Reconn : A cytoscape plug-in for exploring and visualizing reactome

W.P.A. Ligtenberg, D. Bosnacki, P.A.J. Hilbers

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5 Citations (Scopus)
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Abstract

Interface and visualization tools usually provide static representations of biological pathways, which can be a severe limitation: fixed pathway boundaries are used without consensus about the elements that should be included in a particular pathway; one cannot generate new pathways or produce selective views of existing pathways. Also, the tools are not capable of integrating multiple levels that conceptually can be distinguished in biological systems.We present ReConn, an interface and visualization tool for a flexible analysis of large data at multiple biological levels. ReConn (Reactome Connector) is an open source extension to Cytoscape which allows user friendly interaction with the Reactome database. ReConn can use both predefined Reactome pathways as well as generate new pathways. A pathway can be derived by starting from any given metabolite and existing pathways can be extended by adding related reactions. The tool can also retrieve alternative routes between elements of a biological network. Such an option is potentially applicable in the design and analysis of knockout experiments. ReConn displays information about multiple levels of the system in one view. With these dynamic features ReConn addresses all of the above mentioned limitations of the interface tools.
Original languageEnglish
Article number1350004
Pages (from-to)1-17
Number of pages17
JournalJournal of Bioinformatics and Computational Biology
Volume11
Issue number4
DOIs
Publication statusPublished - 2013

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Data Display
Consensus
Databases
Visualization
Biological systems
Metabolites
Experiments

Cite this

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title = "Reconn : A cytoscape plug-in for exploring and visualizing reactome",
abstract = "Interface and visualization tools usually provide static representations of biological pathways, which can be a severe limitation: fixed pathway boundaries are used without consensus about the elements that should be included in a particular pathway; one cannot generate new pathways or produce selective views of existing pathways. Also, the tools are not capable of integrating multiple levels that conceptually can be distinguished in biological systems.We present ReConn, an interface and visualization tool for a flexible analysis of large data at multiple biological levels. ReConn (Reactome Connector) is an open source extension to Cytoscape which allows user friendly interaction with the Reactome database. ReConn can use both predefined Reactome pathways as well as generate new pathways. A pathway can be derived by starting from any given metabolite and existing pathways can be extended by adding related reactions. The tool can also retrieve alternative routes between elements of a biological network. Such an option is potentially applicable in the design and analysis of knockout experiments. ReConn displays information about multiple levels of the system in one view. With these dynamic features ReConn addresses all of the above mentioned limitations of the interface tools.",
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Reconn : A cytoscape plug-in for exploring and visualizing reactome. / Ligtenberg, W.P.A.; Bosnacki, D.; Hilbers, P.A.J.

In: Journal of Bioinformatics and Computational Biology, Vol. 11, No. 4, 1350004, 2013, p. 1-17.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Bosnacki, D.

AU - Hilbers, P.A.J.

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