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PathwayConnector: finding complementary pathways to enhance functional analysis

SUMMARY: PathwayConnector is a web-tool that facilitates the construction of complementary pathway-to-pathway networks and subnetworks of them, based on a reference pathway network derived from the rich information available either in KEGG or Reactome database for pathway mapping. Specifically, for...

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Detalles Bibliográficos
Autores principales: Minadakis, George, Zachariou, Margarita, Oulas, Anastasis, Spyrou, George M
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394395/
https://www.ncbi.nlm.nih.gov/pubmed/30124768
http://dx.doi.org/10.1093/bioinformatics/bty693
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author Minadakis, George
Zachariou, Margarita
Oulas, Anastasis
Spyrou, George M
author_facet Minadakis, George
Zachariou, Margarita
Oulas, Anastasis
Spyrou, George M
author_sort Minadakis, George
collection PubMed
description SUMMARY: PathwayConnector is a web-tool that facilitates the construction of complementary pathway-to-pathway networks and subnetworks of them, based on a reference pathway network derived from the rich information available either in KEGG or Reactome database for pathway mapping. Specifically, for a given set of pathways, PathwayConnector (i) finds all the direct connections between them, (ii) adds a minimum set of complementary pathways required to achieve connectivity between the pathways, leading to informative fully connected networks and (ii) provides a series of clustering methods for the further grouping of pathways in to sub-clusters. The proposed web-tool is a simple yet informative tool towards identifying connected groups of pathways that are significantly related to specific diseases. AVAILABILITY AND IMPLEMENTATION: http://bioinformatics.cing.ac.cy/PathwayConnector SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-63943952019-03-05 PathwayConnector: finding complementary pathways to enhance functional analysis Minadakis, George Zachariou, Margarita Oulas, Anastasis Spyrou, George M Bioinformatics Applications Notes SUMMARY: PathwayConnector is a web-tool that facilitates the construction of complementary pathway-to-pathway networks and subnetworks of them, based on a reference pathway network derived from the rich information available either in KEGG or Reactome database for pathway mapping. Specifically, for a given set of pathways, PathwayConnector (i) finds all the direct connections between them, (ii) adds a minimum set of complementary pathways required to achieve connectivity between the pathways, leading to informative fully connected networks and (ii) provides a series of clustering methods for the further grouping of pathways in to sub-clusters. The proposed web-tool is a simple yet informative tool towards identifying connected groups of pathways that are significantly related to specific diseases. AVAILABILITY AND IMPLEMENTATION: http://bioinformatics.cing.ac.cy/PathwayConnector SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2019-03-01 2018-08-14 /pmc/articles/PMC6394395/ /pubmed/30124768 http://dx.doi.org/10.1093/bioinformatics/bty693 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Minadakis, George
Zachariou, Margarita
Oulas, Anastasis
Spyrou, George M
PathwayConnector: finding complementary pathways to enhance functional analysis
title PathwayConnector: finding complementary pathways to enhance functional analysis
title_full PathwayConnector: finding complementary pathways to enhance functional analysis
title_fullStr PathwayConnector: finding complementary pathways to enhance functional analysis
title_full_unstemmed PathwayConnector: finding complementary pathways to enhance functional analysis
title_short PathwayConnector: finding complementary pathways to enhance functional analysis
title_sort pathwayconnector: finding complementary pathways to enhance functional analysis
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394395/
https://www.ncbi.nlm.nih.gov/pubmed/30124768
http://dx.doi.org/10.1093/bioinformatics/bty693
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