Identifying significantly impacted pathways: a comprehensive review and assessment.

ABSTRACT:

Background

Many high-throughput experiments compare two phenotypes such as disease vs. healthy, with the goal of understanding the underlying biological phenomena characterizing the given phenotype. Because of the importance of this type of analysis, more than 70 pathway analysis methods have been proposed so far. These can be categorized into two main categories: non-topology-based (non-TB) and topology-based (TB). Although some review papers discuss this topic from different aspects, there is no systematic, large-scale assessment of such methods. Furthermore, the majority of the pathway analysis approaches rely on the assumption of uniformity of p values under the null hypothesis, which is often not true.

Results

This article presents the most comprehensive comparative stu

SUBMITTER: Nguyen TM 

PROVIDER: S-EPMC6784345 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature