Search PubMed⌕ Search

Biomedical subjects

Tetsuro Toyoda

Publications and source records attributed to Tetsuro Toyoda.

16 recordsLinked to original sources
PubMed2006

OmicBrowse: a browser of multidimensional omics annotations.

UNLABELLED: OmicBrowse is a browser to explore multiple datasets coordinated in the multidimensional omic space integrating omics knowledge ranging from genomes to phenomes and connecting evolutional correspondences among multiple species. OmicBrowse integrates multiple data servers into a single omic space through secure peer-to-peer server communications, so that a user can easily obtain an integrated view of distributed data servers, e.g. an integrated view of numerous whole-genome tiling-array data retrieved from a user's in-house private-data server, along with various genomic annotations from public internet servers. OmicBrowse is especially appropriate for positional-cloning purposes. It displays both genetic maps and genomic annotations within wide chromosomal intervals and assists a user to select candidate genes by filtering their annotations or associated documents against user-specified keywords or ontology terms. We also show that an omic-space chart effectively represents schemes for integrating multiple datasets of multiple species. AVAILABILITY: OmicBrowse is developed by the Genome-Phenome Superbrain Project and is released as free open-source software under the GNU General Public License at http://omicspace.riken.jp.

Chromosome Mapping↗
PubMed2006

A flexible representation of omic knowledge for thorough analysis of microarray data.

BACKGROUND: In order to understand microarray data reasonably in the context of other existing biological knowledge, it is necessary to conduct a thorough examination of the data utilizing every aspect of available omic knowledge libraries. So far, a number of bioinformatics tools have been developed. However, each of them is restricted to deal with one type of omic knowledge, e.g., pathways, interactions or gene ontology. Now that the varieties of omic knowledge are expanding, analysis tools need a way to deal with any type of omic knowledge. Hence, we have designed the Omic Space Markup Language (OSML) that can represent a wide range of omic knowledge, and also, we have developed a tool named GSCope3, which can statistically analyze microarray data in comparison with the OSML-formatted omic knowledge data. RESULTS: In order to test the applicability of OSML to represent a variety of omic knowledge specifically useful for analysis of Arabidopsis thaliana microarray data, we have constructed a Biological Knowledge Library (BiKLi) by converting eight different types of omic knowledge into OSML-formatted datasets. We applied GSCope3 and BiKLi to previously reported A. thaliana microarray data, so as to extract any additional insights from the data. As a result, we have discovered a new insight that lignin formation resists drought stress and activates transcription of many water channel genes to oppose drought stress; and most of the 20S proteasome subunit genes show similar expression profiles under drought stress. In addition to this novel discovery, similar findings previously reported were also quickly confirmed using GSCope3 and BiKLi. CONCLUSION: GSCope3 can statistically analyze microarray data in the context of any OSML-represented omic knowledge. OSML is not restricted to a specific data type structure, but it can represent a wide range of omic knowledge. It allows us to convert new types of omic knowledge into datasets that can be used for microarray data analysis with GSCope3. In addition to BiKLi, by collecting various types of omic knowledge as OSML libraries, it becomes possible for us to conduct detailed thorough analysis from various biological viewpoints. GSCope3 and BiKLi are available for academic users at our web site http://omicspace.riken.jp.

Journal Article↗
PubMed2005

RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome.

The RIKEN Arabidopsis Genome Encyclopedia (RARGE) database houses information on biological resources ranging from transcriptome to phenome, including RIKEN Arabidopsis full-length (RAFL) complementary DNAs (cDNAs), their promoter regions, Dissociation (Ds) transposon-tagged lines and expression data from microarray experiments. RARGE provides tools for searching by resource code, sequence homology or keyword, and rapid access to detailed information on the resources. We have isolated 245 946 RAFL cDNA clones and collected 11 933 transposon-tagged lines, which are available from the RIKEN Bioresource Center and are stored in RARGE. The RARGE web interface can be accessed at http://rarge.gsc.riken.jp/. Additionally, we report 90 000 new RAFL cDNA clones here.

Arabidopsis↗
PubMed2005

RARTF: database and tools for complete sets of Arabidopsis transcription factors.

