OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice

Similarity of gene expression profiles provides important clues for understanding the biological functions of genes, biological processes and metabolic pathways related to genes. A gene expression network (GEN) is an ideal choice to grasp such expression profile similarities among genes simultaneously. For GEN construction, the Pearson correlation coefficient (PCC) has been widely used as an index to evaluate the similarities of expression profiles for gene pairs. However, calculation of PCCs for all gene pairs requires large amounts of both time and computer resources. Based on correspondence analysis, we developed a new method for GEN construction, which takes minimal time even for large-scale expression data with general computational circumstances. Moreover, our method requires no prior parameters to remove sample redundancies in the data set. Using the new method, we constructed rice GENs from large-scale microarray data stored in a public database. We then collected and integrated various principal rice omics annotations in public and distinct databases. The integrated information contains annotations of genome, transcriptome and metabolic pathways. We thus developed the integrated database OryzaExpress for browsing GENs with an interactive and graphical viewer and principal omics annotations (http://riceball.lab.nig.ac.jp/oryzaexpress/). With integration of Arabidopsis GEN data from ATTED-II, OryzaExpress also allows us to compare GENs between rice and Arabidopsis. Thus, OryzaExpress is a comprehensive rice database that exploits powerful omics approaches from all perspectives in plant science and leads to systems biology

Sister chromatid exchanges in ring chromosomes following X-irradiation of human lymphocytes

Purpose: To examine whether X-rays induce sister chromatid exchanges (SCE).Materials and methods: Peripheral lymphocytes irradiated in vitro or in vivo were cultured and treated with okadaic acid to generate premature chromosome condensation (PCC). When identical spreads were analysed using conventional Giemsa staining and pan-centromeric fluorescence in situ hybridization painting, ring chromosomes were observed. Results: In PCC preparations, cells in the late G2 phase and late M phase were observed. In late M phase cells, 17-20% of ring chromosomes lacked one chromatid (single-chromatid ring), irrespective of dose. Both the distribution patterns of centromeres in rings and intercentromere distances in dicentric rings indicates that a considerable number of single-chromatid rings might be formed by SCE occurring in a chromosome-type ring, therby joining strands of two rings, followed by a transformation into one ring. These single-chromatid rings were less stable in vivo than chromosome-type rings.Conclusion: Single-chromatid rings visualized clearly using PCC techniques indicate SCE in the respective rings. Contrary to the conventional SCE-detecting technique, this approach does not require the use of bromodeoxyuridine, which itself leads to SCE. Some of the observed SCE might be secondary products resulting from the repair of radiation-induced DNA damage, while others may be spontaneous