A database for poplar gene co-expression analysis for systematic understanding of biological processes, including stress responses

• Published in: Journal of wood science Vol. 55; no. 6; pp. 395 - 400
• Main Authors: Ogata, Yoshiyuki, Suzuki, Hideyuki, Shibata, Daisuke
• Format: Journal Article
• Language: English
• Published: Tokyo Springer Japan 01.12.2009; Springer Nature B.V
• Subjects: Arid zones; Aridity; Bioinformatics; Biological activity; Biomedical and Life Sciences; Characterization and Evaluation of Materials; Climate change; data collection; Decoding; Deoxyribonucleic acid; DNA; DNA chips; Flooding; gene banks; Gene expression; Genes; Genomes; Global warming; humid tropics; Hypoxia; Life Sciences; Materials Science; microarray technology; Original Article; Plant species; Poplar; Populus; Populus canescens; Reforestation; stress response; stress tolerance; Stresses; Trees; Tropical environments; Wood Science & Technology; DNA microarray; Database; Poplar; Co-expression; Biological processes
• ISSN: 1435-0211; 1611-4663
• DOI: 10.1007/s10086-009-1058-9

Reforestation in the humid tropics and arid zones, where trees are often subject to stresses, is an effective approach for mitigating global warming. Forestation with Populus species that are tolerant to the stresses in such regions has been conducted. The selection of poplar trees with higher stress tolerance leads to more efficient reforestation. The genome-wide bioinformatics approaches of gene function have been used for revealing the mechanisms of biological processes, including such stress tolerance. The decoding of the poplar genome has been followed by the genome-wide identification of genes and then the inference of gene function for systematic understanding of biological processes. To predict gene function in poplar, we analyzed poplar gene expression data using DNA microarray datasets obtained from the Gene Expression Omnibus database and developed a database for poplar gene co-expression analysis. Using the database, we illustrate the steps to retrieve two groups of co-expressed genes that are specifically expressed in experiments of hypoxic stress response in gray poplar, a flooding-tolerant tree species. Our database allows users to extract genes involved in biological processes, such as stress reaction, and then is useful for understanding such mechanisms in tree species.