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CoExpNetViz: comparative co-expression networks construction and visualization tool

Oren Tzfadia (UGent) , Tim Diels (UGent) , Sam De Meyer (UGent) , Klaas Vandepoele (UGent) , Asaph Aharoni and Yves Van de Peer (UGent)
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Bioinformatics: from nucleotids to networks (N2N)
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 Moreover, in addition, none of the existing pipelines allow plant researchers to make use of their own unpublished gene expression data for performing a comparative co-expression analysis and generate multi-species co-expression networks.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.
Keywords
ELEMENTS, RANKING, ALGORITHM, CYTOSCAPE, INTEGRATION, IDENTIFICATION, GENES, ARABIDOPSIS, PLANT BIOLOGY, plants, cytoscape, networks, comparative genomics, co-expression, MODULES

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Citation

Please use this url to cite or link to this publication:

Chicago
Tzfadia, Oren, Tim Diels, Sam De Meyer, Klaas Vandepoele, Asaph Aharoni, and Yves Van de Peer. 2016. “CoExpNetViz: Comparative Co-expression Networks Construction and Visualization Tool.” Frontiers in Plant Science 6.
APA
Tzfadia, O., Diels, T., De Meyer, S., Vandepoele, K., Aharoni, A., & Van de Peer, Y. (2016). CoExpNetViz: comparative co-expression networks construction and visualization tool. FRONTIERS IN PLANT SCIENCE, 6.
Vancouver
1.
Tzfadia O, Diels T, De Meyer S, Vandepoele K, Aharoni A, Van de Peer Y. CoExpNetViz: comparative co-expression networks construction and visualization tool. FRONTIERS IN PLANT SCIENCE. 2016;6.
MLA
Tzfadia, Oren, Tim Diels, Sam De Meyer, et al. “CoExpNetViz: Comparative Co-expression Networks Construction and Visualization Tool.” FRONTIERS IN PLANT SCIENCE 6 (2016): n. pag. Print.
@article{7081918,
  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 {\textacutedbl}bait{\textacutedbl} 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.},
  articleno    = {1194},
  author       = {Tzfadia, Oren and Diels, Tim and De Meyer, Sam and Vandepoele, Klaas and Aharoni, Asaph and Van de Peer, Yves},
  issn         = {1664-462X},
  journal      = {FRONTIERS IN PLANT SCIENCE},
  keyword      = {ELEMENTS,RANKING,ALGORITHM,CYTOSCAPE,INTEGRATION,IDENTIFICATION,GENES,ARABIDOPSIS,PLANT BIOLOGY,plants,cytoscape,networks,comparative genomics,co-expression,MODULES},
  language     = {eng},
  pages        = {7},
  title        = {CoExpNetViz: comparative co-expression networks construction and visualization tool},
  url          = {http://dx.doi.org/10.3389/fpls.2015.01194},
  volume       = {6},
  year         = {2016},
}

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