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Identification and transition analysis of stable states (attractors) of time-course gene expression of developmental and differentiation system

Research Project

Project/Area Number 22700311
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Bioinformatics/Life informatics
Research InstitutionTohoku University (2012)
Tokyo Medical and Dental University (2010-2011)

Principal Investigator

OGISHIMA Soichi  東北大学, 東北メディカル・メガバンク機構, 講師 (40447496)

Project Period (FY) 2010 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2012: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2011: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2010: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywords生体生命システム情報学 / 発生・分化 / 時系列発現解析 / システム生物 / 時系列遺伝子発現 / アトラクター
Research Abstract

We established a novel method to understand developmental and differentiation process as transition of stable states (attractors) of time-course gene expression. We defined a phase space by principal component analysis on gene expression data during iPS cells differentiations. We then calculated an appearance frequency of each cellular state based on gene expression data, and calculated an occurrence probability of each cellular state as expression potential field showing stability of each cellular state.

Report

(4 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (35 results)

All 2013 2012 2011 2010 Other

All Journal Article (9 results) (of which Peer Reviewed: 9 results) Presentation (24 results) (of which Invited: 3 results) Book (2 results)

  • [Journal Article] A map of Alzheimer'sdisease-signaling pathways: a hope for drug target discovery2013

    • Author(s)
      Ogishima S, Mizuno S, Kikuchi M, Miyashita A, Kuwano R, Tanaka H, Nakaya J.
    • Journal Title

      Clin Pharmacol Ther

      Volume: 93(5) Issue: 5 Pages: 399-401

    • DOI

      10.1038/clpt.2013.37

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies2013

    • Author(s)
      Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M,Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal RJ, Chapman B, Cock PJ, Eriksson T, Gordon PM, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim YJ,Kinjo AR, Konishi F, Kwon KH, Labarga A, Lamprecht AL, Lin Y, Lindenbaum P, McCarthy L, Morita H, Murakami K, Nagao K, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Ono K, Oshita K, Park KJ, Prins P, Saito TL, Samwald M, SatagopamVP, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos RA, Withers D, Yamasaki C, Zmasek CM, Kawamoto S, Okubo K, Asai K, Takagi T.
    • Journal Title

      J Biomed Semantics

      Volume: 4(1) Issue: 1 Pages: 6-6

    • DOI

      10.1186/2041-1480-4-6

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] AlzPathway: a comprehensive map of signaling pathways of Alzheimer'sdisease2012

    • Author(s)
      Mizuno S, Iijima R, Ogishima S, Kikuchi M, Matsuoka Y, Ghosh S, Miyamoto T, Miyashita A, Kuwano R, Tanaka H.
    • Journal Title

      BMC Syst Biol

      Volume: 6 Issue: 1 Pages: 52-52

    • DOI

      10.1186/1752-0509-6-52

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Hub-centered gene network reconstruction using automatic relevance determination2012

    • Author(s)
      Bock M, Ogishima S, Tanaka H, Kramer S, Kaderali L
    • Journal Title

      PLoS One

      Volume: 7(5) Issue: 5 Pages: e35077-e35077

    • DOI

      10.1371/journal.pone.0035077

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Human mesenchymal stem cells in synovial fluid increase in the knee with degenerated cartilage and osteoarthritis.2012

    • Author(s)
      Sekiya I.
    • Journal Title

      JOURNAL OF ORTHOPAEDIC RESEARCH

      Volume: 30(6) Issue: 6 Pages: 943-949

    • DOI

      10.1002/jor.22029

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Omics-based identification of pathophysiological processes2011

    • Author(s)
      Tanaka H, Ogishima S
    • Journal Title

      Methods Mol Biol

      Volume: 719 Pages: 499-509

    • DOI

      10.1007/978-1-61779-027-0_23

    • ISBN
      9781617790263, 9781617790270
    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] The 2nd DBCLS BioHackathon: interoperablebioinformatics Web services for integrated applications2011

    • Author(s)
      Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, Fernandez JM, Fujisawa T, Gordon PM,Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Kinjo AR, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S,Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T.
    • Journal Title

      J Biomed Semantics

      Volume: 2 Issue: 1 Pages: 4-4

    • DOI

      10.1186/2041-1480-2-4

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Suppression of the novel ER protein Maxer by mutant ataxin-1 in Bergman glia contributes to non-cell-autonomous toxicity2010

    • Author(s)
      Shiwaku, H., Yoshimura, N., Tamura, T., Sone, M., Ogishima, S., Watase, K., Tagawa, K., and Okazawa, H.
    • Journal Title

      EMBO J.

