Stabilized COre gene and Pathway Election uncovers pan-cancer shared pathways and a cancer-specific driver.

ABSTRACT: Approaches systematically characterizing interactions via transcriptomic data usually follow two systems: (i) coexpression network analyses focusing on correlations between genes and (ii) 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 marked alterations of outcomes. Here, we propose Stabilized COre gene and Pathway Election (SCOPE), a tool integrating bootstrapped least absolute shrinkage and selection operator and coexpression 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 interact

SUBMITTER: Kossinna P 

PROVIDER: S-EPMC9770999 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature