title: Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure.
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.
authors.affiliation: Environmental Systems Biology Group, Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, RTP, NC 27709, USA.
authors.forename: Reuben
authors.initials: R
authors.lastname: Thomas
authors.forename: Julia M
authors.initials: JM
authors.lastname: Gohlke
authors.forename: Geffrey F
authors.initials: GF
authors.lastname: Stopper
authors.forename: Frederick M
authors.initials: FM
authors.lastname: Parham
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Portier
mesh_terms: D000465:Algorithms; D000818:Animals; D001943:Breast Neoplasms / Q000235:genetics; D003198:Computer Simulation; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods* / Q000706:statistics & numerical data; D005786:Gene Expression Regulation / Q000187:drug effects; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods* / Q000706:statistics & numerical data; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D011506:Proteins / Q000235:genetics / Q000502:physiology; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology; D014704:Veratrum Alkaloids / Q000494:pharmacology; D014982:Xenopus laevis / Q000235:genetics
chemical_list: D011506:Proteins; D014704:Veratrum Alkaloids; C000541:cyclopamine