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BMC Bioinformatics. 2011 Jul 14;12:286. doi: 10.1186/1471-2105-12-286.

Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview.

Author information

1
Bioinformatics and Computational Biosciences Branch (BCBB), Office of Cyber Infrastructure and Computational Biology (OCICB), National Institute of Allergy and Infectious Disease (NIAID), National Institutes if Health (NIH), Bethesda, Maryland, USA.

Abstract

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.

PMID:
21756334
PMCID:
PMC3149583
DOI:
10.1186/1471-2105-12-286
[Indexed for MEDLINE]
Free PMC Article
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