Bibliography of Author: Kawashima, S.

  1. Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A.. "The KEGG databases at GenomeNet." Nucleic Acids Res. 30 (1). 2002. pp. 42-6.
    [ .pdf ] [ PubMed ]

    The Kyoto Encyclopedia of Genes and Genomes (KEGG) is the primary database resource of the Japanese GenomeNet service (http://www.genome.ad.jp/) for understanding higher order functional meanings and utilities of the cell or the organism from its genome information. KEGG consists of the PATHWAY database for the computerized knowledge on molecular interaction networks such as pathways and complexes, the GENES database for the information about genes and proteins generated by genome sequencing projects, and the LIGAND database for the information about chemical compounds and chemical reactions that are relevant to cellular processes. In addition to these three main databases, limited amounts of experimental data for microarray gene expression profiles and yeast two-hybrid systems are stored in the EXPRESSION and BRITE databases, respectively. Furthermore, a new database, named SSDB, is available for exploring the universe of all protein coding genes in the complete genomes and for identifying functional links and ortholog groups. The data objects in the KEGG databases are all represented as graphs and various computational methods are developed to detect graph features that can be related to biological functions. For example, the correlated clusters are graph similarities which can be used to predict a set of genes coding for a pathway or a complex, as summarized in the ortholog group tables, and the cliques in the SSDB graph are used to annotate genes. The KEGG databases are updated daily and made freely available (http://www.genome.ad.jp/kegg/).

    Keywords: Computational Biology ; Computer Graphics ; *Databases Genetic ; *Databases Protein ; Gene Expression Profiling ; *Genome ; Human ; Information Storage and Retrieval ; Internet ; Macromolecular Systems ; Metabolism_genetics ; Multigene Family ; Protein Conformation ; Proteins_chemistry ; Proteins_genetics ; Proteins_metabolism ; Sequence Homology


  2. Kawashima, T., Kawashima, S., Kanehisa, M., Nishida, H., and Makabe, K.W.. "MAGEST: MAboya gene expression patterns and sequence tags." Nucleic Acids Res. 28 (1). 2000. pp. 133-5.
    [ .pdf ] [ PubMed ]

    MAGEST is a database for newly identified maternal cDNAs of the ascidian, Halocynthia roretzi, which aims to examine the population of the mRNAs. We have collected 3' and 5' tag sequences of mRNAs and their expression data from whole-mount in situ hybridi-zation in early embryos. To date, we have determined more than 2000 tag-sequences of H.roretzi cDNAs and input them into public databases. The tag sequences and the expression data as well as additional information can be obtained through MAGEST via the WWW at http://www.genome.ad.jp/magest/

    Keywords: DNA Complementary ; *Databases Factual ; *Expressed Sequence Tags ; *Gene Expression ; Information Storage and Retrieval ; Urochordata_*genetics


  3. Kawashima, T., Kawashima, S., Kohara, Y., Kanehisa, M., and Makabe, K.W.. "Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags." Nucleic Acids Res. 30 (1). 2002. pp. 119-20.
    [ .pdf ] [ PubMed ]

    MAGEST is a database for maternal gene expression information for an ascidian, Halocynthia roretzi. The ascidian has become an animal model in developmental biological research because it shows a simple developmental process, and belongs to one of the chordate groups. Various data are deposited into the MAGEST database, e.g. the 3'- and 5'-tag sequences from the fertilized egg cDNA library, the results of similarity searches against GenBank and the expression data from whole mount in situ hybridization. Over the last 2 years, the data retrieval systems have been improved in several aspects, and the tag sequence entries have increased to over 20 000 clones. Additionally, we constructed a database, translated MAGEST, for the amino acid fragment sequences predicted from the EST data sets. Using this information comprehensively, we should obtain new information on gene functions. The MAGEST database is accessible via the Internet at http://www.genome.ad.jp/magest/.

    Keywords: Amino Acid Sequence ; DNA Complementary_genetics ; *Databases Genetic ; *Expressed Sequence Tags ; Forecasting ; *Gene Expression Regulation ; Developmental ; Gene Library ; In Situ Hybridization ; Information Storage and Retrieval ; Internet ; RNA Messenger Stored_biosynthesis ; Urochordata_*embryology ; Urochordata_*genetics ; Urochordata_metabolism ; Zygote_metabolism