Comparative study on gene set and pathway topology-based enrichment methods.

ABSTRACT:

Background

Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions. In contrast, the new group of so called pathway topology-based methods integrates the topological structure of a pathway into the analysis.

Methods

We comparatively investigated gene set and pathway topology-based enrichment approaches, considering three gene set and four topological methods. These methods were compared in two extensive simulation studies and on a benchmark of 36 real datasets, providing the same pathway input data for all methods.

Results<

SUBMITTER: Bayerlova M 

PROVIDER: S-EPMC4618947 | biostudies-literature | 2015 Oct

REPOSITORIES: biostudies-literature