Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview


Autoria(s): SKINNER, Jeff; KOTLIAROV, Yuri; VARMA, Sudhir; MINE, Karina L.; YAMBARTSEV, Anatoly; SIMON, Richard; HUYEN, Yentram; MORGUN, Andrey
Contribuinte(s)

UNIVERSIDADE DE SÃO PAULO

Data(s)

19/04/2012

19/04/2012

2011

Resumo

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.

Department of Intramural Research (DIR)

Office of the Director (OD) at NIAID, NIH

Identificador

BMC BIOINFORMATICS, LONDON, v.12, 2011

1471-2105

http://producao.usp.br/handle/BDPI/16676

10.1186/1471-2105-12-286

http://dx.doi.org/10.1186/1471-2105-12-286

Idioma(s)

eng

Publicador

BIOMED CENTRAL LTD

LONDON

Relação

BMC Bioinformatics

Direitos

openAccess

Copyright BIOMED CENTRAL LTD

Palavras-Chave #FALSE DISCOVERY RATE #RECEPTOR GENE #BRAIN-TUMORS #EXPRESSION #GROWTH #CANCER #AMPLIFICATION #DEPENDENCY #PROFILES #EGFR #Biochemical Research Methods #Biotechnology & Applied Microbiology #Mathematical & Computational Biology
Tipo

article

original article

publishedVersion