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Gene expression analyses in the mouse digital brain for understanding molecular bases of higher motor disfunction

Research Project

Project/Area Number 26280110
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Okamura-Oho Yuko  国立研究開発法人理化学研究所, 光量子工学研究領域, 客員研究員 (60381571)

Co-Investigator(Kenkyū-buntansha) 横田 秀夫  国立研究開発法人理化学研究所, 光量子工学研究領域, チームリーダー (00261206)
太田 聡史  国立研究開発法人理化学研究所, バイオリソースセンター, 専任研究員 (30391890)
Project Period (FY) 2014-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥15,990,000 (Direct Cost: ¥12,300,000、Indirect Cost: ¥3,690,000)
Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2015: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
Fiscal Year 2014: ¥7,800,000 (Direct Cost: ¥6,000,000、Indirect Cost: ¥1,800,000)
Keywords遺伝子発現 / 随意運動 / モーションキャプチャー / ハンチントン病 / 逆運動学解析 / データベース / 3D 発現地図
Outline of Final Research Achievements

More than 85% of genes are expressed in the brain and maintain the structure and execute neural function. We have invented a TT method for profiling gene expression patterns of the whole brain in the three-dimensional coordinate. We have also developed a high-resolution motion capture method and detected subtle changes of walking motion and describe them with parameters of biomechanics. Using these methods, we analyzed a neuronal inherited disease model mouse with abnormal motion. Then, we found parameter changes in motion of abnormal mice and expression-area changes in gene expression of a group of genes in the beginning stages of the disease.

Report

(5 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • Research Products

    (34 results)

All 2017 2016 2015 2014 Other

All Journal Article (12 results) (of which Peer Reviewed: 11 results,  Open Access: 5 results,  Acknowledgement Compliant: 1 results) Presentation (18 results) (of which Int'l Joint Research: 9 results,  Invited: 9 results) Book (2 results) Remarks (2 results)

  • [Journal Article] Three-Dimensional Observation of Microstructure of Bone Tissue Using High-Precision Machining2017

    • Author(s)
      Furushiro Naomichi、Yokota Hideo、Nakamura Sakiko、Fujisaki Kazuhiro、Yamagata Yutaka、Kokubo Mitsunori、Himeno Ryutaro、Makinouchi Akitake、Higuchi Toshiro、
    • Journal Title

      International Journal of Automation Technology

      Volume: 11 Issue: 6 Pages: 883-894

    • DOI

      10.20965/ijat.2017.p0883

    • NAID

      130007505912

    • ISSN
      1881-7629, 1883-8022
    • Year and Date
      2017-11-05
    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Immobility responses are induced by photoactivation of single glomerular species responsive to fox odour TMT2017

    • Author(s)
      H. Saito, H. Nishizumi, S. Suzuki, H. Matsumoto, N. Ieki, T. Abe, H. Kiyonari, M. Morita, H. Yokota, N. Hirayama, T. Yamazaki, T. Kikusui, K. Mori, H. Sakano
    • Journal Title

      Nature Communications

      Volume: 8 Issue: 1 Pages: 16011-16011

    • DOI

      10.1038/ncomms16011

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Anatomical landmarks for registration of experimental image data to volumetric rodent brain atlasing templates2015

    • Author(s)
      Sergejeva, M, Papp, E. A., Bakker, R., Gaudnek, M. A., Okamura-Oho, Y., Boline, J., Bjaalie, J. G., Hess, A.
    • Journal Title

      J. Neurosci. Methods

      Volume: 240 Pages: 161-169

    • DOI

      10.1016/j.jneumeth.2014.11.005

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Numerical simulation of airflow and microparticle deposition in a synchrotron micro-CT-based pulmonary acinus model2015

    • Author(s)
      T. Sera, K. Uesugi, N. Yagi, and H. Yokota
    • Journal Title

      Computer Methods in Biomechanics and Biomedical Engineering

      Volume: 18 Issue: 13 Pages: 1427-1435

    • DOI

      10.1080/10255842.2014.915030

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Broad Integration of Expression Maps and Co-Expression Networks Compassing Novel Gene Functions in the Brain2014

    • Author(s)
      Okamura-Oho Y, Shimokawa K, Nishimura M, Takemoto S, Sato A, Furuichi T, Yokota H.
    • Journal Title

      Scientific Report

      Volume: 4 Issue: 1 Pages: 6969-6969

    • DOI

      10.1038/srep06969

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Solvable model for chemical oscillations2014

    • Author(s)
      E. Chikayama, Y. Sunaga, S. Noda, H. Yokota
    • Journal Title

      Journal of Mathematical Chemistry

      Volume: 52 Issue: 2 Pages: 399-406

    • DOI

      10.1007/s10910-013-0275-z

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis.2014

    • Author(s)
      Etsuo A. Susaki, Kazuki Tainaka, Dimitri Perrin, Fumiaki Kishino, Takehiro Tawara, Tomonobu M. Watanabe, Chihiro Yokoyama, Hirotaka Onoe, Megumi Eguchi, Shun Yamaguchi, Takaya Abe, Hiroshi Kiyonari, Yoshihiro Shimizu, Atsushi Miyawaki, Hideo Yokota, Hiroki R. Ueda
    • Journal Title

