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Prediction of phosphorylation sites in human protein by machine learning and the functional role of intrinsically disordered regions

Research Project

Project/Area Number 26330336
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionRitsumeikan University

Principal Investigator

NISHIKAWA IKUKO  立命館大学, 情報理工学部, 教授 (90212117)

Research Collaborator NISHIKAWA Ken  
FUKUCHI Satoshi  
TOHSATO Yukako  
Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2016: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2014: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Keywords機械学習 / ヒトタンパク質 / 天然変性領域 / リン酸化 / サポートベクターマシン / 進化的保存度 / オーソログ / 予測 / エントロピー / 進化的保存性 / タンパク質 / 独立成分分析
Outline of Final Research Achievements

Phosphorylation site in human protein is studied, through the prediction by support vector machine. We focus on the difference in evolutional conservation between intrinsically disordered region (IDR) and the domain, and the functional role of IDR in the post-translational modification.
Sequence conservation is known to be generally low in IDR, while the functionally important modifications are often found in IDR. We proposed a measure of site-specific conservation based on multiple ortholog proteins, as PSSM (Position Specific Scoring Matrix), which is often used as a site-specific conservation measure, assumes sequence conservation which does not work in IDR. Then, the site-specific conservation is found to vary within IDR. The conservation is kept high at a phosphorylation site, especially at the phosphorylation with any clarified function. Prediction accuracy improves to 82.1% using both the conservation and the sequence information in IDR for functional phosphorylation sites.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report

Research Products

(18 results)

All 2017 2016 2015 2014

All Journal Article (4 results) (of which Peer Reviewed: 4 results,  Open Access: 3 results,  Acknowledgement Compliant: 1 results) Presentation (14 results) (of which Int'l Joint Research: 1 results)

  • [Journal Article] Efficiency and Sensitivity Analysis on Distributed Solar Power Network based on Linear Programming Model2016

    • Author(s)
      鈴木将義,榊原 一紀,西川 郁子
    • Journal Title

      IEEJ Trans. EIS

      Volume: 136 Issue: 10 Pages: 1445-1453

    • DOI

      10.1541/ieejeiss.136.1445

    • NAID

      130005598360

    • ISSN
      0385-4221, 1348-8155
    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Nuclear detection in 4D microscope images of a developing embryo using an enhanced probability map of top-ranked intensity-ordered descriptors2016

    • Author(s)
      Xiang-Hua Han, Yukako Tohsato, Koji Kyoda, Shuichi Onami, Ikuko Nishikawa and Yen-Wei Chen
    • Journal Title

      IPSJ Transactions on Computer Vision and Applications

      Volume: 8 Pages: 1-15

    • DOI

      10.1186/s41074-016-0010-3

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Agent-based Energy Market toward the Optimal Trading in a Power Network2016

    • Author(s)
      鈴木将義、榊原一紀、瀬尾昌孝、西川郁子
    • Journal Title

      Trans. ISCIE

      Volume: 29 Issue: 2 Pages: 86-92

    • DOI

      10.5687/iscie.29.86

    • NAID

      130005151352

    • ISSN
      1342-5668, 2185-811X
    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] 部分空間学習とB-Spline補間を用いた個人の顔特徴に応じた顔画像の美顔補正の高精度化2015

    • Author(s)
      瀬尾昌孝、西川郁子、陳延偉
    • Journal Title

      日本顔学会誌

      Volume: 15 Pages: 81-91

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] 畳み込み変分オートエンコーダを用いた三次元構造物の認識と生成2017

    • Author(s)
      植田考哉,瀬尾昌孝,西川郁子
    • Organizer
      第61回システム制御情報学会研究発表講演会
    • Place of Presentation
      京都テルサ(京都府・京都市)
    • Year and Date
      2017-05-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] 遺伝的アルゴリズムにおけるヒューリスティック操作の選択的適用2017

    • Author(s)
      石動裕人,陳威,中川大輔,佐田貴浩,吉富信太,瀬尾昌孝,西川郁子
    • Organizer
      第61回システム制御情報学会研究発表講演会
    • Place of Presentation
      京都テルサ(京都府・京都市)
    • Year and Date
      2017-05-24
    • Related Report
      2016 Annual Research Report
  • [Presentation] 分散型電力ネットワークにおける確率計画法に基づく電力運用計画最適化2017

    • Author(s)
      佐藤優馬,瀬尾昌孝,西川郁子
    • Organizer
      第61回システム制御情報学会研究発表講演会
    • Place of Presentation
      京都テルサ(京都府・京都市)
    • Year and Date
      2017-05-23
    • Related Report
      2016 Annual Research Report
  • [Presentation] 畳込みネットワークを用いた局所的な画風転写2017

