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Open Access Software

Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview

Jeff Skinner1, Yuri Kotliarov2, Sudhir Varma1, Karina L Mine3, Anatoly Yambartsev4, Richard Simon5, Yentram Huyen1* and Andrey Morgun6*

Author Affiliations

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

2 Neuro-Oncology Branch (CHIAI), National Cancer Institute (NCI), National Institutes of Neurological Disorder and Stroke (NINDS), National Institutes if Health (NIH), Bethesda, Maryland, USA

3 Setor de Imunogenética, Departamento de Pediatria, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brasil

4 Instituto de Matemática e Estatística (IME), Universidade de São Paulo (USP), São Paulo, Brasil

5 Biometric Research Branch (BRB), Division of Cancer Treatment and Diagnosis (DCTD), National Cancer Institute (NCI), National Institutes if Health (NIH), Bethesda, Maryland, USA

6 "Ghost Lab", T-Cell Tolerance and Memory Section (TCTMS), Laboratory of Cellular and Molecular Immunology (LCMI), National Institute of Allergy and Infectious Disease (NIAID), National Institutes if Health (NIH), Bethesda, Maryland, USA

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BMC Bioinformatics 2011, 12:286  doi:10.1186/1471-2105-12-286

Published: 14 July 2011

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.