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. © 2009 Thomas et al.; licensee BioMed Central Ltd.
Author supplied keywords
- *structural genomics
- *structural proteomics
- DNA polymorphism
- Xenopus
- article
- bioinformatics
- breast cancer
- cancer survival
- cancer susceptibility
- cyclopamine
- gene expression profiling
- gene expression regulation
- gene interaction
- gene structure
- genetic database
- genetic linkage
- genetic model
- human
- lung cancer
- mathematical computing
- microarray analysis
- nonhuman
- null hypothesis
- protein Patched/ec [Endogenous Compound]
- protein structure
- sensitivity and specificity
- signal transduction
- simulation
- sonic hedgehog protein/ec [Endogenous Compound]
- survival time
- transcription initiation
Cite
CITATION STYLE
R., T., J.M., G., G.F., S., F.M., P., & C.J., P. (2009). Choosing the right path: Enhancement of biologically relevant sets of genes or proteins using pathway structure. Genome Biology. C.J. Portier, Environmental Systems Biology Group, Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, United States. E-mail: portier@niehs.nih.gov: BioMed Central Ltd. (Floor 6, 236 Gray’s Inn Road, London WC1X 8HB, United Kingdom). Retrieved from http://ovidsp.ovid.com/ovidweb.cgi?T=JS&PAGE=reference&D=emed9&NEWS=N&AN=2009258180
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