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Development of a method for high-throughput analysisof HiCEP data

Research Project

Project/Area Number 19700273
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Bioinformatics/Life informatics
Research InstitutionThe University of Tokyo

Principal Investigator

KADOTA Koji  The University of Tokyo, 大学院・農学生命科学研究科, 特任助教 (60392221)

Project Period (FY) 2007 – 2008
Project Status Completed (Fiscal Year 2008)
Budget Amount *help
¥1,150,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥150,000)
Fiscal Year 2008: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2007: ¥500,000 (Direct Cost: ¥500,000)
Keywordsバイオインフォマティクス / AFLP / HiCEP / マイクロアレイ
Research Abstract

HiCEP法は、マイクロアレイなど他の技術では不可能であった未知遺伝子を含む転写物の網羅的単離およびプロファイリングが全ての生物で可能な唯一の実験技術であるが、一次元電気泳動(1-DE)パターン比較に基づく発現プロファイル解析法であるため、データ解析に多くの手間と時間がかかっていた。本研究課題によって開発された手法の適用により、データ解析の大部分において自動化が達成できた。

Report

(3 results)
  • 2008 Annual Research Report   Final Research Report ( PDF )
  • 2007 Annual Research Report
  • Research Products

    (38 results)

All 2009 2008 2007 Other

All Journal Article (13 results) (of which Peer Reviewed: 6 results) Presentation (18 results) Book (4 results) Remarks (3 results)

  • [Journal Article] Effect of Quercetin on the Gene Expression Profile of the Mouse Intestine2009

    • Author(s)
      Natsume Y, Kadota K, Satsu H, Shimizu M.
    • Journal Title

      Bioscience, Biotechnology, and Biochemistry 73(3)

      Pages: 722-725

    • NAID

      10027539109

    • Related Report
      2008 Final Research Report
  • [Journal Article] A weighted average difference method for detecting differentially expressed genes from microarray data2008

    • Author(s)
      Kadota K, Nakai Y, Shimizu K.
    • Journal Title

      Algorithms for Molecular Biology 3

      Pages: 8-8

    • Related Report
      2008 Final Research Report
  • [Journal Article] Biochemical and Genomic Analysis of Neoculin Compared to Monocot Mannose-Binding Lectins2008

    • Author(s)
      Shimizu-Ibuka A, Nakai Y, Nakamori K, Morita Y, Nakajima KI, Kadota K, Watanabe H, Okubo S, Terada T, Asakura T, Misaka T, Abe K.
    • Journal Title

      Journal of Agricultural and Food Chemistry 56(13)

      Pages: 5338-5344

    • Related Report
      2008 Final Research Report
  • [Journal Article] Up-regulation of genes related to the ubiquitin-proteasome system in the brown adipose tissue of 24-h-fasted rats2008

    • Author(s)
      Nakai Y, Hashida H., Kadota K, Minami M, Shimizu K, Matsumoto I, Kato H, Abe K.
    • Journal Title

      Bioscience, Biotechnolgy, and Biochemistry 72(1)

      Pages: 139-148

    • NAID

      10027523175

    • Related Report
      2008 Final Research Report
  • [Journal Article] A weighted average difference method for detecting differentially expressed genes from microarrav data2008

    • Author(s)
      Kadota, K.
    • Journal Title

      Algorithms for Molecular Biology 3

      Pages: 5-5

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Biochemical and Genomic Analysis of Neoculin Compared to Monocot Mannose-Binding Lectins2008

    • Author(s)
      Shimizu-Ibuka, A.
    • Journal Title

      Journal of Agricultural and Food Chemistry 56

      Pages: 5338-5344

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Up-regulation of genes related to the ubiquitin-proteasome system in the brown adipose tissue of 24-h-fasted rats2008

    • Author(s)
      Nakai, Y.
    • Journal Title

      Bioscience, Biotechnology, and Biochemistry 72

      Pages: 139-148

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] GOGOT : a method for the identification of differentially expressed fragments from cDNA-AFLP data2007

    • Author(s)
      Kadota K, Araki R, Nakai Y, Abe M.
    • Journal Title

      Algorithms for Molecular Biology 2

      Pages: 5-5

    • Related Report
      2008 Final Research Report
  • [Journal Article] Evaluation of two outlier-detection-based methods for detecting tissue-selective genes from microarray data2007

    • Author(s)
      Kadota K, Konishi T, Shimizu K.
    • Journal Title

      Gene Regulation and Systems Biology 1

      Pages: 9-15

    • Related Report
      2008 Final Research Report
  • [Journal Article] Circadian variations in coagulation and fibrinolytic factors among four different strains of mice2007

