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Development of Bayesian Estimation Method based on Information Geometry for Multi-layered Omics Data Integration

Research Project

Project/Area Number 17K07254
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Medical genome science
Research InstitutionKyoto University

Principal Investigator

Yamada Ryo  京都大学, 医学研究科, 教授 (50301106)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2019: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2018: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2017: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywordsオミックス / 解析手法 / ベイズ / MCMC / ゲノム / MCMC / オミクス / ベイズ推定 / 情報幾何
Outline of Final Research Achievements

Initially we surveyed the appropriate targets of Bayesian integration of multiple omics layers and developed a method and did a poster presentation. Unfortunately a study in the similar frame was published by overseas competitors. Upon this, we re-directed our study targets of MCMC Bayesian approach to the phenotypes that are difficult to handle, 3-dimensional shape and 3-dimensional movement, and successfully developed a method to extract meaningful features from them so that those phenotypes can be readily integrated with single cell omics data set. The finding was proposed in a domestic meeting.

Academic Significance and Societal Importance of the Research Achievements

海外他研究者による先行発表により、当初計画を変更して取り組むことを余儀なくされたが、オミックスデータの定義を拡張し、特に、統計解析の枠組みに乗りにくい表現型である、形態学的情報と3次元移動・軌跡情報とを標的として、MCMCベイズ手法の開発に成功した。このようにして抽出した1細胞の形・動きの特徴量は、いわゆる1細胞情報(とさらに統合するのが容易な状態になっている。その基本的手法の枠組みを維持しつつ、標的に軌道修正を加えることにより、かえって、オミックス研究領域における解析の難しい表現型の解析基盤を整えることに寄与することとなり、有意義なものとなった。

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (6 results)

All 2020 2019 2018 2017 Other

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

  • [Journal Article] A Geometry-Based Multiple Testing Correction for Contingency Tables by Truncated Normal Distribution2020

    • Author(s)
      Basak, T., Nagashima, K., Kajimoto, S., Kawaguchi, T., Tabara, Y., Matsuda, F., Yamada, R.
    • Journal Title

      Statisitcs in Biosciences

      Volume: 12 Issue: 1 Pages: 63-77

    • DOI

      10.1007/s12561-020-09271-6

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Extension of Sinkhorn Method: Optimal Movement Estimation of Agents Moving at Constant Velocity2019

    • Author(s)
      Okada Daigo、Nakamura Naotoshi、Wada Takuya、Iwasaki Ayako、Yamada Ryo
    • Journal Title

      Transactions of the Japanese Society for Artificial Intelligence

      Volume: 34 Issue: 5 Pages: D-J13_1-7

    • DOI

      10.1527/tjsai.D-J13

    • NAID

      130007700234

    • ISSN
      1346-0714, 1346-8030
    • Year and Date
      2019-09-01
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Cell Shape and Movement Analysis in Frenet-Serret Moving Frame2019

    • Author(s)
      Yusri Dwi Heryanto, Ryo Yamada
    • Organizer
      日本分子生物学会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Omics Data Integration Using Bayesian Non-Negative Matrix Factorization2018

    • Author(s)
      Yusri Dwi Heryanto, Ryo Yamada
    • Organizer
      The 63rd Annual Meeting of the Japan Society of Human Genetics
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Bayesian integration of multilayered omics data2017

    • Author(s)
      Satoshi Koyama, Ryo Yamada
    • Organizer
      日本人類遺伝学会
    • Related Report
      2017 Research-status Report
  • [Remarks] Spherization/pvalueCalculation_Botev.R

    • URL

      https://github.com/statgenetJimu/Spherization/blob/master/pvalueCalculation_Botev.R

    • Related Report
      2019 Annual Research Report

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Published: 2017-04-28   Modified: 2021-02-19  

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