Takeshi Obayashi

Summary

Publications

  1. pmc 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
  2. pmc 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
  3. pmc 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. pmc 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. pmc 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. pmc ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants
    Takeshi Obayashi
    Graduate School of Information Sciences, Tohoku University, 6 3 09, Aramaki Aza Aoba, Aoba ku, Sendai, 980 8679 Japan
    Plant Cell Physiol 55:e6. 2014
  7. doi request reprint 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. pmc 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
  9. ncbi request reprint 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
  10. pmc 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

Collaborators

Detail Information

Publications14

  1. pmc 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...
  2. pmc 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...
  3. pmc 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. pmc 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. pmc 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. pmc ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants
    Takeshi Obayashi
    Graduate School of Information Sciences, Tohoku University, 6 3 09, Aramaki Aza Aoba, Aoba ku, Sendai, 980 8679 Japan
    Plant Cell Physiol 55:e6. 2014
    ..With the expanded and newly evaluated coexpression data, ATTED-II represents an important resource for identifying functionally related genes in agriculturally important plants. ..
  7. doi request reprint 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. pmc 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...
  9. ncbi request reprint 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...
  10. pmc 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...
  11. pmc Molecular and cellular features of murine craniofacial and trunk neural crest cells as stem cell-like cells
    Kunie Hagiwara
    Department of Ophthalmology, Tohoku University Graduate School of Medicine, Seiryo cho, Aoba ku, Sendai, Japan Department of Ophthalmology, Osaka University Graduate School of Medicine, Yamadaoka, Suita, Japan
    PLoS ONE 9:e84072. 2014
    ..Furthermore, these newly-identified genes up-regulated in cNCC would provide helpful information on NC-originating tumors, developmental disorders in NCC derivatives, and potential applications of NCCs in regenerative medicine. ..
  12. doi request reprint Dmrta1 regulates proneural gene expression downstream of Pax6 in the mammalian telencephalon
    Takako Kikkawa
    Division of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980 8575, Japan
    Genes Cells 18:636-49. 2013
    ..Our novel findings suggest that dual regulation of proneural genes mediated by Pax6 and Dmrt family members is crucial for cortical neurogenesis. ..
  13. pmc 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...
  14. pmc 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...