Tuyển tập báo cáo các nghiên cứu khoa học quốc tế ngành y học dành cho các bạn tham khảo đề tài: Prospecting for Genes involved in transcriptional regulation of plant defenses, a bioinformatics approach | van Verk et al. BMC Plant Biology 2011 11 88 http 1471-2229 11 88 BMC Plant Biology RESEARCH ARTICLE Open Access Prospecting for Genes involved in transcriptional regulation of plant defenses a bioinformatics approach Marcel C van Verk John F Bol and Huub JM Linthorst Abstract Background In 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. Results Using 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. Conclusions In 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. Keywords Co-expression analysis salicylic acid-induced jasmonic acid-induced ethylene-induced defense response signal transduction Arabidopsis .
