Benchmarking network-based gene prioritization methods for cerebral small vessel disease.

ABSTRACT: Network-based gene prioritization algorithms are designed to prioritize disease-associated genes based on known ones using biological networks of protein interactions, gene-disease associations (GDAs) and other relationships between biological entities. Various algorithms have been developed based on different mechanisms, but it is not obvious which algorithm is optimal for a specific disease. To address this issue, we benchmarked multiple algorithms for their application in cerebral small vessel disease (cSVD). We curated protein-gene interactions (PGIs) and GDAs from databases and assembled PGI networks and disease-gene heterogeneous networks. A screening of algorithms resulted in seven representative algorithms to be benchmarked. Performance of algorithms was assessed using both leave-o

SUBMITTER: Zhang H 

PROVIDER: S-EPMC8425308 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature