Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview

BACKGROUND: DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes. RESULTS: Each significant difference in gene-gene association represents a Differentially Associ...

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Autores principales: Skinner, Jeff, Kotliarov, Yuri, Varma, Sudhir, Mine, Karina L, Yambartsev, Anatoly, Simon, Richard, Huyen, Yentram, Morgun, Andrey
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149583/
https://www.ncbi.nlm.nih.gov/pubmed/21756334
http://dx.doi.org/10.1186/1471-2105-12-286
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author Skinner, Jeff
Kotliarov, Yuri
Varma, Sudhir
Mine, Karina L
Yambartsev, Anatoly
Simon, Richard
Huyen, Yentram
Morgun, Andrey
author_facet Skinner, Jeff
Kotliarov, Yuri
Varma, Sudhir
Mine, Karina L
Yambartsev, Anatoly
Simon, Richard
Huyen, Yentram
Morgun, Andrey
author_sort Skinner, Jeff
collection PubMed
description BACKGROUND: DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes. RESULTS: Each significant difference in gene-gene association represents a Differentially Associated Pair (DAP). Our tools include several choices of filtering methods, gene-gene association metrics, statistical testing methods and multiple comparison adjustments. Network results are easily displayed in Cytoscape. Analyses of glioma experiments and microarray simulations demonstrate the utility of these tools. CONCLUSIONS: DAPfinder is a new friendly-user tool for reconstruction and comparison of biological networks.
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spelling pubmed-31495832011-08-04 Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview Skinner, Jeff Kotliarov, Yuri Varma, Sudhir Mine, Karina L Yambartsev, Anatoly Simon, Richard Huyen, Yentram Morgun, Andrey BMC Bioinformatics Software BACKGROUND: DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes. RESULTS: Each significant difference in gene-gene association represents a Differentially Associated Pair (DAP). Our tools include several choices of filtering methods, gene-gene association metrics, statistical testing methods and multiple comparison adjustments. Network results are easily displayed in Cytoscape. Analyses of glioma experiments and microarray simulations demonstrate the utility of these tools. CONCLUSIONS: DAPfinder is a new friendly-user tool for reconstruction and comparison of biological networks. BioMed Central 2011-07-14 /pmc/articles/PMC3149583/ /pubmed/21756334 http://dx.doi.org/10.1186/1471-2105-12-286 Text en Copyright © 2011 Skinner et al; licensee BioMed Central Ltd. https://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 (https://creativecommons.org/licenses/by/2.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
Skinner, Jeff
Kotliarov, Yuri
Varma, Sudhir
Mine, Karina L
Yambartsev, Anatoly
Simon, Richard
Huyen, Yentram
Morgun, Andrey
Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview
title Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview
title_full Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview
title_fullStr Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview
title_full_unstemmed Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview
title_short Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview
title_sort construct and compare gene coexpression networks with dapfinder and dapview
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149583/
https://www.ncbi.nlm.nih.gov/pubmed/21756334
http://dx.doi.org/10.1186/1471-2105-12-286
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