More than 5% of all genes in the Arabidopsis thaliana genome have been assumed to code for transcription factors. However, it has been difficult to accurately identify them. To construct proper sets of transcription factors, we used PSI-BLAST and InterProScan, and also checked several families manually. Especially to determine major Arabidopsis transcription factors (MYB, AP2/EREBP, bHLH, NAC, MADS, bZIP, WRKY), we compared the PSI-BLAST search results with those in recent reports. Finally, we identified 1968 proteins as transcription factors (7.4% of all Arabidopsis genes). We established a database named RARTF (RIKEN Arabidopsis Transcription Factor database, http://rarge.gsc.riken.jp/rartf/) based on the identified transcription factors. In RARTF, we provide information on the functional motif of transcription factors, full-length cDNAs, alternative pre-mRNA splicing events and Ac/Ds transposon-tagged mutants. We also provide expression profiles of 400 transcription factor genes in six experiments. We will report expression profiles of all transcription factor genes in various plant tissues under various stress and hormone conditions in the near future.

Amino Acid Sequence↗
PubMed2005

Postoperative tomographic assessment of veneer bone grafting with implant placement in the maxillary anterior region.

Various ridge augmentation and sinus lift procedures were performed in severely resorbed alveolar crests of a maxilla to provide some volume for implant treatment. It was reported that the outcome of maxillary sinus lift procedures was evaluated with conventional tomography or computerized tomography, and that grafted bone around implants markedly progressed in resorption, particularly at the implant apex. However, veneer bone grafting with implant placement has not been evaluated after treatment with imaging techniques. Therefore, the purpose of this study was to assess veneer bone grafting after maxillary anterior implant treatment. Seven patients with a mean age of 24 years, with implants placed in the maxillary anterior region with or without autogenous veneer bone grafting were postoperatively examined using conventional tomography. On tomograms, the ratio of bone-to-implant contact and the area of bone were measured in labial bones with bone grafts, and they were compared with the values without bone grafts. In cases with bone grafting, the average ratio of bone-to-implant contact was 63.6%, whereas 81.8% was formed in cases without bone grafting. The average area of bone was 12.9 mm and 23.4 mm in patients with and without bone grafting, respectively. No significant difference was found between the implants with and without bone grafts. Resorbed labial bone was observed in the maxillary anterior region with and without veneer bone grafting.

Adolescent↗
PubMed2005

Tiling array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models.

Tiling arrays of high-density oligonucleotide probes spanning the entire genome are powerful tools for the discovery of new genes. However, it is difficult to determine the structure of the spliced product of a structurally unknown gene from noisy array signals only. Here we introduce a statistical method that estimates the precise splicing points and the exon/intron structure of a structurally unknown gene by maximizing the odds or the ratio of posterior probabilities of the structure under the observation of array signal intensities and nucleic acid sequences. Our method more accurately predicted the gene structures than the simple threshold-based method, and more correctly estimated the expression values of structurally unknown genes than the window-based method. It was observed that the Markov model contributed to the precision of splice points, and that the statistical significance of expression (P-value) represented the reliability of the estimated gene structure and expression value well. We have implemented the method as a program ARTADE (ARabidopsis Tiling Array-based Detection of Exons) and applied it to the Arabidopsis thaliana whole-genome array data analysis. The database of the predicted results and the ARTADE program are available at http://omicspace.riken.jp/ARTADE/.

Arabidopsis↗
PubMed2005

Three-dimensional definition of leaf morphological traits of Arabidopsis in silico phenotypic analysis.

The detection of phenotypic alterations of mutants and variants is one of the bottlenecks that hinder systematic gene functional studies of the model plant Arabidopsis. In an earlier study, we have addressed this problem by proposing a novel methodology for phenome analysis based on in silico analysis of polygon models that are acquired by 3-dimensional (3D) measurement and which precisely reconstruct the actual plant shape. However, 3D quantitative descriptions of morphological traits are rare, whereas conventional 2D descriptions have already been studied but may lack the necessary precision. In this report, we focus on six major leaf morphological traits, which are commonly used in the current manual mutant screens, and propose new 3D quantitative definitions that describe these traits. In experiments to extract the traits, we found significant differences between two variants of Arabidopsis with respect to blade roundness and blade epinasty. Remarkably, the detected difference between variants in the blade roundness trait was undetectable when using conventional 2D descriptions. Thus, the result of the experiment indicates that the proposed definitions with 3D description may lead to new discoveries of phenotypic alteration in gene functional studies that would not be possible using conventional 2D descriptions.

