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Exhaustive Collection of Gene Modules that Changes Functions and Structures of Cells

Research Project

Project/Area Number 18510178
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Applied genomics
Research InstitutionNational Institute of Advanced Industrial Science and Technology

Principal Investigator

FUJIBUCHI Wataru  National Institute of Advanced Industrial Science and Technology, National Institute of Advanced Industrial Science and Technology, Computational Biology Research Center, Team Leader (60273512)

Co-Investigator(Kenkyū-buntansha) OKUBO Kousaku  National Institute of Genetics, Department of Molecular Genetics, Professor (40233069)
Project Period (FY) 2006 – 2007
Project Status Completed (Fiscal Year 2007)
Budget Amount *help
¥1,810,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥210,000)
Fiscal Year 2007: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2006: ¥900,000 (Direct Cost: ¥900,000)
KeywordsCell・Tissue / Gene Expression Regulation
Research Abstract

We performed a research to describe differences of shapes and works of cells by gene modules. First, as a data resource, we obtained expression data of 35,951 genes against 210 cells/tissues in total, from the collaborated researcher. And we obtained microscope images about 100 kinds of cells from the collaborator and others. Second, to measure the shapes of cells, we devised an image processing method that is robust against noise. Third, in order to extract combinatorial patterns of genes and cells exhaustively, we developed a fast biclustering method. With the two methods, we collected gene modules from gene expression data, while measuring parameters related to the contours of cells and nucleuses and the lining of cells. Analyzing the results, we obtained the whole set of gene modules that are commonly or reversely expressed among different cells. We found that this analysis allows us to perform digital differential display in more efficient way, for example, there was an extracted gene module that contained receptors, channels, transcription factors, etc., where genes were expressed reversely between brain and heart cells. Although it was not written in the proposal, to predict the shapes of cells from gene expression states, we performed the Support Vector Machine learning, and were able to predict the shapes of cells with 18 morphological parameters with 69.1 to 78.2% accuracies, against the test cells. We presented these results in two academic meetings, published three journal papers, and opened an Internet web service for retrieving and analyzing gene modules. Currently, we are writing a paper to summarize the whole study. Recognizing the values of the primary and the secondary datasets that we created in this project, our institute proceeded to support the development of the database from the fiscal year of 2008 to open it to public.

Report

(3 results)
  • 2007 Annual Research Report   Final Research Report Summary
  • 2006 Annual Research Report
  • Research Products

    (17 results)

All 2007 2006 Other

All Journal Article (8 results) (of which Peer Reviewed: 3 results) Presentation (5 results) Remarks (2 results) Patent(Industrial Property Rights) (2 results)

  • [Journal Article] A biclustering method for gene expression module discovery using closed itemset enumeration algorithm2007

    • Author(s)
      岡田吉史、藤渕 航、Paul Horton
    • Journal Title

      IPSJ Transactions on Bioinformatics 48・SIG5

      Pages: 39-48

    • NAID

      110006242961

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Exaustive search of maximal biclusters in gene expression data2007

    • Author(s)
      岡田吉史、藤渕 航、Paul Horton
    • Journal Title

      Proceedings of International MultiConference of Engineers and Computer Scientists 2007 1

      Pages: 307-312

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] Exhaustive Search Method of Gene Expression Modules and Its Application to Human Tissue Data2007

    • Author(s)
      Okada, Y., Okubo, K., Horton, P.and Fujibuchi, W.
    • Journal Title

      IAENG International Journal of Computer Science 34

      Pages: 119-126

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
    • Peer Reviewed
  • [Journal Article] A biclustering method for gene expression module discovery using closed itemset enumeration algorithm2007

    • Author(s)
      Okada, et. al.
    • Journal Title

      IPSJ Transactions on Bioinformatics 48・SIG5

      Pages: 39-48

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Exhaustive search of maximal biclusters in gene expression data2007

    • Author(s)
      Okada, et. al.
    • Journal Title

      Proceedings of International MultiConference of Engineers and Computer Scientists 1