    • Author(s)
      Ohkura N, Oishi K, Sakata T, Kadota K, Kasamatsu M, Fukushima N, Kurata A, Tamai Y, Shirai H, Atsumi G Ishida N, Matsuda J, Horie S.
    • Journal Title

      Chronobiology International 24(4)

      Pages: 651-669

    • Related Report
      2008 Final Research Report
  • [Journal Article] GOGOT : a method for the identification of differentially expressed fragments from cDNA-AFLP data2007

    • Author(s)
      Kadota, K.
    • Journal Title

      Algorithms for Molecular Biology 2

      Pages: 5-5

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Circadian variations in coagulation and fibrinolytic factors among four different strains of mice2007

    • Author(s)
      Ohkura, N.
    • Journal Title

      Chronobiology International 24

      Pages: 651-669

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evaluation of two outlier-detection-based methods for detecting tissue-selective genes from microarray data2007

    • Author(s)
      Kadota, K.
    • Journal Title

      Gene Regulation and Systems Biology 1

      Pages: 9-15

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Presentation] マイクロアレイ解析の話 : 発現変動遺伝子検出あたりを中心に2009

    • Author(s)
      門田幸二
    • Organizer
      日本バイオインフォマティクス学会・第5回九州地域部会講習会
    • Place of Presentation
      福岡
    • Year and Date
      2009-02-26
    • Related Report
      2008 Annual Research Report
  • [Presentation] 食餌性亜鉛の欠乏がラット小腸の遺伝子発現に与える影響2009

    • Author(s)
      成川真隆,中井雄治,南道子,門田幸二,三坂巧,阿部啓子
    • Organizer
      日本農芸化学会2009年度大会
    • Place of Presentation
      福岡
    • Related Report
      2008 Final Research Report
  • [Presentation] pCAR1を有することが宿主であるPseudomonas属細菌に鉄欠乏を生じさせる2009

    • Author(s)
      新谷政己,高橋裕里香,徳丸裕樹,門田幸二,原啓文,宮腰昌利,西田洋巳,山根久和,野尻秀昭
    • Organizer
      第3回日本ゲノム微生物学会年会
    • Place of Presentation
      東京
    • Related Report
      2008 Final Research Report
  • [Presentation] IncP-7群プラスミドpCAR1を保持する異種Pseudomonas属細菌の形質およびトランスクリプトーム比較2009

    • Author(s)
      高橋裕里香,新谷政己,徳丸裕樹,門田幸二,原啓文,宮腰昌利,西田洋巳,山根久和,野尻秀昭
    • Organizer
      第3回日本ゲノム微生物学会年会
    • Place of Presentation
      東京
    • Related Report
      2008 Final Research Report
  • [Presentation] マイクロアレイ解析の話:発現変動遺伝子検山あたりを中心に2009

    • Author(s)
      門田幸二
    • Organizer
      日本バイオインフォマティクス学会第5回九州地域部会講習会
    • Place of Presentation
      福岡
    • Related Report
      2008 Final Research Report
  • [Presentation] マイクロアレイデータからの発現変動遺伝子検出法WAD2008

    • Author(s)
      門田幸二
    • Organizer
      日本分子生物学会第31回年会(BMB2008)
    • Place of Presentation
      神戸
    • Year and Date
      2008-12-12
    • Related Report
      2008 Annual Research Report
  • [Presentation] トランスクリプトーム解析手法の開発2008

    • Author(s)
      門田幸二
    • Organizer
      アグリバイオインフォマティクス成果報告シンポジウム
    • Place of Presentation
      東京
    • Year and Date
      2008-12-08
    • Related Report
      2008 Annual Research Report 2008 Final Research Report
  • [Presentation] ニュートリゲノミクス研究におけるDNAマイクロアレイ解析戦略2008

    • Author(s)
      中井雄治,門田幸二
    • Organizer
      日本農芸化学会2008年度大会
    • Place of Presentation
      名古屋
    • Year and Date
      2008-03-29
    • Related Report
      2008 Final Research Report 2007 Annual Research Report
  • [Presentation] Comparison of methods for detecting differentially expressed genes from microarray data2008

    • Author(s)
      Kadota K., Nakai Y, Shimizu K.
    • Organizer
      日本バイオインフォマティクス学会年会
    • Place of Presentation
      大阪
    • Related Report
      2008 Final Research Report
  • [Presentation] マイクロアレイデータからの発現変動遺伝子検出法WAD2008

