Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method.

ABSTRACT: Genes are organized in functional modules (or pathways), thus their action and their dysregulation in diseases may be better understood by the identification of the modules most affected by the disease (aka disease modules, or active subnetworks). We describe how an algorithm based on the Core&Peel method is used to detect disease modules in co-expression networks of genes. We first validate Core&Peel for the general task of functional module detection by comparison with 42 methods participating in the Disease Module Identification DREAM challenge. Next, we use four specific disease test cases (colorectal cancer, prostate cancer, asthma, and rheumatoid arthritis), four state-of-the-art algorithms (ModuleDiscoverer, Degas, KeyPathwayMiner, and ClustEx), and several pathway databases to vali

SUBMITTER: Lucchetta M 

PROVIDER: S-EPMC7573595 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature