Zogopoulos, VL, Saxami, G, Malatras, A et al. (7 more authors) (2021) Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana. iScience, 24 (8). 102848. ISSN 2589-0042
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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2021 The Authors. This is an open access article under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Biological Sciences (Leeds) > School of Molecular and Cellular Biology (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 25 Aug 2021 14:45 |
Last Modified: | 25 Aug 2021 14:45 |
Status: | Published |
Publisher: | Cell Press |
Identification Number: | 10.1016/j.isci.2021.102848 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:177174 |