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

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ViaComplex V.1.0

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ViaComplex is a bioinformatics application that builds landscape maps of gene expression networks. It is released under an open source license and is completely free for any use. The motivation for this software comes from two previous publications:

1. Castro MAA, Mombach JCM, de Almeida RMC, Moreira JCF. Impaired expression of NER gene network in sporadic solid tumors. Nucleic Acids Res., 35(6):1859-67, 2007.

PMID:17332015

2. Castro MAA, Dalmolin RLS, Moreira JCF, Mombach JCM, de Almeida RMC. Evolutionary origins of human apoptosis and genome-stability gene networks. Nucleic Acids Res., 36(19):6269-83, 2008.

PMID:18832373

The first paper presents the network-based model of apoptosis and genome stability pathways and defines a set of genes that characterizes each genetic system. The second paper analyses the model and transfers functional information from several experiments to the network topology. In order to systematize the methods developed in these papers, here ViaComplex provides tools that may help potential users to test different high-throughput experiments in the perspective of six core genome maintenance mechanisms. This model illustrates how different gene networks can be analyzed by the same algorithm.

ViaComplex reference:

Castro MAA et al., Bioinformatics, 25(11):1468-9, 2009. PMID: 19369498

Contact:

Mauro Castro (mauro@ufrgs.br)

Departamento de Bioquímica, Lab32

Universidade Federal do Rio Grande do Sul,

Rua Ramiro Barcelos 2600-anexo,

Porto Alegre 90035-003, Brazil.

José Rybarczyk (jose.rybarczyk@gmail.com)

Instituto de Física, LabCel

Universidade Federal do Rio Grande do Sul,

Av. Bento Gonçalves 9500, PO Box 15051,