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A GWAS study considering multiple genic/invironmental factors

Research Project

Project/Area Number 25700004
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypePartial Multi-year Fund
Research Field Statistical science
Research InstitutionKyushu University (2016)
Kyushu Institute of Technology (2013-2015)

Principal Investigator

Saigo Hiroto  九州大学, システム情報科学研究院, 准教授 (90586124)

Project Period (FY) 2013-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2013: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
KeywordsGWAS / SNP / variable selection / kernel methods / hypothesis testing / model selection / カーネル法 / 特徴選択 / モデル選択 / アイテムセットマイニング / 多重検定 / 線形混合モデル / カーネル / ゲノムワイド相関解析(GWAS) / epistasis / 情報量基準 / 頻出パターンマイニング / 国際情報交換、ドイツ
Outline of Final Research Achievements

(1)Traversing combinatorial space with brand-and-bound search and rigorous multiple testing correction. A combinatorial space spanned by combination of genes contains a large number of false positives. We devised to remove them by employing Tarone’s correction, which resulted in a faster search with higher statistical power.
(2)Estimating the size of combinatorial space by kernel methods: In our computational experiments equipped with polynomial kernels and kernel ridge regression, we have shown that detection of up-to-six degrees interaction was possible. By applying the same method to mouse genotype/phenotype data, we have successfully detected the region in a chromosome that harbors causal genes.

Report

(5 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (22 results)

All 2017 2016 2015 2014 2013 Other

All Journal Article (4 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 4 results,  Open Access: 2 results,  Acknowledgement Compliant: 3 results) Presentation (17 results) (of which Int'l Joint Research: 3 results) Remarks (1 results)

  • [Journal Article] KDSNP: a Kernel-based approach to Detecting high-order SNP interactions2016

    • Author(s)
      Kodama, K., Saigo, H.
    • Journal Title

      Journal of Bioinformatics and Computational Biology

      Volume: 14(5)

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Structural Class Classification of 3D Protein Structure Based on Multi-View 2D Images2016

    • Author(s)
      Suryanto, C. H., Saigo, H., Fukui, K.
    • Journal Title

      IEEE Transactions on Computational Biology and Bioinformatic

      Volume: PP(99) Issue: 1 Pages: 286-299

    • DOI

      10.1109/tcbb.2016.2603987

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Mining discriminative patterns from graph data with multiple labels and its application to QSAR2015

    • Author(s)
      Shao, Z., Hirayama, Y., Yamanishi, Y., Saigo, H.
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 55 Issue: 12 Pages: 2519-2527

    • DOI

      10.1021/acs.jcim.5b00376

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Fast iterative mining using sparsity-inducing loss functions2013

    • Author(s)
      Saigo. H., Kashima. H., Tsuda, K
    • Journal Title

      IEICE Transaction on Information and Systems

      Volume: Vol.E96-D No.8 Pages: 1766-1773

    • NAID

      130003370958

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Presentation] 応答変数が連続値の際の組み合わせ仮説に対する多重検定補正法2017

    • Author(s)
      井ノ口敬章, 永野竜輝, 西郷浩人
    • Organizer
      人工知能基本問題研究会(第103回)
    • Place of Presentation
      大分県湯布院公民館
    • Year and Date
      2017-03-13
    • Related Report
      2016 Annual Research Report
  • [Presentation] KDSNP: a Kernel-based approach to Detecting high-order genetic Epistasis2016

    • Author(s)
      Kodama, K., Saigo, H.
    • Organizer
      International Conference on Genome Informatics (GIW2016)
    • Place of Presentation
      Shanghai, China,
    • Year and Date
      2016-10-03
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Scalable Partial Least Squares Regression on Grammar- Compressed Data Matrices2016

    • Author(s)
      Tabei, Y., Saigo, H., Yamanishi, Y., Puglisi, S.
    • Organizer
      ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD2016)
    • Place of Presentation
      San Francisco, U.S.
    • Year and Date
      2016-08-13
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Efficient enumeration of statically significant SNP interaction2015

    • Author(s)
      Yamaguchi, Saigo
    • Organizer
      IIBMP2015
    • Place of Presentation
      京都大学化学研究所
    • Year and Date
      2015-10-29
    • Related Report
      2015 Research-status Report
  • [Presentation] Drug Side Effects Prediction by Multiple Graph PLS2015

