Lethality: Charting the Landscape of Pairwise Gene Expression States Associated with Survival in Cancer.

ABSTRACT: The phenotypic effect of perturbing a gene's activity depends on the activity level of other genes, reflecting the notion that phenotypes are emergent properties of a network of functionally interacting genes. In the context of cancer, contemporary investigations have primarily focused on just one type of functional relationship between two genes-synthetic lethality (SL). Here, we define the more general concept of "survival-associated pairwise gene expression states" (SPAGEs) as gene pairs whose joint expression levels are associated with survival. We describe a data-driven approach called SPAGE-finder that when applied to The Cancer Genome Atlas (TCGA) data identified 71,946 SPAGEs spanning 12 distinct types, only a minority of which are SLs. The detected SPAGEs explain cancer driver gen

SUBMITTER: Magen A 

PROVIDER: S-EPMC8261641 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature