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2010 Fiscal Year Final Research Report

Construction of ATTED-III, Gene Coexpression Database for Arabidopsis

Research Project

  • PDF
Project/Area Number 21770035
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Plant molecular biology/Plant physiology
Research InstitutionTohoku University

Principal Investigator

OBAYASHI Takeshi  Tohoku University, 大学院・情報科学研究科, 助教 (50397048)

Project Period (FY) 2009 – 2010
Keywords環境応答 / バイオインフォマティクス
Research Abstract

ATTED-II, a coexpressed gene database for Arabidopsis, has been used to find functionally related gene groups. However, this traditional coexpression information cannot provide the detail of gene relationships. In this study, I constructed condition-specific coexpression data and two types of viewers to reveal the situation when and where the genes function together.

  • Research Products

    (12 results)

All 2011 2010 2009

All Journal Article (6 results) (of which Peer Reviewed: 5 results) Presentation (6 results)

  • [Journal Article] Kinoshita K ATTED-II updates : condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.2011

    • Author(s)
      Obayashi T, Nishida K, Kasahara K
    • Journal Title

      Plant Cell Physiol 52

      Pages: 213-219

    • Peer Reviewed
  • [Journal Article] COXPRESdb : a database to compare gene coexpression in seven model animals.2011

    • Author(s)
      Obayashi T, Kinoshita K
    • Journal Title

      Nucleic Acids Res 39

      Pages: D1016-1022

    • Peer Reviewed
  • [Journal Article] 共発現情報から見る遺伝子機能ネットワーク2011

    • Author(s)
      大林武、木下賢吾
    • Journal Title

      化学と生物[KASEAA] 49

      Pages: 48-56

  • [Journal Article] Coexpression landscape in ATTED-II : usage of gene list and gene network for various types of pathways.2010

    • Author(s)
      Obayashi T, Kinoshita K
    • Journal Title

      J. Plant Research 123

      Pages: 311-319

    • Peer Reviewed
  • [Journal Article] Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis.2009

    • Author(s)
      Kinoshita K, Obayashi T
    • Journal Title

      Bioinformatics 25

      Pages: 2677-2684

    • Peer Reviewed
  • [Journal Article] Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression.2009

    • Author(s)
      Obayashi T, Kinoshita K
    • Journal Title

      DNA Research 16

      Pages: 249-260

    • Peer Reviewed
  • [Presentation] How to measure the similarity of gene expression patterns to identify gene function2011

    • Author(s)
      Obayashi T
    • Organizer
      QBIC2011 Bio-Informatics Workshop
    • Place of Presentation
      東京理科大学
    • Year and Date
      2011-03-11
  • [Presentation] Rank of Correlation Coefficient Is a Comparable Measure of Gene Coexpression2010

    • Author(s)
      Obayashi T, Kinoshita K
    • Organizer
      The 2010 Annual Conference of Japanese Society for Bioinformatics
    • Place of Presentation
      九州大学
    • Year and Date
      2010-12-13
  • [Presentation] COXPRESdb : a gene coexpression database for 7 animal species2010

    • Author(s)
      Obayashi T, Kinoshita K
    • Organizer
      4th Asian Young Researchers Conference on Computational and Omics Biology
    • Place of Presentation
      シンガポール、シンガポール共和国
    • Year and Date
      2010-12-01
  • [Presentation] Number of microarray samples to construct effective gene coexpression data2010

    • Author(s)
      Obayashi T, Kinoshita K
    • Organizer
      第51回日本植物生理学会年会
    • Place of Presentation
      熊本大学
    • Year and Date
      2010-03-20
  • [Presentation] Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression2010

    • Author(s)
      Obayashi T, Kinoshita K
    • Organizer
      Asian Young Researchers Conference on Computational and Omics Biology 2010
    • Place of Presentation
      台南、台湾
    • Year and Date
      2010-03-10
  • [Presentation] COXPRESdb : A database of coexpressed gene networks for human, mouse and rat2009

    • Author(s)
      Obayashi T, Kinoshita K
    • Organizer
      International congress of physiological sciences
    • Place of Presentation
      京都
    • Year and Date
      2009-07-27

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Published: 2012-02-13   Modified: 2016-04-21  

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