Breaking free from the chains of pathway annotation: de novo pathway discovery for the analysis of disease processes. (December 2012)

• Record Type: Journal Article
• Authors: Lehne, Benjamin; Schlitt, Thomas
• Is Part Of: Pharmacogenomics. Volume 13:Number 16(2012)
• Page Start: 1967
• Page End: 1978
• Publication Date: 2012-12
• Subjects: disease gene identification -- gene function -- gene network -- genome-wide association studies -- pathway analysis -- protein network; Pharmacogenomics -- Periodicals; 615.1
• DOI: 10.2217/pgs.12.170
• Languages: English
• ISSNs: 1462-2416

Abstract

Interpreting the biological implications of high-throughput experiments such as gene-expression studies, genome-wide association studies and large-scale sequencing studies is not trivial. Gene-set and pathway analyses are useful tools to support the interpretation of such experiments, but rely on curated pathways or gene sets. The recent development of de novo pathway discovery methods aims to overcome this limitation. This article provides an overview of the methods currently available and reviews the advantages and challenges of this approach. In detail, it highlights the particular issues of de novo pathway discovery based on genome-wide association studies data, for which multiple different strategies have been proposed.