Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure

doi:10.1186/gb-2009-10-4-r44

Genome Biology

Volume 10
Issue 4

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Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure

Reuben Thomas¹^* , Julia M Gohlke¹^* , Geffrey F Stopper² , Frederick M Parham¹ and Christopher J Portier¹

¹Environmental Systems Biology Group, Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, RTP, NC 27709, USA

²Department of Biology, Sacred Heart University, Fairfield, CT 06825, USA

author email corresponding author email* Contributed equally

Genome Biology 2009, 10:R44doi:10.1186/gb-2009-10-4-r44


Published:	24 April 2009

Subject areas: Bioinformatics, Genome studies, Methods

Abstract

A method is proposed that finds enriched pathways relevant to a studied condition using the measured molecular data and also the structural information of the pathway viewed as a network of nodes and edges. Tests are performed using simulated data and genomic data sets and the method is compared to two existing approaches. The analysis provided demonstrates the method proposed is very competitive with the current approaches and also provides biologically relevant results.