      Cell

      Volume: 157 Issue: 3 Pages: 726-739

    • DOI

      10.1016/j.cell.2014.03.042

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Prediction of open urinary tract in laparoscopic partial nephrectomy by virtual resection plane visualization2014

    • Author(s)
      D. Ueno, K. Makiyama, H. Yamanaka, T. Ijiri, H. Yokota, and Y. Kubota
    • Journal Title

      BMC Urology

      Volume: 14 Issue: 1 Pages: 47-47

    • DOI

      10.1186/1471-2490-14-47

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Communication Platform for Image Analysis and Sharing in Biology2014

    • Author(s)
      M. Morita, T. Tawara, M. Nishimura, S. Yoshizawa, B. Chou, I. Kuroki, T. Ijiri, Y. Tsujimura, R. Himeno, and H. Yokota
    • Journal Title

      International Journal of Networking and Computing

      Volume: 4 Issue: 2 Pages: 369-391

    • DOI

      10.15803/ijnc.4.2_369

    • NAID

      130004709094

    • ISSN
      2185-2839, 2185-2847
    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Flower Modeling via X-ray Computed Tomography2014

    • Author(s)
      T. Ijiri, S. Yoshizawa, H. Yokota, and T. Igarashi
    • Journal Title

      ACM Transactions on Graphics

      Volume: 33 Issue: 4 Pages: 1-10

    • DOI

      10.1145/2601097.2601124

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Efficient parallel LOD-FDTD method for Debye-dispersive media2014

    • Author(s)
      Tadashi Hemmi, Fumie Costen, Salvador Garcia, Ryutaro Himeno, Hideo Yokota, Mehshan Mustafa
    • Journal Title

      IEEE Transactions on Antennas and Propagation

      Volume: 62 Issue: 3 Pages: 1330-1338

    • DOI

      10.1109/tap.2013.2294860

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] オーダーメ─ド再生医療に向けたコンピュータサイエンス2014

    • Author(s)
      横田秀夫
    • Journal Title

      四国医学雑誌

      Volume: 70 Pages: 208-218

    • Related Report
      2014 Annual Research Report
  • [Presentation] Differential and tissue-specific gene expression in the mouse brain2017

    • Author(s)
      Yuko Okamura-Oho
    • Organizer
      AINI (Advances in Neuroinformatics) 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ViBrism database for gene expression maps and co-expression networks analysis on the 3D brain2017

    • Author(s)
      Kazuro Shimokawa, Masahiko Morita, Masaomi Nishimura, Hideo Yokota, Shuhei Wemler, Yoshihiro Okumura, Yoko Yamaguchi, Yuko Okamura-Oho
    • Organizer
      Annual meeting of Society of Neuroscience 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 3次元Ex Vivo 空間での遺伝子発現分布の測定~TT法で全脳を網羅解析~2016

    • Author(s)
      於保祐子
    • Organizer
      nano tech 2016(国際ナノテクノロジー総合展・技術会議)理研ブース
    • Place of Presentation
      東京ビッグサイト 東ホール
    • Year and Date
      2016-01-27
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Integrated analysis of anatomical and topological maps of gene expression in the mouse brain2016

    • Author(s)
      Yuko Okamura-Oho
    • Organizer
      3rd Japan-EU WS on Neurorobotics
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Ex-vivo transcriptomic analysis on the web: a new platform of ViBrism DB for gene expression mapping and analysis2016

    • Author(s)
      Yuko Okamura-Oho, Masahiko Morita, Kazuro Shimokawa, Masaomi Nishimura, Takahiro Tawara, Hideo Yokota
    • Organizer
      NI(Neuroinformatics)2016
    • Related Report
      2016 Annual Research Report
  • [Presentation] ViBrism DB Platform2016

    • Author(s)
      2.Yuko Okamura-Oho, Masahiko Morita, Masaomi Nishimura, Takahiro Tawara, Shuhei Wemler, Kazuro Shimokawa, Hideo Yokota
    • Organizer
      AINI2016 and INCF Nodes Workshop
    • Related Report
      2016 Annual Research Report
  • [Presentation] Integration of anatomical and topological maps for functional analysis of the brain2015

    • Author(s)
      Yuko Okamura-Oho
    • Organizer
      AINI (Advances in Neuroinformatics) 2015
    • Place of Presentation
      東京大学先端科学技術研究センター エネオスホール、東京 駒場
    • Year and Date
      2015-11-26
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] The homology mapping: interspecies functional morphing2015

    • Author(s)
      Satoshi Oota, Yosuke Ikegami, Koh Ayusawa, Nobunori Kakusho, Atsushi Yoshiki,, Hideo Yokota, Yuko Okamura-Oho, Yoshihiko Nakamura
    • Organizer
      AINI (Advances in Neuroinformatics) 2015
    • Place of Presentation
      東京大学先端科学技術研究センター エネオスホール、東京 駒場
    • Year and Date
      2015-11-26
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] An automatic registration method for ISH images into the 3D standard brain atlas2015

