Takeshi Obayashi

Summary

Publications

  1. ncbi ATTED-II provides coexpressed gene networks for Arabidopsis
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 37:D987-91. 2009
  2. ncbi ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants
    Takeshi Obayashi
    Graduate School of Information Science, Tohoku University, 6 3 09, Aramaki Aza Aoba, Aoba ku, Sendai, 980 8679 Japan
    Plant Cell Physiol 52:213-9. 2011
  3. ncbi Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato ku, Tokyo, Japan
    DNA Res 16:249-60. 2009
  4. ncbi COXPRESdb: a database of coexpressed gene networks in mammals
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo, Japan
    Nucleic Acids Res 36:D77-82. 2008
  5. ncbi Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis
    Kengo Kinoshita
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Bioinformatics 25:2677-84. 2009
  6. ncbi COXPRESdb: a database to compare gene coexpression in seven model animals
    Takeshi Obayashi
    Graduate School of Information Science, Tohoku University, 6 3 09 Aramaki Aza Aoba, Aoba ku, Sendai 980 8679, Japan
    Nucleic Acids Res 39:D1016-22. 2011
  7. ncbi Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways
    Takeshi Obayashi
    Graduate School of Information Science, Tohoku University, 6 3 09 Aramaki Aza Aoba, Aoba ku, Sendai 980 8679, Japan
    J Plant Res 123:311-9. 2010
  8. ncbi A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human
    Yosuke Hatanaka
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1, Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genome Inform 20:212-21. 2008
  9. ncbi COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals
    Takeshi Obayashi
    Graduate School of Information Sciences, Tohoku University, Sendai 980 8679, Japan
    Nucleic Acids Res 41:D1014-20. 2013
  10. ncbi Role of the G-box element in regulation of chlorophyll biosynthesis in Arabidopsis roots
    Koichi Kobayashi
    Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
    Plant Signal Behav 7:922-6. 2012

Detail Information

Publications11

  1. ncbi ATTED-II provides coexpressed gene networks for Arabidopsis
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 37:D987-91. 2009
    ..With these enhanced functions for gene network representation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in Arabidopsis...
  2. ncbi ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants
    Takeshi Obayashi
    Graduate School of Information Science, Tohoku University, 6 3 09, Aramaki Aza Aoba, Aoba ku, Sendai, 980 8679 Japan
    Plant Cell Physiol 52:213-9. 2011
    ..With the ability to investigate condition-specific coexpression and species conservation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in a broad array of plant species...
  3. ncbi Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato ku, Tokyo, Japan
    DNA Res 16:249-60. 2009
    ..This observation was evaluated by large-scale gene expression data for four species: Arabidopsis, human, mouse and rat...
  4. ncbi COXPRESdb: a database of coexpressed gene networks in mammals
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo, Japan
    Nucleic Acids Res 36:D77-82. 2008
    ..COXPRESdb also provides a view to compare the human and mouse coexpression patterns to estimate the conservation between the two species...
  5. ncbi Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis
    Kengo Kinoshita
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Bioinformatics 25:2677-84. 2009
    ..We observed the correlation changes when the first ten principal components were subtracted step-by-step in large-scale Arabidopsis expression data...
  6. ncbi COXPRESdb: a database to compare gene coexpression in seven model animals
    Takeshi Obayashi
    Graduate School of Information Science, Tohoku University, 6 3 09 Aramaki Aza Aoba, Aoba ku, Sendai 980 8679, Japan
    Nucleic Acids Res 39:D1016-22. 2011
    ..With the functions for gene network representation, COXPRESdb can help researchers to clarify the functional and regulatory networks of genes in a broad array of animal species...
  7. ncbi Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways
    Takeshi Obayashi
    Graduate School of Information Science, Tohoku University, 6 3 09 Aramaki Aza Aoba, Aoba ku, Sendai 980 8679, Japan
    J Plant Res 123:311-9. 2010
    ..In addition, we will discuss the coexpression effectiveness for various types of gene sets...
  8. ncbi A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human
    Yosuke Hatanaka
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1, Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genome Inform 20:212-21. 2008
    ..We also applied basket method analysis for seeking combinatorial activities of those conserved TFBSs...
  9. ncbi COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals
    Takeshi Obayashi
    Graduate School of Information Sciences, Tohoku University, Sendai 980 8679, Japan
    Nucleic Acids Res 41:D1014-20. 2013
    ..With these updates, COXPRESdb will become a more powerful tool for analyses of functional and regulatory networks of genes in a variety of animal species...
  10. ncbi Role of the G-box element in regulation of chlorophyll biosynthesis in Arabidopsis roots
    Koichi Kobayashi
    Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
    Plant Signal Behav 7:922-6. 2012
    ..Our data suggest that transcription factors and cis-elements participating chlorophyll biosynthesis are substantially changed during organ differentiation, which may be linked to the differentiation of plastids...
  11. ncbi Corticotropin-releasing hormone receptor 1 gene variants in irritable bowel syndrome
    Naoko Sato
    Department of Behavioral Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
    PLoS ONE 7:e42450. 2012
    ..We tested the hypothesis that genetic polymorphisms and haplotypes of CRH-R1 moderate the IBS phenotype and negative emotion in IBS patients...