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Published (Version of record)CC BY V4.0, Open Access
Journal article
CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool
Frontiers in Plant Science, Vol.6, 1194
05/Jan/2016
Abstract
Motivation: 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 Moreover, in addition, none of the existing pipelines allow plant researchers to make use of their own unpublished gene expression data for performing a comparative co-expression analysis and generate multi-species co-expression networks.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. Availability: 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.
Details
- Title
- CoExpNetViz; Comparative Co-Expression Networks Construction and Visualization Tool
- Creators
- Oren Tzfadia (null) - Ghent UniversityTim Diels (null) - Ghent UniversityMeyer, Sam De Meyer (null) - Ghent UniversityKlaas Vandepoele (null) - Ghent UniversityAsaph Aharoni (null) - 972WIS_INST___110de Peer, Yves Van de Peer (null) - Ghent University
- Resource Type
- Journal article
- Publication Details
- Frontiers in Plant Science, Vol.6, 1194; 05/Jan/2016
- Number of pages
- 7
- Language
- English
- DOI
- https://doi.org/10.3389/fpls.2015.01194
- Grant note
- European Research Council grant SAMIT [204575]; Ghent University [01MR0310W]; European Union under European Research Council [322739] The work in the AA lab was supported by the European Research Council grant SAMIT (no. 204575). We thank the Tom and Sondra Rykof Family Foundation for supporting the AA lab activity. AA is the incumbent of the Peter J. Cohn Professorial Chair. KV and YP acknowledge the Multidisciplinary Research Partnership "Bioinformatics: from nucleotides to networks" Project (no 01MR0310W) of Ghent University. YVdP also acknowledges support from the European Union Seventh Framework Programme (FP7/2007-2013) under European Research Council Advanced Grant Agreement 322739 "DOUBLE-UP." The Authors would like to thank Thomas Van Parys and Michiel Van Bel for technical assistance. OT designed the project, analyzed the data and wrote the MS. TD developed the web tool, SD developed the Cytoscape plug-in, KV analyzed the data, wrote the MS. AA designed the project, analyzed the data, wrote the MS. YP analyzed the data, wrote the MS. All authors read, revised and approved the MS._ALMAME_DELIMITER_
- Record Identifier
- 993264326003596
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