CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool

Frontiers in Plant Science
Oren TzfadiaYves Van de Peer

Abstract

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 Moreover, in addition, none of the existing pipelines allow plant researchers to make use of their own unpublished gene expression data for performing a comparative co-expression analysis and generate multi-species co-expression networks.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 C...Continue Reading

References

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Citations

Apr 20, 2016·Frontiers in Plant Science·Elise A R SerinWilco Ligterink
Jan 28, 2017·Trends in Plant Science·Colin RuprechtMarek Mutwil
Oct 3, 2017·Bioinformatics·Kristoffer ForslundUNKNOWN Quest for Orthologs Consortium
Feb 1, 2018·The Plant Journal : for Cell and Molecular Biology·Navot GalpazNurit Katzir
Jul 4, 2018·Plant Signaling & Behavior·N MokshinaT Gorshkova
Nov 27, 2018·Physiologia Plantarum·Natalia MokshinaTatyana Gorshkova
Jan 9, 2019·BMC Bioinformatics·Minzhe ZhangGuanghua Xiao
May 4, 2017·BMC Bioinformatics·Zakhar Sergeevich MustafinDmitry Arkadievich Afonnikov
Dec 14, 2017·Frontiers in Plant Science·Satoru KodaKeiichi Mochida
May 3, 2018·Nucleic Acids Research·Sebastian Proost, Marek Mutwil
Mar 22, 2019·Frontiers in Genetics·Lucas E CardozoHelder I Nakaya
May 20, 2020·Nature Chemical Biology·Adam JozwiakAsaph Aharoni
Feb 6, 2017·The Plant Journal : for Cell and Molecular Biology·Colin RuprechtMarek Mutwil
Apr 5, 2018·Frontiers in Plant Science·Arthur ZwaenepoelOren Tzfadia
May 3, 2018·Nucleic Acids Research·Camilla FerrariMarek Mutwil
Aug 1, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Weilong KongXiaopeng Fu
Oct 31, 2020·Plant, Cell & Environment·Caryn N OatesSanushka Naidoo
Jan 30, 2021·Frontiers in Plant Science·Riccardo Delli-PontiMarek Mutwil
Mar 16, 2021·Plant Physiology·Maria-Angelica SanclementeKaren E Koch
Mar 13, 2021·Journal of Experimental Botany·Antonio MauceriAntonio Lupini
Oct 26, 2021·Frontiers in Cell and Developmental Biology·Tao ZhangKun Liu
Dec 14, 2021·Frontiers in Genetics·Chiranjib SarkarAnil Rai

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Software Mentioned

Complex
Perl
ATED
GeneCAT
Linux
PODC
Windows
BLAST
II
SAMIT

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