title: CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool.
abstract: BACKGROUND
  Comparative transcriptomics is a common approach in functional gene discovery efforts. It allows for finding conserved co-expression patterns between orthologous genes in closely related plant species, suggesting that these genes potentially share similar function and regulation. Several efficient co-expression-based tools have been commonly used in plant research but most of these pipelines are limited to data from model systems, which greatly limit their utility. Moreover, in addition, none of the existing pipelines allow plant researchers to make use of their own unpublished gene expression data for performing a comparative co-expression analysis and generate multi-species co-expression networks.
  
  
  RESULTS
  We introduce CoExpNetViz, a computational tool that uses a set of query or "bait" genes as an input (chosen by the user) and a minimum of one pre-processed gene expression dataset. The CoExpNetViz algorithm proceeds in three main steps; (i) for every bait gene submitted, co-expression values are calculated using mutual information and Pearson correlation coefficients, (ii) non-bait (or target) genes are grouped based on cross-species orthology, and (iii) output files are generated and results can be visualized as network graphs in Cytoscape.
  
  
  BACKGROUND
  The CoExpNetViz tool is freely available both as a PHP web server (link: http://bioinformatics.psb.ugent.be/webtools/coexpr/) (implemented in C++) and as a Cytoscape plugin (implemented in Java). Both versions of the CoExpNetViz tool support LINUX and Windows platforms.
authors.affiliation: Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium; Bioinformatics Institute Ghent, Ghent UniversityGhent, Belgium.
authors.forename: Oren
authors.initials: O
authors.lastname: Tzfadia
authors.affiliation: Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium; Bioinformatics Institute Ghent, Ghent UniversityGhent, Belgium.
authors.forename: Tim
authors.initials: T
authors.lastname: Diels
authors.affiliation: Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium.
authors.forename: Sam
authors.initials: S
authors.lastname: De Meyer
authors.affiliation: Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium; Bioinformatics Institute Ghent, Ghent UniversityGhent, Belgium.
authors.forename: Klaas
authors.initials: K
authors.lastname: Vandepoele
authors.affiliation: Department of Plant Sciences and the Environment, Weizmann Institute of Science Rehovot, Israel.
authors.forename: Asaph
authors.initials: A
authors.lastname: Aharoni
authors.affiliation: Department of Plant Systems Biology, Vlaams Instituut voor BiotechnologieGhent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium; Bioinformatics Institute Ghent, Ghent UniversityGhent, Belgium; Genomics Research Institute, University of PretoriaPretoria, South Africa.
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
keywords: co-expression; comparative genomics; cytoscape; networks; plants