Network Methods for Pathway Analysis of Genomic Data

摘要: Rapid advances in high-throughput technologies have led to considerable interest analyzing genome-scale data the context of biological pathways, with goal identifying functional systems that are involved a given phenotype. In most common approaches, pathways modeled as simple sets genes, neglecting network interactions comprising pathway and treating all genes equally important pathway's function. Recently, number new methods been proposed integrate topology analyses, harnessing existing knowledge enabling more nuanced models complex systems. However, there is little guidance available researches choosing between these methods. this review, we discuss eight topology-based methods, comparing their methodological approaches appropriate use cases. addition, present results application curated set ten gene expression profiling studies using annotations. We report computational efficiency consistency across help guide users method. also challenges future outlook for improved analysis methodologies.