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.
Bibliographical noteFunding 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 ).
© 2021 The Authors
- Gene co-expression
- Gene co-expression networks
- Plant genetics
- Plant bioinformatics