      Pages: 307-312

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] Exhaustive search method of gene expression modules and its application to human tissue data2007

    • Author(s)
      Okada, et. al.
    • Journal Title

      IAENG International Journal of Computer Science 34

      Pages: 119-126

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Journal Article] A biclustering method for gene expression module discovery using closed itemset enumeration algorithm2007

    • Author(s)
      岡田吉史, 藤渕航, Paul Horton
    • Journal Title

      IPSJ Transactions on Bioinformatics 48・SIG5

      Pages: 39-48

    • NAID

      110006242961

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Exaustive search of maximal biclusters in gene expression data2007

    • Author(s)
      岡田吉史, 藤渕航, Paul Horton
    • Journal Title

      Proceedings of International MultiCongerence of Engineers and Computer Scienitists 2007 1

      Pages: 307-312

    • Related Report
      2006 Annual Research Report
  • [Presentation] Global and Local Similarity Searches of Gene Expression Data2007

    • Author(s)
      Fujibuchi, W., Okada, Y., and Horton, P.
    • Organizer
      Japanese Society of Bioinformatics
    • Place of Presentation
      日本科学未来館(東京)
    • Year and Date
      2007-12-19
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Presentation] Global and Local Similarity Searches of Gene Expression Data2007

    • Author(s)
      Fujibuchi, et. al.
    • Organizer
      Japanese Society of Bioinformatics
    • Place of Presentation
      Tokyo
    • Year and Date
      2007-12-19
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Mining a Large-scale Microarray Database for Similar Gene Expression Modules to Find Distant Relationships between Down Syndrome and Huntington's Disease2007

    • Author(s)
      Okada, Y.and Fujibuchi, W.
    • Organizer
      Critical Assessment of Microarray Data Analysis 07
    • Place of Presentation
      Valencia,Spain
    • Year and Date
      2007-12-14
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Mining a large-scale microarray database for similar gene expression modules to find distant relationships between Down syndrome and Huntington's disease2007

    • Author(s)
      Okada, et. al.
    • Organizer
      Critical Assessment of Microarray Data Analysis 07
    • Place of Presentation
      Valencia, Spain
    • Year and Date
      2007-12-14
    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2007 Final Research Report Summary
  • [Presentation] Mming a Large-scale Microarray Database for Similar Gene Expression Modules to Find Distant Relationships between Down Syndrome andHuntingtonIs Disease2007

    • Author(s)
      Okada, Y.and Fujibuchi, W.
    • Organizer
      Critical Assessment of Microarray Data Analysis 07
    • Place of Presentation
      Valencia, Spain
    • Year and Date
      2007-12-14
    • Related Report
      2007 Annual Research Report
  • [Remarks] 「研究成果報告書概要(和文)」より

    • URL

      http://cellmontage.cbrc.jp/samurai/

    • Related Report
      2007 Final Research Report Summary
  • [Remarks]

    • URL

      http://cellmontage.cbrc.jp/samurai/

    • Related Report
      2007 Annual Research Report
  • [Patent(Industrial Property Rights)] 遺伝子発現モジュール探索装置、遺伝子発現モジュール探索方法及び遺伝子発現モジュール探索プログラム2007

    • Inventor(s)
      岡田 吉史, 藤渕 航
    • Industrial Property Rights Holder
      独立行政法人産業技術総合研究所
    • Industrial Property Number
      2007-320636
    • Filing Date
      2007-12-12
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Annual Research Report 2007 Final Research Report Summary
  • [Patent(Industrial Property Rights)] 細胞輪郭抽出装置、細胞輪郭抽出方法およびプログラム2006

    • Inventor(s)
      藤渕 航
    • Industrial Property Rights Holder
      独立行政法人産業技術総合研究所
    • Industrial Property Number
      2006-331416
    • Filing Date
      2006-12-08
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2007 Final Research Report Summary 2006 Annual Research Report

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Published: 2006-04-01   Modified: 2016-04-21  

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