BioNetBuilder2.0: bringing systems biology to chicken and other model organisms

Persistent Link:
http://hdl.handle.net/10150/610006
Title:
BioNetBuilder2.0: bringing systems biology to chicken and other model organisms
Author:
Konieczka, Jay; Drew, Kevin; Pine, Alex; Belasco, Kevin; Davey, Sean; Yatskievych, Tatiana; Bonneau, Richard; Antin, Parker
Affiliation:
Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA; Courant Institute, New York University, New York, NY, USA; Department of Biology, New York University, New York, NY, USA; Department of Cell Biology & Anatomy, University of Arizona, Tucson, AZ, USA
Issue Date:
2009
Publisher:
BioMed Central
Citation:
BMC Genomics 2009, 10(Suppl 2):S6 doi:10.1186/1471-2164-10-S2-S6
Journal:
BMC Genomics
Rights:
© 2009 Konieczka et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:Systems Biology research tools, such as Cytoscape, have greatly extended the reach of genomic research. By providing platforms to integrate data with molecular interaction networks, researchers can more rapidly begin interpretation of large data sets collected for a system of interest. BioNetBuilder is an open-source client-server Cytoscape plugin that automatically integrates molecular interactions from all major public interaction databases and serves them directly to the user's Cytoscape environment. Until recently however, chicken and other eukaryotic model systems had little interaction data available.RESULTS:Version 2.0 of BioNetBuilder includes a redesigned synonyms resolution engine that enables transfer and integration of interactions across species; this engine translates between alternate gene names as well as between orthologs in multiple species. Additionally, BioNetBuilder is now implemented to be part of the Gaggle, thereby allowing seamless communication of interaction data to any software implementing the widely used Gaggle software. Using BioNetBuilder, we constructed a chicken interactome possessing 72,000 interactions among 8,140 genes directly in the Cytoscape environment. In this paper, we present a tutorial on how to do so and analysis of a specific use case.CONCLUSION:BioNetBuilder 2.0 provides numerous user-friendly systems biology tools that were otherwise inaccessible to researchers in chicken genomics, as well as other model systems. We provide a detailed tutorial spanning all required steps in the analysis. BioNetBuilder 2.0, the tools for maintaining its data bases, standard operating procedures for creating local copies of its back-end data bases, as well as all of the Gaggle and Cytoscape codes required, are open-source and freely available at http://err.bio.nyu.edu/cytoscape/bionetbuilder/ webcite.
EISSN:
1471-2164
DOI:
10.1186/1471-2164-10-S2-S6
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/10/S2/S6

Full metadata record

DC FieldValue Language
dc.contributor.authorKonieczka, Jayen
dc.contributor.authorDrew, Kevinen
dc.contributor.authorPine, Alexen
dc.contributor.authorBelasco, Kevinen
dc.contributor.authorDavey, Seanen
dc.contributor.authorYatskievych, Tatianaen
dc.contributor.authorBonneau, Richarden
dc.contributor.authorAntin, Parkeren
dc.date.accessioned2016-05-20T08:56:16Z-
dc.date.available2016-05-20T08:56:16Z-
dc.date.issued2009en
dc.identifier.citationBMC Genomics 2009, 10(Suppl 2):S6 doi:10.1186/1471-2164-10-S2-S6en
dc.identifier.doi10.1186/1471-2164-10-S2-S6en
dc.identifier.urihttp://hdl.handle.net/10150/610006-
dc.description.abstractBACKGROUND:Systems Biology research tools, such as Cytoscape, have greatly extended the reach of genomic research. By providing platforms to integrate data with molecular interaction networks, researchers can more rapidly begin interpretation of large data sets collected for a system of interest. BioNetBuilder is an open-source client-server Cytoscape plugin that automatically integrates molecular interactions from all major public interaction databases and serves them directly to the user's Cytoscape environment. Until recently however, chicken and other eukaryotic model systems had little interaction data available.RESULTS:Version 2.0 of BioNetBuilder includes a redesigned synonyms resolution engine that enables transfer and integration of interactions across speciesen
dc.description.abstractthis engine translates between alternate gene names as well as between orthologs in multiple species. Additionally, BioNetBuilder is now implemented to be part of the Gaggle, thereby allowing seamless communication of interaction data to any software implementing the widely used Gaggle software. Using BioNetBuilder, we constructed a chicken interactome possessing 72,000 interactions among 8,140 genes directly in the Cytoscape environment. In this paper, we present a tutorial on how to do so and analysis of a specific use case.CONCLUSION:BioNetBuilder 2.0 provides numerous user-friendly systems biology tools that were otherwise inaccessible to researchers in chicken genomics, as well as other model systems. We provide a detailed tutorial spanning all required steps in the analysis. BioNetBuilder 2.0, the tools for maintaining its data bases, standard operating procedures for creating local copies of its back-end data bases, as well as all of the Gaggle and Cytoscape codes required, are open-source and freely available at http://err.bio.nyu.edu/cytoscape/bionetbuilder/ webcite.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/10/S2/S6en
dc.rights© 2009 Konieczka et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleBioNetBuilder2.0: bringing systems biology to chicken and other model organismsen
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentDepartment of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USAen
dc.contributor.departmentCourant Institute, New York University, New York, NY, USAen
dc.contributor.departmentDepartment of Biology, New York University, New York, NY, USAen
dc.contributor.departmentDepartment of Cell Biology & Anatomy, University of Arizona, Tucson, AZ, USAen
dc.identifier.journalBMC Genomicsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
All Items in UA Campus Repository are protected by copyright, with all rights reserved, unless otherwise indicated.