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

Abstract

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.

Gene coexpression analysis in Arabidopsis thaliana based on public microarray data

“…The advantages described in this protocol include: the hierarchical clustering approach for displaying gene coexpression which outperforms the more commonly used gene coexpression list output ( Obayashi et al., 2018 ; Yim et al., 2013 ), the automatic quality control procedure and the meticulous representative sample selection which eliminates tissue bias, as well as the usage of modern normalization algorithms along with up-to-date CDFs. Execution of this protocol has resulted in several use-cases, where a gene of interest was discovered to be grouped with genes of similar functions, which are supported by already existing bibliography ( Zogopoulos et al., 2021 ).…”

“…Because the computational analysis described here is highly dependent on sample quality, we detail an automatic quality control approach. For complete details on the use and execution of this protocol, please refer to Zogopoulos et al. (2021) .…”

“…For complete details on the use and execution of this protocol, please refer to Zogopoulos et al. (2021) .…”

Approaches in Gene Coexpression Analysis in Eukaryotes

“…Finally, the top coexpressed partners to a gene of interest are portrayed as coexpression networks in the gene's information page (Figure 3). [23,140,141] studies gene coexpression in 21,273 Arabidopsis thaliana genes using high-quality healthy microarray samples. The latest version of ACT is based on 3500 Affymetrix Arabidopsis ATH1 Genome Array GeneChip samples from ArrayExpress, GEO and NASCArrays.…”

“…Currently, there are several gene coexpression webtools and standalone applications focusing on a variety of model species of animals [ 13 , 17 , 18 , 19 , 20 , 21 ], plants [ 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ] and fungi [ 30 , 31 ].…”