title: Identification of rice genes associated with cosmic-ray response via co-expression gene network analysis.
abstract: 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.
authors.affiliation: Plant Genomics Lab., Department of Applied Plant Sciences, Kangwon National University, Chuncheon 200-713, South Korea.
authors.forename: Sun-Goo
authors.initials: SG
authors.lastname: Hwang
authors.affiliation: Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk 580-185, South Korea.
authors.forename: Dong Sub
authors.initials: DS
authors.lastname: Kim
authors.affiliation: Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 1266 Sinjeong, Jeongeup, Jeonbuk 580-185, South Korea.
authors.forename: Jung Eun
authors.initials: JE
authors.lastname: Hwang
authors.affiliation: Plant Genomics Lab., Department of Applied Plant Sciences, Kangwon National University, Chuncheon 200-713, South Korea.
authors.forename: A-Reum
authors.initials: AR
authors.lastname: Han
authors.affiliation: Plant Genomics Lab., Department of Applied Plant Sciences, Kangwon National University, Chuncheon 200-713, South Korea. Electronic address: csjang@kangwon.ac.kr.
authors.forename: Cheol Seong
authors.initials: CS
authors.lastname: Jang
mesh_terms: D003359:Cosmic Radiation; D015536:Down-Regulation; D005720:Gamma Rays; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects; D053263:Gene Regulatory Networks; D017343:Genes, Plant / Q000235:genetics / Q000528:radiation effects; D059372:Nucleotide Motifs; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity; D012275:Oryza / Q000235:genetics* / Q000502:physiology / Q000528:radiation effects; D013312:Stress, Physiological; D059467:Transcriptome; D015854:Up-Regulation
keywords: Co-expression network; Cosmic ray; Gamma ray; Ion beam; Irradiations; Rice