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Open Access Method

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*

Author Affiliations

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

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

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Genome Biology 2009, 10:R44  doi:10.1186/gb-2009-10-4-r44

Published: 24 April 2009

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.