Prospecting for Genes involved in transcriptional regulation of plant defenses, a bioinformatics approach

BMC Plant Biology

Research Article

John F Bol¹  Marcel C van Verk¹  Huub JM Linthorst¹ 

[1] Institute of Biology, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333, BE Leiden, The Netherlands;

关键词: Co-expression analysis;    salicylic acid-induced;    jasmonic acid-induced;    ethylene-induced;    defense response;    signal transduction;    Arabidopsis;    transcription factors;   

DOI  :  10.1186/1471-2229-11-88

 received in 2010-12-22, accepted in 2011-05-19,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundIn order to comprehend the mechanisms of induced plant defense, knowledge of the biosynthesis and signaling pathways mediated by salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) is essential. Potentially, many transcription factors could be involved in the regulation of these pathways, although finding them is a difficult endeavor. Here we report the use of publicly available Arabidopsis microarray datasets to generate gene co-expression networks.ResultsUsing 372 publicly available microarray data sets, a network was constructed in which Arabidopsis genes for known components of SA, JA and ET pathways together with the genes of over 1400 transcription factors were assayed for co-expression. After determining the Pearson Correlation Coefficient cutoff to obtain the most probable biologically relevant co-expressed genes, the resulting network confirmed the presence of many genes previously reported in literature to be relevant for stress responses and connections that fit current models of stress gene regulation, indicating the potential of our approach. In addition, the derived network suggested new candidate genes and associations that are potentially interesting for future research to further unravel their involvement in responses to stress.ConclusionsIn this study large sets of stress related microarrays were used to reveal co-expression networks of transcription factors and signaling pathway components. These networks will benefit further characterization of the signal transduction pathways involved in plant defense.

【 授权许可】

Unknown   
© van Verk et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.