Comparative Co-expression Networks Construction and Visualization.
CoExpNetViz is 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.
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.
Tzfadia O, Diels T, De Meyer S, Vandepoele K, Aharoni A and Van de Peer Y (2015). CoExpNetViz: Comparative Co-expression Networks Construction and Visualization Tool. Front. Plant Sci. 6:1194. doi: 10.3389/fpls.2015.01194