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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 (2016) FRONTIERS IN PLANT SCIENCE. 6.
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 Moreover, in addition, none of the existing pipelines allow plant researchers to make use of their own unpublished gene expression data for performing a comparative co-expression analysis and generate multi-species co-expression networks.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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
ELEMENTS, RANKING, ALGORITHM, CYTOSCAPE, INTEGRATION, IDENTIFICATION, GENES, ARABIDOPSIS, PLANT BIOLOGY, plants, cytoscape, networks, comparative genomics, co-expression, MODULES
journal title
FRONTIERS IN PLANT SCIENCE
Front. Plant Sci.
volume
6
article number
1194
pages
7 pages
Web of Science type
Article
Web of Science id
000367653200001
JCR category
PLANT SCIENCES
JCR impact factor
4.298 (2016)
JCR rank
20/211 (2016)
JCR quartile
1 (2016)
ISSN
1664-462X
DOI
10.3389/fpls.2015.01194
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
7081918
handle
http://hdl.handle.net/1854/LU-7081918
date created
2016-02-11 14:53:00
date last changed
2017-03-02 13:42:10
@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},
}

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.