CoExpNetViz

CoExpNetViz is a computational tool for comparative transcriptomics that allows plant researchers to perform a comparative co-expression analysis and generate multi-species co-expression networks using a set of query or "bait" genes as input and a minimum of one pre-processed gene expression dataset. The algorithm proceeds in three main steps, calculating co-expression values, grouping non-bait genes based on cross-species orthology, and generating output files and network graphs in Cytoscape. CoExpNetViz is freely available as a PHP web server and as a Cytoscape plugin for LINUX and Windows platforms.

Topic

Gene expression;Comparative genomics

Detail

  • Operation: Pathway or network analysis

  • Software interface: Web application;Graphical user interface

  • Language: The CoExpNetViz Cytoscape plugin was written in Java-OpenJDK (http:--openjdk.java.net).

  • License: GNU Lesser General Public License v3.0

  • Cost: Free

  • Version name: 2.1.5

  • Credit: The European Research Council grant SAMIT, the Tom and Sondra Rykof Family Foundation, the European Union Seventh Framework Programme (FP7-2007-2013).

  • Input: CSV

  • Output: -

  • Contact: yves.vandepeer@psb.vib-ugent.be

  • Collection: -

  • Maturity: Stable

Publications

  • CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool.
  • Tzfadia O, et al. CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool. CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool. 2015; 6:1194. doi: 10.3389/fpls.2015.01194
  • https://doi.org/10.3389/fpls.2015.01194
  • PMID: 26779228
  • PMC: PMC4700130

Download and documentation

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