    • Author(s)
      谷口元希,瀬尾昌孝,西川郁子
    • Organizer
      2017年電子情報通信学会総合大会
    • Place of Presentation
      名城大学 天白キャンパス(愛知県・名古屋市)
    • Year and Date
      2017-03-24
    • Related Report
      2016 Annual Research Report
  • [Presentation] 確率計画法によるHEMS の買電・蓄電スケジューリング2016

    • Author(s)
      佐藤優馬,瀬尾昌孝,榊原一紀,西川郁子
    • Organizer
      平成28年電気関係学会関西連合大会
    • Place of Presentation
      大阪府立大学 中百舌鳥キャンパス(大阪府・堺市)
    • Year and Date
      2016-11-22
    • Related Report
      2016 Annual Research Report
  • [Presentation] 電力ネットワーク上の融通と蓄電による電力利用効率化2016

    • Author(s)
      佐藤優馬、瀬尾昌孝、西川郁子
    • Organizer
      第60回システム制御情報学会研究発表講演会(SCI’16)
    • Place of Presentation
      京都テルサ (京都府、京都市)
    • Year and Date
      2016-05-27
    • Related Report
      2015 Research-status Report
  • [Presentation] Deep畳み込みニューラルネットワークによる実験データ分類の事例研究2016

    • Author(s)
      谷口元希、瀬尾昌孝、西川郁子
    • Organizer
      第60回システム制御情報学会研究発表講演会(SCI’16)
    • Place of Presentation
      京都テルサ (京都府、京都市)
    • Year and Date
      2016-05-27
    • Related Report
      2015 Research-status Report
  • [Presentation] 複雑な組合せ構造をもつ最適化問題における可能解領域の推定2016

    • Author(s)
      石動裕人、中川大輔、佐田貴浩、吉富信太、瀬尾昌孝、西川郁子
    • Organizer
      第60回システム制御情報学会研究発表講演会(SCI’16)
    • Place of Presentation
      京都テルサ (京都府、京都市)
    • Year and Date
      2016-05-26
    • Related Report
      2015 Research-status Report
  • [Presentation] Nuclear Detection in 4D Microscope Images of Developing Embryo Using Enhanced Probability Map of Top-ranked Intensity-ordered Descriptor2015

    • Author(s)
      Xian-Hua Han, Yukako Tohsato, Koji Kyoda, Shuichi Onami, Ikuko Nishikawa and Yen-Wei Chen
    • Organizer
      The 3rd IAPR Asian Conference on Pattern Recognition (ACPR2015)
    • Place of Presentation
      Kuala Lumpur(Malaysia)
    • Year and Date
      2015-11-05
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] Prediction of Post-Translational Modification onHuman Protein in Intrinsically Disordered Region by Support Vector Machine2014

    • Author(s)
      Ikuko Nishikawa, Tomoki Ishino, Yukako Tohsato, Satoshi Fukuchi and Ken Nishikawa
    • Organizer
      11th Neural Coding Workshop
    • Place of Presentation
      Versailles (France)
    • Year and Date
      2014-10-08
    • Related Report
      2014 Research-status Report
  • [Presentation] ネットワーク構造に着目した電力網の脆弱性の解析2014

    • Author(s)
      宮澤渉,西川郁子
    • Organizer
      電子情報通信学会 第3回情報ネットワーク科学研究会・複雑コミュニケーションサイエンス研究会 合同ワークショップ
    • Place of Presentation
      丸駒温泉旅館 (北海道)
    • Year and Date
      2014-08-07
    • Related Report
      2014 Research-status Report
  • [Presentation] 電力融通ネットワークにおける強化学習を用いた電力価格決定制度の設計2014

    • Author(s)
      鈴木将義,カモン・スパポン,西川郁子
    • Organizer
      電子情報通信学会 第3回情報ネットワーク科学研究会・複雑コミュニケーションサイエンス研究会 合同ワークショップ
    • Place of Presentation
      丸駒温泉旅館 (北海道)
    • Year and Date
      2014-08-07
    • Related Report
      2014 Research-status Report
  • [Presentation] SVMによるタンパク質天然変性領域上の機能性リン酸化部位の予測2014

    • Author(s)
      石野友喜,西川郁子, 遠里由佳子,福地佐斗志,西川建
    • Organizer
      第58回システム制御情報学会研究発表講演会(SCI'14)
    • Place of Presentation
      京都テルサ (京都府)
    • Year and Date
      2014-05-22
    • Related Report
      2014 Research-status Report
  • [Presentation] 強化学習を用いた電力取引エージェントに依る電力価格決定制度の設計2014

    • Author(s)
      鈴木将義,中谷隆次,西川郁子
    • Organizer
      第58回システム制御情報学会研究発表講演会(SCI'14)
    • Place of Presentation
      京都テルサ (京都府)
    • Year and Date
      2014-05-22
    • Related Report
      2014 Research-status Report

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Published: 2014-04-04   Modified: 2018-03-22  

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