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Bioinformatics Advance Access published online on April 15, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp246
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ViaComplex: software for landscape analysis of gene expression networks in genomic context

Mauro A. A. Castro 1,*, José L. Rybarczyk Filho 2, Rodrigo J. S. Dalmolin 1, Marialva Sinigaglia 3, José C. F. Moreira 1, José C. M. Mombach 4 and Rita M. C. de Almeida 2

1Unidade de Bioinformática, Departamento de Bioquímica, 2Instituto de Física and 3Núcleo de Bioinformática, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos 2600-anexo, Porto Alegre 90035-003, Brazil. 4Departamento de Física, Universidade Federal de Santa Maria, Santa Maria 97105-900, Brazil.

*To whom correspondence should be addressed. Dr. Mauro Alves Castro, E-mail: mauro{at}ufrgs.br


  Abstract

Summary: ViaComplex is an open-source application that builds landscape maps of gene expression networks. The motivation for this software comes from two previous publications (Nucleic Acids Res, 35(6):1859-67, 2007; Nucleic Acids Res, 36(19):6269-83, 2008). The first paper presents a network-based model of genome stability pathways where we defined a set of genes that characterizes each genetic system. In the second paper we analyzed this model by projecting functional information from several experiments onto the gene network topology. In order to systematize the methods developed in these papers, ViaComplex provides tools that may help potential users to assess different high-throughput experiments in the context of six core genome maintenance mechanisms. This model illustrates how different gene networks can be analyzed by the same algorithm.

Availability: http://lief.if.ufrgs.br/pub/biosoftwares/viacomplex.

Contact: M.A.A.C. (mauro{at}ufrgs.br) or R.M.C.A. (rita{at}if.ufrgs.br).

Associate Editor: Prof. Thomas Lengauer

Received on January 13, 2009; revised on March 22, 2009; accepted on April 6, 2009

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