    • Author(s)
      Daisuke Miyamoto, Yuko Okamura-Oho, Teiichi Furuichi, Ryohei Kanzaki, Hidetoshi Ikeno
    • Organizer
      AINI (Advances in Neuroinformatics) 2015
    • Place of Presentation
      東京大学先端科学技術研究センター エネオスホール、東京 駒場
    • Year and Date
      2015-11-26
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Ex-vivo transcriptomic analysis on the web: a new platform of ViBrism DB for gene expression mapping and analysis2015

    • Author(s)
      Yuko Okamura-Oho, Masahiko Morita, Kazuro Shimokawa, Masaomi Nishimura, Takahiro Tawara, Hideo Yokota
    • Organizer
      Neuroinformatics 2015
    • Place of Presentation
      Cairns, Australia
    • Year and Date
      2015-08-20 – 2015-08-22
    • Related Report
      2014 Annual Research Report
  • [Presentation] Ex-vivo transcriptomic analysis on the web: a new platform of ViBrism DB for gene expression mapping and analysis2015

    • Author(s)
      Yuko Okamura-Oho, Masahiko Morita, Kazuro Shimokawa, Masaomi Nishimura, Takahiro Tawara, Hideo Yokota
    • Organizer
      NI(Neuroinformatics)2015
    • Place of Presentation
      Cairns, Australia
    • Year and Date
      2015-08-20
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Network analysis of 3D gene expression pattern, using microtomy based transcriptomic data sets in ViBrism DB2015

    • Author(s)
      Kazuro Shimokawa, Masahiko Morita, Masaomi Nishimura, Hideo Yokota, Yuko Okamura-Oho
    • Organizer
      NI(Neuroinformatics)2015
    • Place of Presentation
      Cairns, Australia
    • Year and Date
      2015-08-20
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Neuromuscular Modeling by Bridging Mouse and Human2015

    • Author(s)
      Satoshi Oota
    • Organizer
      Japan-EU Workshop on Neurorobotics
    • Place of Presentation
      Ichijyo Hall, Yayoi Auditorium, The University of Tokyo,Tokyo
    • Year and Date
      2015-04-18
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 3次元内部構造顕微鏡による3次元計測の生物・材料分野への挑戦と展開2015

    • Author(s)
      於保祐子
    • Organizer
      RIKENシンポジウム
    • Place of Presentation
      理化学研究所 仁科センター 大会議室、和光市、埼玉県
    • Year and Date
      2015-02-06
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Transcriptome tomography: mapping genes onto 3D brain structures2014

    • Author(s)
      Yuko Okamura-Oho, Kazuro Shimokawa, Sakiko Nakamura, Yuki Tsujimura, Masaomi Nishimura, Satoko Takemoto, Masahiko Morita, Takashi Ijiri, Takehiro Tawara, Hideo Yokota
    • Organizer
      Annual meeting of Society of Neuroscience 2014
    • Place of Presentation
      Washington DC, USA
    • Year and Date
      2014-11-15 – 2014-11-19
    • Related Report
      2014 Annual Research Report
  • [Presentation] Integrated Analysis of Expression Maps and Co-Expression Networks Using a Dataset of ViBrism DB2014

    • Author(s)
      Yuko Okamura-Oho, Kazuro Shimokawa, Masaomi Nishimura, Satoko Takemoto, Masahiko Morita, Hideo Yokota
    • Organizer
      AINI2014
    • Place of Presentation
      Wako, Japan
    • Year and Date
      2014-09-25 – 2014-09-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] Novel genes located in the co-expression networks detected with Transcriptome Tomography2014

    • Author(s)
      Yuko Okamura-Oho, Kazuro Shimokawa, Masaomi Nishimura, Satoko Takemoto, Akira Sato, Teiichi Furuichi, Hideo Yokota
    • Organizer
      Neuroinformatics 2014
    • Place of Presentation
      Leiden, Nederland
    • Year and Date
      2014-08-25 – 2014-08-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] トランスクリプトーム・トモグラフィーを用いた遺伝子発現に基づく全脳地図作成2014

    • Author(s)
      於保祐子
    • Organizer
      科学技術振興機構主催 理化学研究所新技術説明会
    • Place of Presentation
      JST 東京本部別館ホール、市ヶ谷、東京
    • Year and Date
      2014-06-12 – 2014-06-13
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Book] バイオ画像解析手取り足取りガイド,第3章,5)2014

    • Author(s)
      森田正彦,西村将臣,横田秀夫
    • Publisher
      羊土社
    • Related Report
      2014 Annual Research Report
  • [Book] ビッグデータ時代のゲノミクス情報処理2014

    • Author(s)
      北上始, 斉藤成也, 太田聡史
    • Total Pages
      226
    • Publisher
      コロナ社
    • Related Report
      2014 Annual Research Report
  • [Remarks] ViBrism DB

    • URL

      https://vibrism.neuroinf.jp/

    • Related Report
      2017 Annual Research Report 2016 Annual Research Report
  • [Remarks] ViBrism DB

    • URL

      http://vibrism.neuroinf.jp/

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report

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Published: 2014-04-04   Modified: 2019-03-29  

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