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

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...

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Detalles Bibliográficos
Autores principales: Thomas, Reuben, Gohlke, Julia M, Stopper, Geffrey F, Parham, Frederick M, Portier, Christopher J
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688935/
https://www.ncbi.nlm.nih.gov/pubmed/19393085
http://dx.doi.org/10.1186/gb-2009-10-4-r44
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author Thomas, Reuben
Gohlke, Julia M
Stopper, Geffrey F
Parham, Frederick M
Portier, Christopher J
author_facet Thomas, Reuben
Gohlke, Julia M
Stopper, Geffrey F
Parham, Frederick M
Portier, Christopher J
author_sort Thomas, Reuben
collection PubMed
description 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.
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spelling pubmed-26889352009-06-02 Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure Thomas, Reuben Gohlke, Julia M Stopper, Geffrey F Parham, Frederick M Portier, Christopher J Genome Biol Method 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. BioMed Central 2009 2009-04-24 /pmc/articles/PMC2688935/ /pubmed/19393085 http://dx.doi.org/10.1186/gb-2009-10-4-r44 Text en Copyright © 2009 Thomas et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Thomas, Reuben
Gohlke, Julia M
Stopper, Geffrey F
Parham, Frederick M
Portier, Christopher J
Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure
title Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure
title_full Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure
title_fullStr Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure
title_full_unstemmed Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure
title_short Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure
title_sort choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688935/
https://www.ncbi.nlm.nih.gov/pubmed/19393085
http://dx.doi.org/10.1186/gb-2009-10-4-r44
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