    • Author(s)
      Hirayama, Saigo
    • Organizer
      IIBMP2015
    • Place of Presentation
      京都大学化学研究所
    • Year and Date
      2015-10-29
    • Related Report
      2015 Research-status Report
  • [Presentation] A branch-and-bound algorithm for searching a block with interacting SNPs2015

    • Author(s)
      Matsumoto, Saigo
    • Organizer
      IIBMP2015
    • Place of Presentation
      京都大学化学研究所
    • Year and Date
      2015-10-29
    • Related Report
      2015 Research-status Report
  • [Presentation] An extended linear mixture model approach to modeling population structure2015

    • Author(s)
      Michizoe, Saigo
    • Organizer
      IIBMP2015
    • Place of Presentation
      京都大学化学研究所
    • Year and Date
      2015-10-29
    • Related Report
      2015 Research-status Report
  • [Presentation] Estimating the number of interacting SNPs in case control study2015

    • Author(s)
      Koyanagi, Saigo
    • Organizer
      IIBMP2015
    • Place of Presentation
      京都大学化学研究所
    • Year and Date
      2015-10-29
    • Related Report
      2015 Research-status Report
  • [Presentation] RF-NR: Random forest based approach for improved classification of Nuclear Receptors2015

    • Author(s)
      Ismail, H.D., Saigo, H., Bahadur, K.C.D.
    • Organizer
      International Conference on Genome Informatics & International Conference on Bioinformatics (GIW/InCoB2015)
    • Place of Presentation
      Odaiba, Tokyo
    • Year and Date
      2015-09-09
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] カイ二乗検定によるp値の下限値を利用した遺伝子相互作用の効率的な数え上げ2015

    • Author(s)
      山口、西郷
    • Organizer
      第42回バイオ情報学研究会
    • Place of Presentation
      沖縄科学技術先端大学院大学
    • Year and Date
      2015-06-23
    • Related Report
      2015 Research-status Report
  • [Presentation] SNP間相互作用を効率的に検出するアルゴリズム開発2014

    • Author(s)
      山口拓郎
    • Organizer
      情報論的学習理論(IBIS)ワークショップ2014
    • Place of Presentation
      名古屋大学
    • Year and Date
      2014-11-16 – 2014-11-19
    • Related Report
      2014 Research-status Report
  • [Presentation] gplsによる薬の候補探索2014

    • Author(s)
      邵正
    • Organizer
      情報論的学習理論(IBIS)ワークショップ2014
    • Place of Presentation
      名古屋大学
    • Year and Date
      2014-11-16 – 2014-11-19
    • Related Report
      2014 Research-status Report
  • [Presentation] カーネル法によるSNP間相互作用数の推定法2014

    • Author(s)
      児玉研人
    • Organizer
      生命医薬情報学連合大会(IIBMP)2014
    • Place of Presentation
      宮城県仙台市 仙台国際センター
    • Year and Date
      2014-10-02 – 2014-10-04
    • Related Report
      2014 Research-status Report
  • [Presentation] Mining discriminative patterns from graph data with multiple labels2014

    • Author(s)
      Saigo. H
    • Organizer
      BMIRC International Symposium
    • Place of Presentation
      Iizuka, Fukuoka, Japan
    • Related Report
      2013 Research-status Report
  • [Presentation] SNP間相互作用探索アルゴリズム2013

    • Author(s)
      池田直人、西郷浩人
    • Organizer
      第16回情報論的学習理論ワークショップ
    • Place of Presentation
      東京工業大学
    • Related Report
      2013 Research-status Report
  • [Presentation] カーネル法によるSNP間相互作用数の推定法2013

    • Author(s)
      児玉研人、西郷浩人
    • Organizer
      第16回情報論的学習理論ワークショップ
    • Place of Presentation
      東京工業大学
    • Related Report
      2013 Research-status Report
  • [Presentation] Comparison of clustering algorithms towards efficient virtual screening2013

    • Author(s)
      Hiroyuki Iguchi, Hiroto Saigo
    • Organizer
      日本バイオインフォマティクス学会 2013年年会
    • Place of Presentation
      タワーホール船越
    • Related Report
      2013 Research-status Report
  • [Remarks] 西郷浩人のWebpage

    • URL

      http://www.i.kyushu-u.ac.jp/~saigo/

    • Related Report
      2016 Annual Research Report

URL: 

Published: 2013-05-21   Modified: 2019-07-29  

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