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Development of a method to examine the relationship between phenotype and individual differences in gene expression without the need for gene expression data from a large number of people.

Research Project

Project/Area Number 19K20394
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 62010:Life, health and medical informatics-related
Research InstitutionUniversity of Tsukuba

Principal Investigator

Ozaki Haruka  筑波大学, 医学医療系, 准教授 (10743346)

Project Period (FY) 2019-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2021: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2020: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2019: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Keywords機械学習 / 遺伝子発現 / 深層学習 / 表現型予測 / ゲノム配列 / シングルセルRNA-seq
Outline of Research at the Start

本研究では、機械学習技術を応用し、大人数の個人発現量データを必要とせずに、個々人のゲノムデータから遺伝子発現量の個人差を予測し、遺伝子発現量と表現型の関連解析を行う方法を開発し、個人から採取が困難な組織・細胞型の遺伝子発現量と表現型の関連を発見することを目指す。

Outline of Final Research Achievements

We aimed to develop a method to investigate the relationship between individual differences in gene expression and phenotype. In this context, we succeeded in predicting the effects of individual differences in genome sequence on transcription factor binding based on large-scale epigenomic data. In addition, to investigate the effect of the in vivo environment on gene expression variation, we evaluated the effect of surrounding cells on gene expression variation in each cell in organ-derived single-cell spatial transcriptome data. Furthermore, to gain insight into the relationship between individual differences in gene expression and phenotype, we extracted cell-cell interactions in which high or low expression levels affect survival time from bulk RNA-seq data derived from a large cohort of cancer tissues and single-cell RNA-seq data derived from a small number of cancer tissues to determine the relationship with prognosis.

Academic Significance and Societal Importance of the Research Achievements

ヒト疾患関連変異の大半はタンパク質のアミノ酸配列を変えない非コード変異である。これらの非コード変異は主に遺伝子発現量の違いを通じて表現型の違いを生み出すため、さまざまな臓器での発現量の個人差が表現型とどのように関連するかを調べることは、疾患発症リスクや精密医療の観点から重要である。本研究では特に、ゲノムの個人差と転写因子結合の関係や遺伝子発現変動と細胞間相互作用の関係を明らかにすることで、大量の個人ゲノムデータが蓄積しつつある現代社会において、ヒト疾患研究の基盤を与えると期待される。

Report

(5 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Research-status Report
  • 2020 Research-status Report
  • 2019 Research-status Report
  • Research Products

    (12 results)

All 2022 2021 2020 Other

All Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 6 results,  Open Access: 5 results) Presentation (4 results) (of which Invited: 1 results) Remarks (1 results)

  • [Journal Article] In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states.2022

    • Author(s)
      Kokaji T, Eto M, Hatano A, Yugi K, Morita K, Ohno S, Fujii M, Hironaka KI, Ito Y, Egami R, Uematsu S, Terakawa A, Pan Y, Maehara H, Li D, Bai Y, Tsuchiya T, Ozaki H, Inoue H, Kubota H, Suzuki Y, Hirayama A, Soga T, Kuroda S.
    • Journal Title

      Sci Rep

      Volume: 12 Issue: 1 Pages: 13719-13719

    • DOI

      10.1038/s41598-022-17964-9

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] CCPLS reveals cell-type-specific spatial dependence of transcriptomes in single cells2022

    • Author(s)
      Tsuchiya Takaho、Hori Hiroki、Ozaki Haruka
    • Journal Title

      Bioinformatics

      Volume: 38 Issue: 21 Pages: 4868-4877

    • DOI

      10.1093/bioinformatics/btac599

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Cell-to-cell interaction analysis of prognostic ligand-receptor pairs in human pancreatic ductal adenocarcinoma2021

    • Author(s)
      Suzuki Sayaka R.、Kuno Akihiro、Ozaki Haruka
    • Journal Title

      Biochemistry and Biophysics Reports

      Volume: 28 Pages: 101126-101126

    • DOI

      10.1016/j.bbrep.2021.101126

    • Related Report
      2021 Research-status Report
  • [Journal Article] Integrated analysis of glycan and RNA in single cells2021

    • Author(s)
      Minoshima Fumi、Ozaki Haruka、Odaka Haruki、Tateno Hiroaki
    • Journal Title

      iScience

      Volume: 24 Issue: 8 Pages: 102882-102882

    • DOI

      10.1016/j.isci.2021.102882

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle2021

    • Author(s)
      Egami Riku、Kokaji Toshiya、Hatano Atsushi、et al.
    • Journal Title

      iScience

      Volume: 24 Issue: 3 Pages: 102217-102217

    • DOI

      10.1016/j.isci.2021.102217

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Stability of RNA sequences derived from the coronavirus genome in human cells2020

    • Author(s)
      Wakida Hiroyasu、Kawata Kentaro、Yamaji Yuta、Hattori Emi、Tsuchiya Takaho、Wada Youichiro、Ozaki Haruka、Akimitsu Nobuyoshi
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 527 Issue: 4 Pages: 993-999

    • DOI

      10.1016/j.bbrc.2020.05.008

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Journal Article] Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity2020

    • Author(s)
      Kokaji Toshiya、Hatano Atsushi、Ito Yuki、et al.
    • Journal Title

      Science Signaling

      Volume: 13 Issue: 660 Pages: 1236-1236

    • DOI

      10.1126/scisignal.aaz1236

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] MOCCS profile analysis clarifies the cell type dependency of transcription factor-binding sequences and cis-regulatory SNPs in humans2022

    • Author(s)
      Saeko Tahara, Takaho Tsuchiya, Hirotaka Matsumoto, Haruka Ozaki
    • Organizer
      2022年日本バイオインフォマティクス学会年会・第11回生命医薬情報学連合大会(IIBMP2022)
    • Related Report
      2022 Annual Research Report
  • [Presentation] Predicting SNPs' effects on transcriptional factor binding and cell-type specificity using a crowd of ChIP-seq data2022

    • Author(s)
      田原沙絵子, 土屋貴穂, 松本拡高, 尾崎遼
    • Organizer
      日本人類遺伝学会第67回大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] MOCCS-DB: ヒト転写因子認識配列の多様性データベース2022

    • Author(s)
      田原沙絵子, 土屋貴穂, 松澤亮輔, 尾崎遼
    • Organizer
      トーゴーの日シンポジウム2022
    • Related Report
      2022 Annual Research Report
  • [Presentation] NGSデータ解析における生命現象のモデル化と自動化2021

    • Author(s)
      尾崎遼
    • Organizer
      バイオDXの最前線 - JST戦略的創造研究推進事業 CREST「データ駆動・AI駆動を中心としたデジタルトランスフォーメーションによる生命科学研究の革新[バイオDX]」キックオフシンポジウム
    • Related Report
      2021 Research-status Report
    • Invited
  • [Remarks] コロナウイルスの遺伝情報に秘められた機能を解明

    • URL

      https://www.tsukuba.ac.jp/journal/medicine-health/20200512140015.html

    • Related Report
      2020 Research-status Report

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Published: 2019-04-18   Modified: 2024-01-30  

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