Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview

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Data
2011-07-14
Autores
Skinner, Jeff
Kotliarov, Yuri
Varma, Sudhir
Mine, Karina Lumi [UNIFESP]
Yambartsev, Anatoly
Simon, Richard
Huyen, Yentram
Morgun, Andrey
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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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Bmc Bioinformatics. London: Biomed Central Ltd, v. 12, 8 p., 2011.
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