      Volume: 29 Issue: 14 Pages: 2446-2460

    • DOI

      10.1038/emboj.2010.116

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Suppression of the novel ER protein Maxer by mutant ataxin-1 in Bergman glia contributes to non-cell-autonomous toxicity.2010

    • Author(s)
      Hiroki Shiwaku
    • Journal Title

      EMBO Journal

      Volume: 29 Pages: 2446-60

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] (2013)システムバイオロジーの動向とクリニカルシステムシステムバイオロジーへの展開2013

    • Author(s)
      荻島創一
    • Organizer
      日本バイオインフォマティクス学会生命システム理論研究会
    • Place of Presentation
      京都大学化学研究所
    • Year and Date
      2013-01-15
    • Related Report
      2012 Final Research Report
  • [Presentation] (2012)10年後に期待されるバイオメディカルを支えるオープンバイオ技術2012

    • Author(s)
      荻島創一
    • Organizer
      次世代シーケンス現場の会・オープンバイオ研究会・生命情報科学若手の会・定量生物学の会4会合同シンポジウム「これからの生命科学を考える」
    • Place of Presentation
      タワーホール船堀
    • Year and Date
      2012-10-17
    • Related Report
      2012 Final Research Report
  • [Presentation] (2012)臨床オミックスデータのシステム生物学的解析と統合生物学的解析-アルツハイマー病および希少性疾患における取り組み2012

    • Author(s)
      荻島創一
    • Organizer
      第329回情報計算化学生物学会研究講演会
    • Place of Presentation
      東京大学山上会館
    • Year and Date
      2012-08-03
    • Related Report
      2012 Final Research Report
  • [Presentation] (2012)"Expression trajectories" of reprogramming and differentiation on expression potential field2012

    • Author(s)
      宮本直,荻島創一,中谷純,田中博
    • Organizer
      生命医薬情報学連合大会
    • Place of Presentation
      タワーホール船堀
    • Related Report
      2012 Final Research Report
  • [Presentation] “Expression trajectories” of reprogramming and differentiation on expression potential field2012

    • Author(s)
      宮本直, 荻島創一, 中谷純, 田中博
    • Organizer
      生命医薬情報学連合大会
    • Place of Presentation
      タワーホール船堀
    • Related Report
      2012 Annual Research Report
  • [Presentation] (2011)アルツハイマー病のシグネチャ遺伝子の遺伝子調節ネットワークの疾患アトラクターとしての推定2011

    • Author(s)
      荻島創一,菊地正隆,田中博
    • Organizer
      日本分子生物学会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2011-12-12
    • Related Report
      2012 Final Research Report
  • [Presentation] アルツハイマー病のシグネチャ遺伝子の遺伝子調節ネットワークの疾患アトラクターとしての推定2011

    • Author(s)
      荻島創一, 菊地正隆, 田中博
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2011-12-12
    • Related Report
      2011 Annual Research Report
  • [Presentation] BioCichlid : central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network2011

    • Author(s)
      Soichi Ogishima
    • Organizer
      InCoB 2010
    • Place of Presentation
      Waseda Univ, Tokyo(Japan)
    • Year and Date
      2011-09-26
    • Related Report
      2010 Annual Research Report
  • [Presentation] (2011)オミックスデータの統合による疾患システム生物学研究の現状2011

    • Author(s)
      荻島創一,田中博
    • Organizer
      日本バイオインフォマティクス学会糖鎖インフォマティクス若手の会
    • Place of Presentation
      立命館大学びわこ・くさつキャンパス
    • Year and Date
      2011-08-27
    • Related Report
      2012 Final Research Report
  • [Presentation] オミックスデータの統合による疾患システム生物学研究の現状2011

    • Author(s)
      荻島創一, 田中博
    • Organizer
      日本バイオインフォマティクス学会糖鎖インフォマティクス若手の会
    • Place of Presentation
      立命館大学びわこ・くさつキャンパス
    • Year and Date
      2011-08-27
    • Related Report
      2011 Annual Research Report
  • [Presentation] (2011)先制医療のためのバイオマーカーのシステム生物学的アプローチによる探索2011

    • Author(s)
      荻島創一,田中博
    • Organizer
      日本バイオインフォマティクス学会応用システムバイオロジー第3回研究会
    • Place of Presentation
      九州大学
    • Year and Date
      2011-06-27
    • Related Report
      2012 Final Research Report
  • [Presentation] 先制医療のためのバイオマーカーのシステム生物学的アプローチによる探索2011

    • Author(s)
      荻島創一, 田中博
    • Organizer
      日本バイオインフォマティクス学会応用システムバイオロジー第3回研究会
    • Place of Presentation
      九州大学
    • Year and Date
      2011-06-27
    • Related Report
      2011 Annual Research Report
  • [Presentation] (2011) Inference of DiseaseAttractors and Gene Regulatory Network of Disease Progression2011

