Shin Kawano

Publications of Shin Kawano

• The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

  Authors: Toshiaki Katayama, Mark D Wilkinson, Rutger Vos, Takeshi Kawashima, Shuichi Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong-Woo Chun, Atsuko Yamaguchi, Shin Kawano [......] Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi

  Journal of biomedical semantics. 08/2011; 2:4.

  ABSTRACT: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperabilityABSTRACT: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.

• Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans.

  Authors: Kosuke Hashimoto, Toshiaki Tokimatsu, Shin Kawano, Akiyasu C Yoshizawa, Shujiro Okuda, Susumu Goto, Minoru Kanehisa

  Carbohydrate research. 04/2009;

  Glycosyltransferases comprise highly divergent groups of enzymes, which play a central role in the synthesis of complex glycans. Because the repertoire of glycosyltransferases in the genomeGlycosyltransferases comprise highly divergent groups of enzymes, which play a central role in the synthesis of complex glycans. Because the repertoire of glycosyltransferases in the genome determines the range of synthesizable glycans, and because the increasing amount of genome sequence data is now available, it is essential to examine these enzymes across organisms to explore possible structures and functions of the glycoconjugates. In this study, we systematically investigated 36 eukaryotic genomes and obtained 3426 glycosyltransferase homologs for biosynthesis of major glycans, classified into 53 families based on sequence similarity. The families were further grouped into six functional categories based on the biosynthetic pathways, which revealed characteristic patterns among organism groups in the degree of conservation and in the number of paralogs. The results also revealed a strong correlation between the number of glycosyltransferases and the number of coding genes in each genome. We then predicted the ability to synthesize major glycan structures including N-glycan precursors and GPI-anchors in each organism from the combination of the glycosyltransferase families. This indicates that not only parasitic protists but also some algae are likely to synthesize smaller structures than the structures known to be conserved among a wide range of eukaryotes. Finally we discuss the functions of two large families, sialyltransferases and beta4-glycosyltransferases, by performing finer classifications into subfamilies. Our findings suggest that universality and diversity of glycans originate from two types of evolution of glycosyltransferase families, namely conserved families with few paralogs and diverged families with many paralogs.

• KEGG as a glycome informatics resource.

  Authors: Kosuke Hashimoto, Susumu Goto, Shin Kawano, Kiyoko F Aoki-Kinoshita, Nobuhisa Ueda, Masami Hamajima, Toshisuke Kawasaki, Minoru Kanehisa

  Glycobiology. 06/2006; 16(5):63R-70R.

  Bioinformatics approaches to carbohydrate research have recently begun using large amounts of protein and carbohydrate data. In this field called glycome informatics, the foremost necessity is aBioinformatics approaches to carbohydrate research have recently begun using large amounts of protein and carbohydrate data. In this field called glycome informatics, the foremost necessity is a comprehensive resource for genome-scale bioinformatics analysis of glycan data. Although the accumulation of experimental data may be useful as a reference of biological and biochemical information on carbohydrates, this is insufficient for bioinformatics analysis. Thus, we have developed a glycome informatics resource (http://www.genome.jp/kegg/glycan/) in KEGG (Kyoto Encyclopedia of Genes and Genomes), an integrated knowledge base of protein networks, genomic information, and chemical information. This review describes three noteworthy features: (1) GLYCAN, a database of carbohydrate structures; (2) glycan-related pathways; and (3) Composite Structure Map (CSM), a map illustrating all possible variations of carbohydrate structures within organisms. GLYCAN includes two useful tools: an intuitive drawing tool called KegDraw, and an efficient glycan search and alignment tool called KEGG Carbohydrate Matcher (KCaM). KEGG's glycan biosynthesis and metabolism pathways, integrating carbohydrate structures, proteins, and reactions, are also a pivotal resource. CSM is constructed as a bridge between carbohydrate functions and structures. CSM is able to display, for example, expression data of glycosyltransferases in a compact manner. In all the KEGG resources, various objects including KEGG pathways, chemical compounds, as well as carbohydrate structures are commonly represented as graphs, which are widely studied and utilized in the computer science field.

• Prediction of glycan structures from gene expression data based on glycosyltransferase reactions.

  Authors: Shin Kawano, Kosuke Hashimoto, Takashi Miyama, Susumu Goto, Minoru Kanehisa

  Bioinformatics (Oxford, England). 12/2005; 21(21):3976-82.

  MOTIVATION: Glycan chains are synthesized by a combination of several kinds of glycosyltransferases (GTs). Thus, once we know the repertoire of GTs in the genome, in the transcriptome or in theMOTIVATION: Glycan chains are synthesized by a combination of several kinds of glycosyltransferases (GTs). Thus, once we know the repertoire of GTs in the genome, in the transcriptome or in the proteome, it should in principle be possible to predict the repertoire of possible glycan structures in an organism or at a specific stage of the cell. Here, we show that a repertoire of glycan structures can be predicted from the set of GTs in the transcriptome. That is, using knowledge about glycan structure characteristics, we can predict glycan structures from incomplete or noisy data such as DNA microarray data. RESULTS: First, we constructed a reaction pattern library consisting of bond-formation patterns of GT reactions and investigated the co-occurrence frequencies of all reaction patterns in the glycan database. This was followed by the prediction of glycan structures using this library and a co-occurrence score. A penalty score was also implemented in the prediction method. Then we examined the performance of prediction by the leave-one-out cross validation method using individual reaction pattern profiles in the KEGG GLYCAN database as virtual expression profiles. The accuracy of prediction was 81%. Finally, we applied the prediction method to real expression data. Using expression profiles from the human carcinoma cell, glycan structures with sialic acid and sialyl Lewis X epitope were predicted, which corresponded well with experimental results.

• A global representation of the carbohydrate structures: a tool for the analysis of glycan.

  Authors: Kosuke Hashimoto, Shin Kawano, Susumu Goto, Kiyoko F Aoki-Kinoshita, Masayuki Kawashima, Minoru Kanehisa

  Genome informatics. International Conference on Genome Informatics. 02/2005; 16(1):214-22.

  Glycan resources have been developed of late, such as carbohydrate databases, analysis tools, and algorithms for analysis of carbohydrate features. With this background, bioinformatics approaches toGlycan resources have been developed of late, such as carbohydrate databases, analysis tools, and algorithms for analysis of carbohydrate features. With this background, bioinformatics approaches to carbohydrate research have recently begun using a large amount of protein and carbohydrate data. This paper introduces one of these projects that elucidates the range of carbohydrate structures. In this study, the variety of carbohydrate structures have been enumerated in a global tree structure called variation trees, using the KEGG GLYCAN database, which is a public-domain glycan resource for bioinformatics analysis. Additionally, a glycosyltransferase mapping list of glycosyltransferases and their catalyzing glycosidic linkages was constructed. From this, we present the composite structure map (CSM), which is a structural variation map integrating its variation trees and glycosyltransferase map list. CSM is able to display, for example, expression data of glycosyltransferases in a compact manner, illustrating its versatility as a new bioinformatics resource and tool capable of analyzing carbohydrate structures on a global scale. These resources are available at http://www.genome.jp/kegg/glycan/.