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 languageEnglish
Article number102848
JournaliScience
Volume24
Issue number8
Early online date10 Jul 2021
DOIs
Publication statusPublished - 20 Aug 2021

Keywords

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

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