کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
2816470 1159936 2014 10 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Identification of rice genes associated with cosmic-ray response via co-expression gene network analysis
ترجمه فارسی عنوان
شناسایی ژن های برنج مرتبط با پاسخ کیهانی اشعه با تجزیه و تحلیل شبکه ژن مشترک
موضوعات مرتبط
علوم زیستی و بیوفناوری بیوشیمی، ژنتیک و زیست شناسی مولکولی ژنتیک
چکیده انگلیسی


• We conducted the co-expression network analysis with module detection method.
• We evaluated the gene–gene functional interactions between 680 CR-response probes.
• We found 243 IR-response probes between CR, GR and IB.
• We identified the co-regulations between several IR-response genes.

In order to better understand the biological systems that are affected in response to cosmic ray (CR), we conducted weighted gene co-expression network analysis using the module detection method. By using the Pearson's correlation coefficient (PCC) value, we evaluated complex gene–gene functional interactions between 680 CR-responsive probes from integrated microarray data sets, which included large-scale transcriptional profiling of 1000 microarray samples. These probes were divided into 6 distinct modules that contained 20 enriched gene ontology (GO) functions, such as oxidoreductase activity, hydrolase activity, and response to stimulus and stress. In particular, modules 1 and 2 commonly showed enriched annotation categories such as oxidoreductase activity, including enriched cis-regulatory elements known as ROS-specific regulators. These results suggest that the ROS-mediated irradiation response pathway is affected by CR in modules 1 and 2. We found 243 ionizing radiation (IR)-responsive probes that exhibited similarities in expression patterns in various irradiation microarray data sets. The expression patterns of 6 randomly selected IR-responsive genes were evaluated by quantitative reverse transcription polymerase chain reaction following treatment with CR, gamma rays (GR), and ion beam (IB); similar patterns were observed among these genes under these 3 treatments. Moreover, we constructed subnetworks of IR-responsive genes and evaluated the expression levels of their neighboring genes following GR treatment; similar patterns were observed among them. These results of network-based analyses might provide a clue to understanding the complex biological system related to the CR response in plants.

Identification of Rice Genes Associated with Cosmic-Ray Response via Co-expression Gene Network Analysis.Figure optionsDownload high-quality image (415 K)Download as PowerPoint slide

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Gene - Volume 541, Issue 2, 15 May 2014, Pages 82–91
نویسندگان
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