Algorithms↗
PubMed2005

In silico phenotypic screening method of mutants based on statistical modeling of genetically mixed samples.

In comprehensive functional genomics projects, systematic analysis of phenotypes is vital. However, conventional phenotypic screening is done mainly by imprecise visual observation of qualitative traits, and, therefore, in silico screening techniques for quantitative traits are required. In this report, we propose in silico phenotypic screening method that utilizes a Gaussian mixture model for the trait distribution in the offspring of a mutagenized line and the likelihood ratio test between the estimated Gaussian mixture model and the wild-type single Gaussian model. In order to evaluate the proposed method, we performed a screening experiment using real trait data of Arabidopsis. In this experiment, the proposed screening method properly distinguished the mutant line from the wild-type line. Furthermore, we conducted power analysis of the proposed method and two conventional methods under various simulated conditions of sample size and distribution of trait frequency. The result of the power analysis confirmed the effectiveness of the proposed method compared to the conventional methods.

Algorithms↗
PubMed2004

Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences.

We mapped RIKEN Arabidopsis full-length (RAFL) cDNAs to the Arabidopsis thaliana genome to search for alternative splicing events. We used 278,734 full-length and 3'/5' terminal reads of the sequences of 220,214 RAFL cDNA clones for the analysis. Eighty-nine percent of the cDNA sequences could be mapped to the genome and were clustered in 17,130 transcription units (TUs). Alternative splicing events were found in 1764 out of 15,214 TUs (11.6%) with multiple sequences. We collected full-length cDNA clones from plants grown under various environmental conditions or from various organs. We then analyzed the correlation between alternative splicing events and environmental stress conditions. Alternative splicing profiles changed according to environmental stress conditions and the various developmental stages of plant organs. In particular, cold-stress conditions affected alternative splicing profiles. The change in alternative splicing profiles under cold stress may be mediated by alternative splicing and transcriptional regulation of splicing factors.

Alternative Splicing↗
PubMed2004

TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks.

MOTIVATION: Most ordinary traits are well described by multiple measurable parameters. Thus, in the course of elucidating the genes responsible for a given trait, it is necessary to conduct and integrate the genetic mapping of each parameter. However, the integration of multiple mapping results from different publications is prevented by the fact that they are conventionally published and accumulated in printed forms or graphics which are difficult for computers to reuse for further analyses. RESULTS: We have defined an XML-based schema as a container of genetic mapping results, and created a database named TraitMap containing curator-checked data records based on published papers of mapping results in Homosapiens, Mus musculus, and Arabidopsis thaliana. TraitMap is the first database of mapping charts in genetics, and is integrated in a web-based retrieval framework: termed Genome <--> Phenome Superhighway (GPS) system, where it is possible to combine and visualize multiple mapping records in a two-dimensional display. Since most traits are regulated by multiple genes, the system associates every combination of genetic loci to biomolecular networks, and thus helps us to estimate molecular-level candidate networks responsible for a given trait. It is demonstrated that a combined analysis of two diabetes-related traits (susceptibility to insulin resistance and non-HDL cholesterol level) suggests that molecular-level relationships such as the interaction among leptin receptor (Lepr), peroxisome proliferators-activated receptor-gamma (Pparg) and insulin receptor substrate 1 (Irs1), are candidate causal networks affecting the traits in a multigenic manner. AVAILABILITY: TraitMap database and GPS are accessible at http://omicspace.riken.jp/gps/

Chromosome Mapping↗
PubMed2004

Omic space: coordinate-based integration and analysis of genomic phenomic interactions.

