Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana

Vasileios Zogopoulos; Saxami Georgia; Apostolos Malatras; Antonia Angelopoulou; Chih-Hung Jen; William Duddy; Gerasimos Daras; Polydefkis Hatzopoulos; David Westhead; Ioannis Michalopoulos

doi:10.1016/j.isci.2021.102848

Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana

Vasileios Zogopoulos, Saxami Georgia, Apostolos Malatras, Antonia Angelopoulou, Chih-Hung Jen, William Duddy, Gerasimos Daras, Polydefkis Hatzopoulos, David Westhead, Ioannis Michalopoulos

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Abstract

Gene coexpression analysis refers to the discovery of sets of genes which exhibit similar expression patterns across multiple transcriptomic data sets, such as microarray experiment data of public repositories. Arabidopsis Coexpression Tool (ACT), a gene coexpression analysis web tool for Arabidopsis thaliana, identifies genes which are correlated to a driver gene. Primary microarray data from ATH1 Affymetrix platform were processed with Single-Channel Array Normalization algorithm and combined to produce a coexpression tree which contains ∼21,000 A. thaliana genes. ACT was developed to present subclades of coexpressed genes, as well as to perform gene set enrichment analysis, being unique in revealing enriched transcription factors targeting coexpressed genes. ACT offers a simple and user-friendly interface producing working hypotheses which can be experimentally verified for the discovery of gene partnership, pathway membership, and transcriptional regulation. ACT analyses have been successful in identifying not only genes with coordinated ubiquitous expressions but also genes with tissue-specific expressions.

Original language	English
Article number	102848
Journal	iScience
Volume	24
Issue number	8
Early online date	10 Jul 2021
DOIs	https://doi.org/10.1016/j.isci.2021.102848
Publication status	Published (in print/issue) - 20 Aug 2021

Bibliographical note

Funding Information:
We acknowledge support of this work by the project “ ELIXIR-GR: Managing and Analysing Life Sciences Data ” (MIS: 5002780) which is implemented under the Action “ Reinforcement of the Research and Innovation Infrastructure ”, funded by the Operational Programme “ Competitiveness, Entrepreneurship and Innovation ” (NSRF 2014-2020) and co-financed by Greece and the European Union ( European Regional Development Fund ).

Publisher Copyright:
© 2021 The Authors

Keywords

Gene co-expression
Gene co-expression networks
Arabidopsis
Plant genetics
Plant bioinformatics
Bioinformatics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Cite this

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title = "Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana",

abstract = "Gene coexpression analysis refers to the discovery of sets of genes which exhibit similar expression patterns across multiple transcriptomic data sets, such as microarray experiment data of public repositories. Arabidopsis Coexpression Tool (ACT), a gene coexpression analysis web tool for Arabidopsis thaliana, identifies genes which are correlated to a driver gene. Primary microarray data from ATH1 Affymetrix platform were processed with Single-Channel Array Normalization algorithm and combined to produce a coexpression tree which contains ∼21,000 A. thaliana genes. ACT was developed to present subclades of coexpressed genes, as well as to perform gene set enrichment analysis, being unique in revealing enriched transcription factors targeting coexpressed genes. ACT offers a simple and user-friendly interface producing working hypotheses which can be experimentally verified for the discovery of gene partnership, pathway membership, and transcriptional regulation. ACT analyses have been successful in identifying not only genes with coordinated ubiquitous expressions but also genes with tissue-specific expressions.",

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Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana

Abstract

Bibliographical note

Keywords

UN SDGs

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