A critical comparison of topology-based pathway analysis methods.

ABSTRACT: One of the aims of high-throughput gene/protein profiling experiments is the identification of biological processes altered between two or more conditions. Pathway analysis is an umbrella term for a multitude of computational approaches used for this purpose. While in the beginning pathway analysis relied on enrichment-based approaches, a newer generation of methods is now available, exploiting pathway topologies in addition to gene/protein expression levels. However, little effort has been invested in their critical assessment with respect to their performance in different experimental setups. Here, we assessed the performance of seven representative methods identifying differentially expressed pathways between two groups of interest based on gene expression data with prior knowledge of p

SUBMITTER: Ihnatova I 

PROVIDER: S-EPMC5784953 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature