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Construction of analyses basis for understanding rare variants using protein structural information

Research Project

Project/Area Number 15H02773
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionTohoku University

Principal Investigator

Kinoshita Kengo  東北大学, 情報科学研究科, 教授 (60332293)

Co-Investigator(Renkei-kenkyūsha) SHIRAI TSUYOSHI  長浜バイオ大学, バイオサイエンス学部, 教授 (00262890)
OHTA MOTONORI  名古屋大学, 大学院情報科学研究科, 教授 (40290895)
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥15,470,000 (Direct Cost: ¥11,900,000、Indirect Cost: ¥3,570,000)
Fiscal Year 2017: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2016: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2015: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Keywords低頻度変異 / タンパク質立体構造 / ホモロジーモデリング / ヒトタンパク質 / レアバリアント / 変異の意味づけ / ゲノム変異 / 蛋白質立体構構造 / バイオインフォマティクス / 蛋白質立体構造 / ヒトゲノム / 変異
Outline of Final Research Achievements

We could construct the proposed systems as planned, which can map genetic variations onto protein structures, and the results are available through the web site called snvmap. For the purpose, we generated model structures of human proteins, if they are not available in PDB.
By using the mapping results, we performed statistical analyses and found some interesting rare variations related with the metabolism of oseltamivir, an anti-virus drug, which specific for east Asian populations.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (15 results)

All 2017 2016 2015 2014 Other

All Journal Article (8 results) (of which Peer Reviewed: 8 results,  Open Access: 8 results,  Acknowledgement Compliant: 6 results) Presentation (6 results) (of which Int'l Joint Research: 4 results,  Invited: 2 results) Remarks (1 results)

  • [Journal Article] New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)2017

    • Author(s)
      Kinjo Akira R.、Bekker Gert-Jan、Wako Hiroshi、Endo Shigeru、Tsuchiya Yuko、Sato Hiromu、Nishi Hafumi、Kinoshita Kengo、Suzuki Hirofumi、Kawabata Takeshi、Yokochi Masashi、Iwata Takeshi、Kobayashi Naohiro、Fujiwara Toshimichi、Kurisu Genji、Nakamura Haruki
    • Journal Title

      Protein Science

      Volume: 27 Issue: 1 Pages: 95-102

    • DOI

      10.1002/pro.3273

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population2016

    • Author(s)
      Matsuyuki Shirota and Kengo Kinoshita
    • Journal Title

      Database

      Volume: 1 Pages: 1-15

    • DOI

      10.1093/database/baw124

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] NCMine: Core-peripheral based functional module detection using near-clique mining2016

    • Author(s)
      Shu Tadaka and Kengo Kinoshita
    • Journal Title

      Bioinformatics

      Volume: 32 Issue: 22 Pages: 3454-3460

    • DOI

      10.1093/bioinformatics/btw488

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] NLDB: a database for 3D protein-ligand interactions in enzymatic reactions2016

    • Author(s)
      Yoichi Murakami, Satoshi Omori, and Kengo Kinoshita
    • Journal Title

      J Struct Funct Genomics

      Volume: 17 Issue: 4 Pages: 101-110

    • DOI

      10.1007/s10969-016-9206-0

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels2016

    • Author(s)
      Kota Kasahara and Kengo Kinoshita
    • Journal Title

      Plos One

      Volume: 11 Issue: 12 Pages: e0167524-e0167524

    • DOI

      10.1371/journal.pone.0167524

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Distribution of single nucleotide variants on protein-protein interaction sites and its relation to minor allele frequency2016

    • Author(s)
      Hafumi Nishi, Junichi Nakata, and Kengo Kinoshita
    • Journal Title

      Protein Science

      Volume: 25 Issue: 2 Pages: 316-321

    • DOI

      10.1002/pro.2845

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins2016

    • Author(s)
      Kazunori D. Yamada, Hafumi Nishi, Junichi Nakata, Kengo Kinoshita
    • Journal Title

      Biophysics and Physicobiology

      Volume: 印刷中

    • NAID

      130005165370

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes2014

    • Author(s)
      Kasahara K and Kinoshita K
    • Journal Title

      BMC Bioinformatics

      Volume: 15 Issue: 1 Pages: 12-12

    • DOI

      10.1186/1471-2105-15-12

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] A Challenge to Understand Functional Impacts of Rare Variants Using Protein Structural Information2017

    • Author(s)
      Kengo Kinoshita
    • Organizer
      2nd Karolinska-Tohoku Joint Symposium on Medical Sciences
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Development and application of a simple yet flexible framework for construction of gene-pair relationship database2016

    • Author(s)
      Shu Tadaka and Kengo KInoshita
    • Organizer
      生命医薬情報学連合大会
    • Place of Presentation
      東京国際交流プラザ平成(東京都江東区)
    • Year and Date
      2016-09-29
    • Related Report
      2016 Annual Research Report
  • [Presentation] Distribution of human single nucleotide variants at protein functional sites and its relation to minor allele frequency2016

    • Author(s)
      Hafumi Nishi, Kazunori D Yamada, Junichi Nakata, Kengo Kinoshita
    • Organizer
      Gordon Conference
    • Place of Presentation
      South Hadley, MA, USA.
    • Year and Date
      2016-06-13
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Prediction of biological and biochemical functions of uncharacterized genes2015

    • Author(s)
      Kengo Kinoshita
    • Organizer
      Data Science in Life Science and Engineering Collaboration and Symposium
    • Place of Presentation
      Case western university, USA
    • Year and Date
      2015-07-30
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Distribution of single nucleotide variants on protein-protein interaction sites2015

    • Author(s)
      Hafumi Nishi, Junichi Nakata, Kengo Kinoshita
    • Organizer
      3Dsig2015, 23rd Annual International Conference on Intelligent Systems for Molecular Biology
    • Place of Presentation
      Dublin, Ireland
    • Year and Date
      2015-07-13
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ヒトゲノム一塩基変異のタンパク質間相互作用面上での分布2015

    • Author(s)
      西羽美、中田純一、木下賢吾
    • Organizer
      第15回日本蛋白質科学会
    • Place of Presentation
      あわぎんホール、徳島県
    • Year and Date
      2015-06-25
    • Related Report
      2015 Annual Research Report
  • [Remarks] SNVMap

    • URL

      https://sahg.hgc.jp

    • Related Report
      2017 Annual Research Report

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Published: 2015-04-16   Modified: 2019-03-29  

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