Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana
Vasileios L. Zogopoulos,
Georgia Saxami,
Apostolos Malatras,
Antonia Angelopoulou,
Chih-Hung Jen,
William J. Duddy,
Gerasimos Daras,
Polydefkis Hatzopoulos,
David R. Westhead,
Ioannis Michalopoulos
Affiliations
Vasileios L. Zogopoulos
Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens 11527, Greece
Georgia Saxami
Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens 11527, Greece
Apostolos Malatras
Center for Research in Myology, Sorbonne Université, Paris 75013, France
Antonia Angelopoulou
Department of Biotechnology, Agricultural University of Athens, Athens 11855, Greece
Chih-Hung Jen
Cold Spring Biotech Corp, Da Hu Science Park, New Taipei City, Taiwan
William J. Duddy
Center for Research in Myology, Sorbonne Université, Paris 75013, France; Northern Ireland Centre for Stratified Medicine, Altnagelvin Hospital Campus, Ulster University, Londonderry BT52 1SJ, UK
Gerasimos Daras
Department of Biotechnology, Agricultural University of Athens, Athens 11855, Greece
Polydefkis Hatzopoulos
Department of Biotechnology, Agricultural University of Athens, Athens 11855, Greece
David R. Westhead
School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
Ioannis Michalopoulos
Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens 11527, Greece; Corresponding author
Summary: 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.
