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of the existing pipelines allow plant researchers to make use of their own unpublished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.
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.
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.
, Diels, T.
, De Meyer, S., Vandepoele, K.
, Aharoni, A., Van de Peer, Y.
CoExpNetViz: the Construction and Vizualisation of Co-expression Networks. Frontiers in Plant Science 6:1194.