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

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, 1859–1867, 2007; Nucleic Acids Res., 36, 6269–6283, 2008). The first article presents a network-based model...

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Bibliographic Details
Published in:Bioinformatics 2009-06, Vol.25 (11), p.1468-1469
Main Authors: Castro, Mauro A. A., Filho, José L. Rybarczyk, Dalmolin, Rodrigo J. S., Sinigaglia, Marialva, Moreira, José C. F., Mombach, José C. M., de Almeida, Rita M. C.
Format: Article
Language:English
Subjects:
Biological and medical sciences
Fundamental and applied biological sciences. Psychology
Gene Expression
Gene Expression Profiling - methods
Gene Regulatory Networks - genetics
General aspects
Genome - genetics
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Software
User-Computer Interface
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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, 1859–1867, 2007; Nucleic Acids Res., 36, 6269–6283, 2008). The first article presents a network-based model of genome stability pathways where we defined a set of genes that characterizes each genetic system. In the second article 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 articles, 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 Supplementary information: Supplementary data are available at Bioinformatics online. Contact: mauro@ufrgs.br or rita@if.ufrgs.br
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btp246