    • Author(s)
      門田幸二,中井雄治,清水謙多郎
    • Organizer
      日本分子生物学会第31会年会(BMB2008)
    • Place of Presentation
      神戸
    • Related Report
      2008 Final Research Report
  • [Presentation] Comparison of methods for detecting differentially expressed genes from microarray data2008

    • Author(s)
      門田幸二
    • Organizer
      2008年日本バイオインフォマティクス学会年会
    • Place of Presentation
      大阪
    • Related Report
      2008 Annual Research Report
  • [Presentation] HiCEPデータのマイクロアレイ様データへの変換:HiCEPもアレイ用解析手法が利用可能です2007

    • Author(s)
      門田幸二
    • Organizer
      放射線医学総合研究所第14回重粒子医科学センター研究交流会
    • Place of Presentation
      千葉
    • Year and Date
      2007-07-19
    • Related Report
      2008 Final Research Report
  • [Presentation] HiCEPデータのマイクロアレイ様データへの変換 : HiCEPもアレイ用解析手法が利用可能です2007

    • Author(s)
      門田幸二
    • Organizer
      放射線医学総合研究所第14回重粒子医科学センター研究交流会
    • Place of Presentation
      千葉
    • Year and Date
      2007-07-19
    • Related Report
      2007 Annual Research Report
  • [Presentation] マイクロアレイ解析手法あれこれ2007

    • Author(s)
      門田幸二
    • Organizer
      日本バイオインフォマティクス学会第2会機能ゲノミクス研究会
    • Place of Presentation
      東京
    • Year and Date
      2007-04-12
    • Related Report
      2008 Final Research Report
  • [Presentation] Genes Related to the Ubiquitin-Proteasome System Are Up-regulated in the Brown Adipose Tissue of 24 h-Fasted Rats2007

    • Author(s)
      Nakai Y, Hashida H, Kadota K, Minami M, Shimizu K, Matsumoto I, Kato H, Abe K.
    • Organizer
      The University of Tokyo International Symposium "Frontier of Microbial and Plant Biotechnology in Environmental and Life Sciences"
    • Place of Presentation
      東京
    • Related Report
      2008 Final Research Report
  • [Presentation] A new method for detecting tissue-selective genes from microarray data and its comparative study2007

    • Author(s)
      Kadota K, Ye J, Nakai Y, Terada T, Shimizu K.
    • Organizer
      The University of Tokyo International Symposium "Frontier of Microbial and Plant Biotechnology in Environmental and Life Sciences"
    • Place of Presentation
      東京
    • Related Report
      2008 Final Research Report
  • [Presentation] The effect of quercetin on ER stress at intestinal epithelia2007

    • Author(s)
      Natsume Y, Ito S, Satsu H, Kadota K, Ohsawa K, Shimizu M.
    • Organizer
      3rd International Conference on Polyphenols and Health (ICPH2007)
    • Place of Presentation
      京都
    • Related Report
      2008 Final Research Report
  • [Presentation] Rでお手軽にアレイ解析2007

    • Author(s)
      門田幸二
    • Organizer
      特定領域研究「植物ゲノム障壁」マイクロアレイワークショップ
    • Place of Presentation
      東京
    • Related Report
      2008 Final Research Report
  • [Book] 有意差検定とマーカー遺伝子の意義(他),(藤渕航・堀本勝久/編)実験医学別冊 マイクロアレイデータ統計解析プロトコール2008

    • Author(s)
      門田幸二
    • Publisher
      羊土社
    • Related Report
      2008 Final Research Report
  • [Book] マイクロアレイデータ統計解析プロトコール2008

    • Author(s)
      門田幸二
    • Publisher
      羊土社
    • Related Report
      2008 Annual Research Report
  • [Book] 書評(統計解析環境Rによるバイオインフォマティクスデータ解析),バイオサイエンスとインダストリー65(11),282007

    • Author(s)
      門田幸二
    • Total Pages
      28
    • Related Report
      2008 Final Research Report
  • [Book] バイオサイエンスとインダストリー2007

    • Author(s)
      門田幸二
    • Publisher
      バイオインダストリー協会
    • Related Report
      2007 Annual Research Report
  • [Remarks] 研究代表者ホームページ

    • URL

      http://www.iu.a.u-tokyo.ac.jp/~kadota/

    • Related Report
      2008 Final Research Report
  • [Remarks]

    • URL

      http://www.iu.a.u-tokyo.ac.jp/~kadota/

    • Related Report
      2008 Annual Research Report
  • [Remarks]

    • URL

      http://www.iu.a.u-tokyo.ac.jp/~kadota/

    • Related Report
      2007 Annual Research Report

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Published: 2007-04-01   Modified: 2016-04-21  

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