    • Author(s)
      Ogishima S
    • Organizer
      CDB Symposium2011
    • Place of Presentation
      RIKEN CDB, Kobe, Japan
    • Year and Date
      2011-03-14
    • Related Report
      2012 Final Research Report
  • [Presentation] Inference of Disease Attractors and Gene Regulatory Network of Disease Progression2011

    • Author(s)
      Soichi Ogishima
    • Organizer
      CDB Symposium 2011
    • Place of Presentation
      理化学研究所発生・再生科学総合研究センター(神戸)
    • Year and Date
      2011-03-14
    • Related Report
      2010 Annual Research Report
  • [Presentation] (2011) Network-based inference of signature genes of Alzheimer's disease progression2011

    • Author(s)
      Ogishima S, Kikuchi M, Miyashita T, Kuwano R, Tanaka H.
    • Organizer
      International Conferenceon Systems Biology 2011
    • Place of Presentation
      Heidelberg, Germany
    • Related Report
      2012 Final Research Report
  • [Presentation] (2011) Inference of the master regulators in the gene regulatory network of Alzheimer'sdisease progression2011

    • Author(s)
      Ogishima S
    • Organizer
      Asia Pacific Bioinformatics Conference 2011
    • Place of Presentation
      Incheon, Korea
    • Related Report
      2012 Final Research Report
  • [Presentation] Network-based inference of signature genes of Alzheimer's disease progression2011

    • Author(s)
      Ogishima, S., Kikuchi, M., Miyashita, T., Kuwano, R., Tanaka, H.
    • Organizer
      International Conference on Systems Biology 2011
    • Place of Presentation
      Heidelberg, Germany
    • Related Report
      2011 Annual Research Report
  • [Presentation] Inference of the master regulators in the gene regulatory network of Alzheimer's disease progression2011

    • Author(s)
      Soichi Ogishima
    • Organizer
      Asia Pacific Bioinformatics Conference 2011
    • Place of Presentation
      Incheon(Korea)
    • Related Report
      2010 Annual Research Report
  • [Presentation] (2010)AlzPathway:アルツハイマー病のリスク遺伝子探索や分子機序の解明のための網羅的パスウエイマップ2010

    • Author(s)
      荻島創一
    • Organizer
      第33回日本分子生物学会年会
    • Place of Presentation
      神戸国際会議場
    • Year and Date
      2010-12-09
    • Related Report
      2012 Final Research Report
  • [Presentation] AlzPathway:アルツハイマー病のリスク遺伝子探索や分子機序の解明のための網羅的パスウエイマップ2010

    • Author(s)
      荻島創一
    • Organizer
      第33回日本分子生物学会年会
    • Place of Presentation
      神戸国際会議場
    • Year and Date
      2010-12-09
    • Related Report
      2010 Annual Research Report
  • [Presentation] (2010) BioCichlid : central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network2010

    • Author(s)
      Ogishima S
    • Organizer
      InCoB 2010
    • Place of Presentation
      Waseda Univ, Tokyo, Japan
    • Year and Date
      2010-09-26
    • Related Report
      2012 Final Research Report
  • [Presentation] システムバイオロジーの動向とクリニカルシステムバイオロジーへの展開

    • Author(s)
      荻島創一
    • Organizer
      日本バイオインフォマティクス学会 生命システム理論研究会
    • Place of Presentation
      京都大学化学研究所
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 臨床オミックスデータのシステム生物学的解析と統合生物学的解析 - アルツハイマー病および希少性疾患における取り組み

    • Author(s)
      荻島創一
    • Organizer
      第329回情報計算化学生物学会研究講演会
    • Place of Presentation
      東京大学山上会館
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 10年後に期待されるバイオメディカルを支えるオープンバイオ技術

    • Author(s)
      荻島創一
    • Organizer
      次世代シーケンス現場の会・オープンバイオ研究会・生命情報科学若手の会・定量生物学の会 4会合同シンポジウム「これからの生命科学を考える」
    • Place of Presentation
      タワーホール船堀
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Book] (2012) 先制医療と創薬のための疾患システムバイオロジー-オミックス医療からシステム分子医学へ2012

    • Author(s)
      田中博,茂櫛薫,荻島創一,高井貴子
    • Publisher
      培風館
    • Related Report
      2012 Final Research Report
  • [Book] (2012)バイオ実験に絶対使える統計の基本Q&A~論文が書ける読めるデータが見える!2012

    • Author(s)
      秋山徹(監修),井元清哉(編集),河府和義(編集),藤渕航(編集),荻島創一
    • Publisher
      培風館
    • Related Report
      2012 Final Research Report

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Published: 2010-08-23   Modified: 2019-07-29  

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