MOTIVATION: With the recent progress in genomics, various data sets of omic interactions describing networks of omic elements have become available. In order to obtain reliable hypotheses from the data, it is effective to integrate interactions from different sorts of data sets. In order to facilitate a coordinate-based integration and analysis of omic interactions, we introduce the concept of an omic space comprising a comprehensive set of omic planes. Genomic, transcriptomic, proteomic, metabolomic, phenomic and other omic planes are defined by two orthogonal genomic-coordinate axes. RESULTS: We show that the omic space concept helps us to assimilate biological findings comprehensively into hypotheses or models combining higher-order phenomena and lower-order mechanisms by demonstrating that a comprehensive ranking of correspondences among interactions in the space can be used effectively for estimating candidates of responsible gene pairs for epistatic interacting loci of tumors in mice. We also show that the omic space offers a convenient framework for database integration, by presenting a system named the 'Genome <==> Phenome Superhighway' (GPS) that serves as a framework for integration and visualization of omic interactions based on omic spaces of some model species including Homo sapiens, Mus musculus, Caenorhabditis elegans and Arabidopsis thaliana. AVAILABILITY: For the GPS web site, see http://omicspace.riken.jp/gps/.

Algorithms↗
PubMed2004

Two missense mutations in the IRF6 gene in two Japanese families with Van der Woude syndrome.

Van der Woude syndrome (VWS) is a common autosomal dominant disorder with cleft lip and/or palate and lower lip pits. Its prevalence is estimated to be 1/33,600 in the Finnish Population, and 1/47,813 in the Japanese. We performed mutation analysis of the IRF6 gene by direct sequencing in 2 unrelated Japanese families that consist of a total of 3 affected members with cleft lip and palate associated with lower lip pits. Consequently, we found novel base substitutions, 25C>T, in IRF6-exon 3 in a boy, his mother, and his phenotypically normal maternal grandmother in one of the families. A known mutation, 250C>T, was identified in exon 4 of a girl and her unaffected father in the other family. The same mutations were never observed among 190 healthy Japanese. The results indicate incomplete penetrance and variable expressivity in the families. Because 25C>T and 250C>T predict to lead to R9W and R84C substitutions, respectively, at the most conserved DNA binding domain of IRF6, and because arginine at positions 9 and 84 is highly conserved among IRFs, the 2 mutations may lead to abolish the DNA binding activity in the developing craniofacial region. To our knowledge, this is the first report of IRF6 mutations observed in Japanese VWS patients.

Amino Acid Sequence↗
PubMed2004

Automatic quantification of morphological traits via three-dimensional measurement of Arabidopsis.

Many mutants have been isolated from the model plant Arabidopsis thaliana, and recent important genetic resources, such as T-DNA knockout lines, facilitate the speed of identifying new mutants. However, present phenotypic analysis of mutant screens depends mainly on qualitative descriptions after visual observation of morphological traits. We propose a novel method of phenotypic analysis based on precise three-dimensional (3D) measurement by a laser range finder (LRF) and automatic data processing. We measured the 3D surfaces of young plants of two Arabidopsis ecotypes and successfully defined two new traits, the direction of the blade surface and epinasty of the blade, quantitatively. The proposed method enables us to obtain quantitative and precise descriptions of plant morphologies compared to conventional 2D measurement. The method will open a way to find new traits from mutant pools or natural ecotypes based on 3D data.

Algorithms↗
PubMed2003

KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data.

UNLABELLED: KnowledgeEditor is a graphical workbench for biological experts to model biomolecular network graphs. The modeled network data are represented by SRML, and can be published via the internet with the help of plug-in module 'GSCope'. KnowledgeEditor helps us to model and analyze biological pathways based on microarray data. It is possible to analyze the drawn networks by simulating up-down regulatory cascade in molecular interactions. AVAILABILITY: KnowledgeEditor is available at http://gscope.gsc.riken.go.jp/.

Cluster Analysis↗
PubMed2003

GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs.

UNLABELLED: A graphical tool to visualize highly complicated biomolecular network graphs is described. It helps us to understand the graphs from macroscopic and microscopic viewpoints by incorporating continuous transition from global to clipped hyperbolic projection. GSCope also helps us to find a molecule in the graphs by offering several searching functions. It is useful to publish biomolecular network graphs on the internet. AVAILABILITY: GSCope is available at http://gscope.gsc.riken.go.jp.

Computer Graphics↗